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* helm-bibtex questions
@ 2015-06-17 18:08 Xebar Saram
  2015-06-17 20:02 ` Titus von der Malsburg
  0 siblings, 1 reply; 26+ messages in thread
From: Xebar Saram @ 2015-06-17 18:08 UTC (permalink / raw)
  To: Titus von der Malsburg, org mode

[-- Attachment #1: Type: text/plain, Size: 976 bytes --]

Hi Titus

I have been exploring helm-bibtex a bit today and have some questions. btw
is this the preferred way to make requests/ask questions or is
github preferred?

in any case i was wondering a few things:

1. is it possible to have custom sorting? i want all views to sort by
Author, year, month

2. i would really like a way to have stored smart groups (like the jabref
dynamic groups if your aware of that). that is for example create a group
that auto selects all publications i have (by my first/last name) and shows
the count (in numbers) of these publications.
Another example is a group to keep track of all the papers im working on or
invloved with by matching keyword author and prep/*other key word

3.is it possible to ass an option to auto generate a bibkey for a selected
citation based on user criteria such as author(date)short-title?

thx so much in advance, you and john have given me confidence to finally
dive into the whole latex/bibteX world

best

Z

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^ permalink raw reply	[flat|nested] 26+ messages in thread

• * Re: helm-bibtex questions
    2015-06-17 18:08 helm-bibtex questions Xebar Saram
  @ 2015-06-17 20:02 ` Titus von der Malsburg
    2015-06-18 11:32   ` Xebar Saram
    2015-06-19 21:08   ` John Kitchin
    0 siblings, 2 replies; 26+ messages in thread
  From: Titus von der Malsburg @ 2015-06-17 20:02 UTC (permalink / raw)
    To: Xebar Saram; +Cc: org mode
  
  [-- Attachment #1: Type: text/plain, Size: 3302 bytes --]
  
  
  On 2015-06-17 Wed 11:08, Xebar Saram wrote:
  > Hi Titus
  >
  > I have been exploring helm-bibtex a bit today and have some questions. btw
  > is this the preferred way to make requests/ask questions or is
  > github preferred?
  
  Helm-bibtex is not part of org (although it tries to work well with
  org).  So I’m not sure whether this list is the best place for
  discussing it.  For now the issue tracker on Github might be a better
  option:
  
    https://github.com/tmalsburg/helm-bibtex/issues
  
  > in any case i was wondering a few things:
  >
  > 1. is it possible to have custom sorting? i want all views to sort by
  > Author, year, month
  
  I prefer to see the entries in the (inverse) order in which they appear
  in the BibTeX file.  This way, recent additions show up at the
  top.  However, I agree that sorting would be useful (see issues #5 and
  #21); it just doesn’t have high priority for me.  Pull requests welcome.
  
  > 2. i would really like a way to have stored smart groups (like the jabref
  > dynamic groups if your aware of that). that is for example create a group
  > that auto selects all publications i have (by my first/last name) and shows
  > the count (in numbers) of these publications.
  
  I’m not familiar with smart groups but it seems that all helm-bibtex is
  doing is giving you very flexible smart groups defined by your search
  expressions.  For example, if you want a list of your publications, you
  can simple enter your name.  And if you want a list of your articles,
  you can enter your name + “article”.  If you want all your articles from
  2010, enter your name + “articles 2010”.  And so on.  The number of
  matches will be displayed in the mode line.  If you don’t want to type
  these search expressions, you could create a command that invokes
  helm-bibtex with a default search expression and that command could be
  bound to a keyboard shortcut.
  
  > Another example is a group to keep track of all the papers im working on or
  > invloved with by matching keyword author and prep/*other key word
  
  I use two BibTeX fields to tag entries: “keywords” for keywords
  describing the content of the paper (as usual) and “tags” for meta
  data.  Values that I use in tags are “own”, “manuscript”, “poster”,
  “talk”, … So if I want a list of all articles in progress, I search for
  “own manuscript”.  Since the tags field is non-standard, it has to be
  added to `helm-bibtex-additional-search-fields`.
  
  Another solution would be to use the pubstate field and to search for
  your name and “forthcoming” (add pubstate to
  helm-bibtex-additional-search-fields for this to work).
  
  > 3.is it possible to ass an option to auto generate a bibkey for a selected
  > citation based on user criteria such as author(date)short-title?
  
  Maintaining the content of the BibTeX file not really in the scope of
  helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
  org-ref or ebib can help here?  Once you have a function that generates
  a new key and inserts it in the BibTeX file, you can easily add it to
  the list of actions in helm-bibtex.
  
  Hope that helps.
  
    Titus
  
  > thx so much in advance, you and john have given me confidence to finally
  > dive into the whole latex/bibteX world
  >
  > best
  >
  > Z
  
  
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  ^ permalink raw reply	[flat|nested] 26+ messages in thread

• • * Re: helm-bibtex questions
      2015-06-17 20:02 ` Titus von der Malsburg
    @ 2015-06-18 11:32   ` Xebar Saram
      2015-06-18 18:38     ` Titus von der Malsburg
      2015-06-19 21:08   ` John Kitchin
      1 sibling, 1 reply; 26+ messages in thread
    From: Xebar Saram @ 2015-06-18 11:32 UTC (permalink / raw)
      To: Titus von der Malsburg, org mode
    
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    Hi Titus and thx so much for the answers!
    
    i will in the future use the github page to make requests.
    
    "The number of matches will be displayed in the mode line. "
    
    i see that now thx! :) the problem was(is) that its colored black on my
    black modline BG which makes it invisible ;-) i assume thats an helm config
    i need to change
    
    
    "If you don’t want to type these search expressions, you could create a
    command that invokes helm-bibtex with a default search expression and that
    command could be bound to a keyboard shortcut."
    
    that would be prefect for me and a solution to my issue. would you mind
    giving an example of such a code chunk. unfortunately i dont know elisp though
    as john recommended i will do my best this summer when the semester ends to
    try and pick it up :)
    
    i will definitely use your tag system as you recommended, sounds perfect
    for me
    
    thanks again for your kind help and the amazing app ;-)
    
    best
    
    Z
    
    
    
    On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <malsburg@posteo.de
    > wrote:
    
    >
    > On 2015-06-17 Wed 11:08, Xebar Saram wrote:
    > > Hi Titus
    > >
    > > I have been exploring helm-bibtex a bit today and have some questions.
    > btw
    > > is this the preferred way to make requests/ask questions or is
    > > github preferred?
    >
    > Helm-bibtex is not part of org (although it tries to work well with
    > org).  So I’m not sure whether this list is the best place for
    > discussing it.  For now the issue tracker on Github might be a better
    > option:
    >
    >   https://github.com/tmalsburg/helm-bibtex/issues
    >
    > > in any case i was wondering a few things:
    > >
    > > 1. is it possible to have custom sorting? i want all views to sort by
    > > Author, year, month
    >
    > I prefer to see the entries in the (inverse) order in which they appear
    > in the BibTeX file.  This way, recent additions show up at the
    > top.  However, I agree that sorting would be useful (see issues #5 and
    > #21); it just doesn’t have high priority for me.  Pull requests welcome.
    >
    > > 2. i would really like a way to have stored smart groups (like the jabref
    > > dynamic groups if your aware of that). that is for example create a group
    > > that auto selects all publications i have (by my first/last name) and
    > shows
    > > the count (in numbers) of these publications.
    >
    > I’m not familiar with smart groups but it seems that all helm-bibtex is
    > doing is giving you very flexible smart groups defined by your search
    > expressions.  For example, if you want a list of your publications, you
    > can simple enter your name.  And if you want a list of your articles,
    > you can enter your name + “article”.  If you want all your articles from
    > 2010, enter your name + “articles 2010”.  And so on.  The number of
    > matches will be displayed in the mode line.  If you don’t want to type
    > these search expressions, you could create a command that invokes
    > helm-bibtex with a default search expression and that command could be
    > bound to a keyboard shortcut.
    >
    > > Another example is a group to keep track of all the papers im working on
    > or
    > > invloved with by matching keyword author and prep/*other key word
    >
    > I use two BibTeX fields to tag entries: “keywords” for keywords
    > describing the content of the paper (as usual) and “tags” for meta
    > data.  Values that I use in tags are “own”, “manuscript”, “poster”,
    > “talk”, … So if I want a list of all articles in progress, I search for
    > “own manuscript”.  Since the tags field is non-standard, it has to be
    > added to `helm-bibtex-additional-search-fields`.
    >
    > Another solution would be to use the pubstate field and to search for
    > your name and “forthcoming” (add pubstate to
    > helm-bibtex-additional-search-fields for this to work).
    >
    > > 3.is it possible to ass an option to auto generate a bibkey for a
    > selected
    > > citation based on user criteria such as author(date)short-title?
    >
    > Maintaining the content of the BibTeX file not really in the scope of
    > helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
    > org-ref or ebib can help here?  Once you have a function that generates
    > a new key and inserts it in the BibTeX file, you can easily add it to
    > the list of actions in helm-bibtex.
    >
    > Hope that helps.
    >
    >   Titus
    >
    > > thx so much in advance, you and john have given me confidence to finally
    > > dive into the whole latex/bibteX world
    > >
    > > best
    > >
    > > Z
    >
    >
    
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    ^ permalink raw reply	[flat|nested] 26+ messages in thread

  • • * Re: helm-bibtex questions
        2015-06-18 11:32   ` Xebar Saram
      @ 2015-06-18 18:38     ` Titus von der Malsburg
        2015-06-19 10:56       ` Xebar Saram
        0 siblings, 1 reply; 26+ messages in thread
      From: Titus von der Malsburg @ 2015-06-18 18:38 UTC (permalink / raw)
        To: Xebar Saram; +Cc: org mode
      
      [-- Attachment #1: Type: text/plain, Size: 5532 bytes --]
      
      
      On 2015-06-18 Thu 04:32, Xebar Saram wrote:
      > Hi Titus and thx so much for the answers!
      >
      > i will in the future use the github page to make requests.
      >
      > "The number of matches will be displayed in the mode line. "
      >
      > i see that now thx! :) the problem was(is) that its colored black on my
      > black modline BG which makes it invisible ;-) i assume thats an helm config
      > i need to change
      >
      >
      > "If you don’t want to type these search expressions, you could create a
      > command that invokes helm-bibtex with a default search expression and that
      > command could be bound to a keyboard shortcut."
      >
      > that would be prefect for me and a solution to my issue. would you mind
      > giving an example of such a code chunk. unfortunately i dont know elisp though
      > as john recommended i will do my best this summer when the semester ends to
      > try and pick it up :)
      
      Sure, here you go:
      
      #+BEGIN_SRC elisp
      ;; Define helm-search with predefined search expression:
      (defun helm-bibtex-my-publications ()
        "Search BibTeX entries authored by Xebar Saram."
        (interactive)
        (helm :sources '(helm-source-bibtex)
              :full-frame t
              :input "xebar saram"
              :candidate-number-limit 500))
      
      ;; Bind this search function to Ctrl-x p:
      (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
      #+END_SRC
      
      > i will definitely use your tag system as you recommended, sounds perfect
      > for me
      
      The tag system also comes in handy when generating publication lists for
      CVs and web pages because BibTeX does not distinguish between conference
      papers, posters, and talks.  If you have tags for that, it’s relatively
      easy to create separate sections for these types of publications using
      biblatex or bib2bib and bibtex2html in the case of web pages.
      
      > thanks again for your kind help and the amazing app ;-)
      
      You are welcome.
      
        Titus
      
      >
      > best
      >
      > Z
      >
      >
      >
      > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <malsburg@posteo.de
      >> wrote:
      >
      >>
      >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
      >> > Hi Titus
      >> >
      >> > I have been exploring helm-bibtex a bit today and have some questions.
      >> btw
      >> > is this the preferred way to make requests/ask questions or is
      >> > github preferred?
      >>
      >> Helm-bibtex is not part of org (although it tries to work well with
      >> org).  So I’m not sure whether this list is the best place for
      >> discussing it.  For now the issue tracker on Github might be a better
      >> option:
      >>
      >>   https://github.com/tmalsburg/helm-bibtex/issues
      >>
      >> > in any case i was wondering a few things:
      >> >
      >> > 1. is it possible to have custom sorting? i want all views to sort by
      >> > Author, year, month
      >>
      >> I prefer to see the entries in the (inverse) order in which they appear
      >> in the BibTeX file.  This way, recent additions show up at the
      >> top.  However, I agree that sorting would be useful (see issues #5 and
      >> #21); it just doesn’t have high priority for me.  Pull requests welcome.
      >>
      >> > 2. i would really like a way to have stored smart groups (like the jabref
      >> > dynamic groups if your aware of that). that is for example create a group
      >> > that auto selects all publications i have (by my first/last name) and
      >> shows
      >> > the count (in numbers) of these publications.
      >>
      >> I’m not familiar with smart groups but it seems that all helm-bibtex is
      >> doing is giving you very flexible smart groups defined by your search
      >> expressions.  For example, if you want a list of your publications, you
      >> can simple enter your name.  And if you want a list of your articles,
      >> you can enter your name + “article”.  If you want all your articles from
      >> 2010, enter your name + “articles 2010”.  And so on.  The number of
      >> matches will be displayed in the mode line.  If you don’t want to type
      >> these search expressions, you could create a command that invokes
      >> helm-bibtex with a default search expression and that command could be
      >> bound to a keyboard shortcut.
      >>
      >> > Another example is a group to keep track of all the papers im working on
      >> or
      >> > invloved with by matching keyword author and prep/*other key word
      >>
      >> I use two BibTeX fields to tag entries: “keywords” for keywords
      >> describing the content of the paper (as usual) and “tags” for meta
      >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
      >> “talk”, … So if I want a list of all articles in progress, I search for
      >> “own manuscript”.  Since the tags field is non-standard, it has to be
      >> added to `helm-bibtex-additional-search-fields`.
      >>
      >> Another solution would be to use the pubstate field and to search for
      >> your name and “forthcoming” (add pubstate to
      >> helm-bibtex-additional-search-fields for this to work).
      >>
      >> > 3.is it possible to ass an option to auto generate a bibkey for a
      >> selected
      >> > citation based on user criteria such as author(date)short-title?
      >>
      >> Maintaining the content of the BibTeX file not really in the scope of
      >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
      >> org-ref or ebib can help here?  Once you have a function that generates
      >> a new key and inserts it in the BibTeX file, you can easily add it to
      >> the list of actions in helm-bibtex.
      >>
      >> Hope that helps.
      >>
      >>   Titus
      >>
      >> > thx so much in advance, you and john have given me confidence to finally
      >> > dive into the whole latex/bibteX world
      >> >
      >> > best
      >> >
      >> > Z
      >>
      >>
      
      
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      ^ permalink raw reply	[flat|nested] 26+ messages in thread

    • • * Re: helm-bibtex questions
          2015-06-18 18:38     ` Titus von der Malsburg
        @ 2015-06-19 10:56       ` Xebar Saram
          2015-06-19 21:02         ` John Kitchin
          2015-06-21 18:29         ` Titus von der Malsburg
          0 siblings, 2 replies; 26+ messages in thread
        From: Xebar Saram @ 2015-06-19 10:56 UTC (permalink / raw)
          To: Titus von der Malsburg; +Cc: org mode
        
        [-- Attachment #1: Type: text/plain, Size: 6271 bytes --]
        
        Hi again Titus
        
        2 quick questions that arose from using helm-bitex today extensively:
        
        how does one exclude in the search items? for example i want to search for
        xebar without keyword "progress" (I want to exclude in progress articles
        not published yet)
        
        is it possible to define default enter command in helm-bibtex ?
        
        best
        
        Z
        
        On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <malsburg@posteo.de>
        wrote:
        
        >
        > On 2015-06-18 Thu 04:32, Xebar Saram wrote:
        > > Hi Titus and thx so much for the answers!
        > >
        > > i will in the future use the github page to make requests.
        > >
        > > "The number of matches will be displayed in the mode line. "
        > >
        > > i see that now thx! :) the problem was(is) that its colored black on my
        > > black modline BG which makes it invisible ;-) i assume thats an helm
        > config
        > > i need to change
        > >
        > >
        > > "If you don’t want to type these search expressions, you could create a
        > > command that invokes helm-bibtex with a default search expression and
        > that
        > > command could be bound to a keyboard shortcut."
        > >
        > > that would be prefect for me and a solution to my issue. would you mind
        > > giving an example of such a code chunk. unfortunately i dont know elisp
        > though
        > > as john recommended i will do my best this summer when the semester ends
        > to
        > > try and pick it up :)
        >
        > Sure, here you go:
        >
        > #+BEGIN_SRC elisp
        > ;; Define helm-search with predefined search expression:
        > (defun helm-bibtex-my-publications ()
        >   "Search BibTeX entries authored by Xebar Saram."
        >   (interactive)
        >   (helm :sources '(helm-source-bibtex)
        >         :full-frame t
        >         :input "xebar saram"
        >         :candidate-number-limit 500))
        >
        > ;; Bind this search function to Ctrl-x p:
        > (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
        > #+END_SRC
        >
        > > i will definitely use your tag system as you recommended, sounds perfect
        > > for me
        >
        > The tag system also comes in handy when generating publication lists for
        > CVs and web pages because BibTeX does not distinguish between conference
        > papers, posters, and talks.  If you have tags for that, it’s relatively
        > easy to create separate sections for these types of publications using
        > biblatex or bib2bib and bibtex2html in the case of web pages.
        >
        > > thanks again for your kind help and the amazing app ;-)
        >
        > You are welcome.
        >
        >   Titus
        >
        > >
        > > best
        > >
        > > Z
        > >
        > >
        > >
        > > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
        > malsburg@posteo.de
        > >> wrote:
        > >
        > >>
        > >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
        > >> > Hi Titus
        > >> >
        > >> > I have been exploring helm-bibtex a bit today and have some questions.
        > >> btw
        > >> > is this the preferred way to make requests/ask questions or is
        > >> > github preferred?
        > >>
        > >> Helm-bibtex is not part of org (although it tries to work well with
        > >> org).  So I’m not sure whether this list is the best place for
        > >> discussing it.  For now the issue tracker on Github might be a better
        > >> option:
        > >>
        > >>   https://github.com/tmalsburg/helm-bibtex/issues
        > >>
        > >> > in any case i was wondering a few things:
        > >> >
        > >> > 1. is it possible to have custom sorting? i want all views to sort by
        > >> > Author, year, month
        > >>
        > >> I prefer to see the entries in the (inverse) order in which they appear
        > >> in the BibTeX file.  This way, recent additions show up at the
        > >> top.  However, I agree that sorting would be useful (see issues #5 and
        > >> #21); it just doesn’t have high priority for me.  Pull requests welcome.
        > >>
        > >> > 2. i would really like a way to have stored smart groups (like the
        > jabref
        > >> > dynamic groups if your aware of that). that is for example create a
        > group
        > >> > that auto selects all publications i have (by my first/last name) and
        > >> shows
        > >> > the count (in numbers) of these publications.
        > >>
        > >> I’m not familiar with smart groups but it seems that all helm-bibtex is
        > >> doing is giving you very flexible smart groups defined by your search
        > >> expressions.  For example, if you want a list of your publications, you
        > >> can simple enter your name.  And if you want a list of your articles,
        > >> you can enter your name + “article”.  If you want all your articles from
        > >> 2010, enter your name + “articles 2010”.  And so on.  The number of
        > >> matches will be displayed in the mode line.  If you don’t want to type
        > >> these search expressions, you could create a command that invokes
        > >> helm-bibtex with a default search expression and that command could be
        > >> bound to a keyboard shortcut.
        > >>
        > >> > Another example is a group to keep track of all the papers im working
        > on
        > >> or
        > >> > invloved with by matching keyword author and prep/*other key word
        > >>
        > >> I use two BibTeX fields to tag entries: “keywords” for keywords
        > >> describing the content of the paper (as usual) and “tags” for meta
        > >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
        > >> “talk”, … So if I want a list of all articles in progress, I search for
        > >> “own manuscript”.  Since the tags field is non-standard, it has to be
        > >> added to `helm-bibtex-additional-search-fields`.
        > >>
        > >> Another solution would be to use the pubstate field and to search for
        > >> your name and “forthcoming” (add pubstate to
        > >> helm-bibtex-additional-search-fields for this to work).
        > >>
        > >> > 3.is it possible to ass an option to auto generate a bibkey for a
        > >> selected
        > >> > citation based on user criteria such as author(date)short-title?
        > >>
        > >> Maintaining the content of the BibTeX file not really in the scope of
        > >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
        > >> org-ref or ebib can help here?  Once you have a function that generates
        > >> a new key and inserts it in the BibTeX file, you can easily add it to
        > >> the list of actions in helm-bibtex.
        > >>
        > >> Hope that helps.
        > >>
        > >>   Titus
        > >>
        > >> > thx so much in advance, you and john have given me confidence to
        > finally
        > >> > dive into the whole latex/bibteX world
        > >> >
        > >> > best
        > >> >
        > >> > Z
        > >>
        > >>
        >
        >
        
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        ^ permalink raw reply	[flat|nested] 26+ messages in thread

      • • * Re: helm-bibtex questions
            2015-06-19 10:56       ` Xebar Saram
          @ 2015-06-19 21:02         ` John Kitchin
            2015-06-21 18:29         ` Titus von der Malsburg
            1 sibling, 0 replies; 26+ messages in thread
          From: John Kitchin @ 2015-06-19 21:02 UTC (permalink / raw)
            To: Xebar Saram; +Cc: org mode, Titus von der Malsburg
          
          
          Xebar Saram writes:
          
          > Hi again Titus
          >
          > 2 quick questions that arose from using helm-bitex today extensively:
          >
          > how does one exclude in the search items? for example i want to search for
          > xebar without keyword "progress" (I want to exclude in progress articles
          > not published yet)
          
          Try this in the helm search:
          
          xebar !progress
          
          >
          > is it possible to define default enter command in helm-bibtex ?
          
          >
          > best
          >
          > Z
          >
          > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <malsburg@posteo.de>
          > wrote:
          >
          >>
          >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
          >> > Hi Titus and thx so much for the answers!
          >> >
          >> > i will in the future use the github page to make requests.
          >> >
          >> > "The number of matches will be displayed in the mode line. "
          >> >
          >> > i see that now thx! :) the problem was(is) that its colored black on my
          >> > black modline BG which makes it invisible ;-) i assume thats an helm
          >> config
          >> > i need to change
          >> >
          >> >
          >> > "If you don’t want to type these search expressions, you could create a
          >> > command that invokes helm-bibtex with a default search expression and
          >> that
          >> > command could be bound to a keyboard shortcut."
          >> >
          >> > that would be prefect for me and a solution to my issue. would you mind
          >> > giving an example of such a code chunk. unfortunately i dont know elisp
          >> though
          >> > as john recommended i will do my best this summer when the semester ends
          >> to
          >> > try and pick it up :)
          >>
          >> Sure, here you go:
          >>
          >> #+BEGIN_SRC elisp
          >> ;; Define helm-search with predefined search expression:
          >> (defun helm-bibtex-my-publications ()
          >>   "Search BibTeX entries authored by Xebar Saram."
          >>   (interactive)
          >>   (helm :sources '(helm-source-bibtex)
          >>         :full-frame t
          >>         :input "xebar saram"
          >>         :candidate-number-limit 500))
          >>
          >> ;; Bind this search function to Ctrl-x p:
          >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
          >> #+END_SRC
          >>
          >> > i will definitely use your tag system as you recommended, sounds perfect
          >> > for me
          >>
          >> The tag system also comes in handy when generating publication lists for
          >> CVs and web pages because BibTeX does not distinguish between conference
          >> papers, posters, and talks.  If you have tags for that, it’s relatively
          >> easy to create separate sections for these types of publications using
          >> biblatex or bib2bib and bibtex2html in the case of web pages.
          >>
          >> > thanks again for your kind help and the amazing app ;-)
          >>
          >> You are welcome.
          >>
          >>   Titus
          >>
          >> >
          >> > best
          >> >
          >> > Z
          >> >
          >> >
          >> >
          >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
          >> malsburg@posteo.de
          >> >> wrote:
          >> >
          >> >>
          >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
          >> >> > Hi Titus
          >> >> >
          >> >> > I have been exploring helm-bibtex a bit today and have some questions.
          >> >> btw
          >> >> > is this the preferred way to make requests/ask questions or is
          >> >> > github preferred?
          >> >>
          >> >> Helm-bibtex is not part of org (although it tries to work well with
          >> >> org).  So I’m not sure whether this list is the best place for
          >> >> discussing it.  For now the issue tracker on Github might be a better
          >> >> option:
          >> >>
          >> >>   https://github.com/tmalsburg/helm-bibtex/issues
          >> >>
          >> >> > in any case i was wondering a few things:
          >> >> >
          >> >> > 1. is it possible to have custom sorting? i want all views to sort by
          >> >> > Author, year, month
          >> >>
          >> >> I prefer to see the entries in the (inverse) order in which they appear
          >> >> in the BibTeX file.  This way, recent additions show up at the
          >> >> top.  However, I agree that sorting would be useful (see issues #5 and
          >> >> #21); it just doesn’t have high priority for me.  Pull requests welcome.
          >> >>
          >> >> > 2. i would really like a way to have stored smart groups (like the
          >> jabref
          >> >> > dynamic groups if your aware of that). that is for example create a
          >> group
          >> >> > that auto selects all publications i have (by my first/last name) and
          >> >> shows
          >> >> > the count (in numbers) of these publications.
          >> >>
          >> >> I’m not familiar with smart groups but it seems that all helm-bibtex is
          >> >> doing is giving you very flexible smart groups defined by your search
          >> >> expressions.  For example, if you want a list of your publications, you
          >> >> can simple enter your name.  And if you want a list of your articles,
          >> >> you can enter your name + “article”.  If you want all your articles from
          >> >> 2010, enter your name + “articles 2010”.  And so on.  The number of
          >> >> matches will be displayed in the mode line.  If you don’t want to type
          >> >> these search expressions, you could create a command that invokes
          >> >> helm-bibtex with a default search expression and that command could be
          >> >> bound to a keyboard shortcut.
          >> >>
          >> >> > Another example is a group to keep track of all the papers im working
          >> on
          >> >> or
          >> >> > invloved with by matching keyword author and prep/*other key word
          >> >>
          >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
          >> >> describing the content of the paper (as usual) and “tags” for meta
          >> >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
          >> >> “talk”, … So if I want a list of all articles in progress, I search for
          >> >> “own manuscript”.  Since the tags field is non-standard, it has to be
          >> >> added to `helm-bibtex-additional-search-fields`.
          >> >>
          >> >> Another solution would be to use the pubstate field and to search for
          >> >> your name and “forthcoming” (add pubstate to
          >> >> helm-bibtex-additional-search-fields for this to work).
          >> >>
          >> >> > 3.is it possible to ass an option to auto generate a bibkey for a
          >> >> selected
          >> >> > citation based on user criteria such as author(date)short-title?
          >> >>
          >> >> Maintaining the content of the BibTeX file not really in the scope of
          >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
          >> >> org-ref or ebib can help here?  Once you have a function that generates
          >> >> a new key and inserts it in the BibTeX file, you can easily add it to
          >> >> the list of actions in helm-bibtex.
          >> >>
          >> >> Hope that helps.
          >> >>
          >> >>   Titus
          >> >>
          >> >> > thx so much in advance, you and john have given me confidence to
          >> finally
          >> >> > dive into the whole latex/bibteX world
          >> >> >
          >> >> > best
          >> >> >
          >> >> > Z
          >> >>
          >> >>
          >>
          >>
          
          --
          Professor John Kitchin
          Doherty Hall A207F
          Department of Chemical Engineering
          Carnegie Mellon University
          Pittsburgh, PA 15213
          412-268-7803
          @johnkitchin
          http://kitchingroup.cheme.cmu.edu
          
          ^ permalink raw reply	[flat|nested] 26+ messages in thread

        • * Re: helm-bibtex questions
            2015-06-19 10:56       ` Xebar Saram
            2015-06-19 21:02         ` John Kitchin
          @ 2015-06-21 18:29         ` Titus von der Malsburg
            2015-06-21 18:40           ` John Kitchin
            1 sibling, 1 reply; 26+ messages in thread
          From: Titus von der Malsburg @ 2015-06-21 18:29 UTC (permalink / raw)
            To: Xebar Saram; +Cc: org mode
          
          [-- Attachment #1: Type: text/plain, Size: 7406 bytes --]
          
          
          On 2015-06-19 Fri 03:56, Xebar Saram wrote:
          > Hi again Titus
          >
          > 2 quick questions that arose from using helm-bitex today extensively:
          >
          > how does one exclude in the search items? for example i want to search for
          > xebar without keyword "progress" (I want to exclude in progress articles
          > not published yet)
          >
          > is it possible to define default enter command in helm-bibtex ?
          
          Yes.  Helm uses the first action as the default action.  To move an
          action to the top of the list you can use the following code:
          
            (helm-delete-action-from-source "Insert BibTeX key" helm-source-bibtex)
            (helm-add-action-to-source "Insert BibTeX key" 'helm-bibtex-insert-key helm-source-bibtex 0)
          
          The second argument in the second line is the function that executes the
          action.  Here is a list of all actions and their functions:
            
            Open PDF file (if present): helm-bibtex-open-pdf
            Open URL or DOI in browser: helm-bibtex-open-url-or-doi
            Insert citation: helm-bibtex-insert-citation
            Insert reference: helm-bibtex-insert-reference
            Insert BibTeX key: helm-bibtex-insert-key
            Insert BibTeX entry: helm-bibtex-insert-bibtex
            Attach PDF to email: helm-bibtex-add-PDF-attachment
            Edit notes: helm-bibtex-edit-notes
            Show entry: helm-bibtex-show-entry
          
          Best,
          
            Titus
          
          >
          > best
          >
          > Z
          >
          > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <malsburg@posteo.de>
          > wrote:
          >
          >>
          >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
          >> > Hi Titus and thx so much for the answers!
          >> >
          >> > i will in the future use the github page to make requests.
          >> >
          >> > "The number of matches will be displayed in the mode line. "
          >> >
          >> > i see that now thx! :) the problem was(is) that its colored black on my
          >> > black modline BG which makes it invisible ;-) i assume thats an helm
          >> config
          >> > i need to change
          >> >
          >> >
          >> > "If you don’t want to type these search expressions, you could create a
          >> > command that invokes helm-bibtex with a default search expression and
          >> that
          >> > command could be bound to a keyboard shortcut."
          >> >
          >> > that would be prefect for me and a solution to my issue. would you mind
          >> > giving an example of such a code chunk. unfortunately i dont know elisp
          >> though
          >> > as john recommended i will do my best this summer when the semester ends
          >> to
          >> > try and pick it up :)
          >>
          >> Sure, here you go:
          >>
          >> #+BEGIN_SRC elisp
          >> ;; Define helm-search with predefined search expression:
          >> (defun helm-bibtex-my-publications ()
          >>   "Search BibTeX entries authored by Xebar Saram."
          >>   (interactive)
          >>   (helm :sources '(helm-source-bibtex)
          >>         :full-frame t
          >>         :input "xebar saram"
          >>         :candidate-number-limit 500))
          >>
          >> ;; Bind this search function to Ctrl-x p:
          >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
          >> #+END_SRC
          >>
          >> > i will definitely use your tag system as you recommended, sounds perfect
          >> > for me
          >>
          >> The tag system also comes in handy when generating publication lists for
          >> CVs and web pages because BibTeX does not distinguish between conference
          >> papers, posters, and talks.  If you have tags for that, it’s relatively
          >> easy to create separate sections for these types of publications using
          >> biblatex or bib2bib and bibtex2html in the case of web pages.
          >>
          >> > thanks again for your kind help and the amazing app ;-)
          >>
          >> You are welcome.
          >>
          >>   Titus
          >>
          >> >
          >> > best
          >> >
          >> > Z
          >> >
          >> >
          >> >
          >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
          >> malsburg@posteo.de
          >> >> wrote:
          >> >
          >> >>
          >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
          >> >> > Hi Titus
          >> >> >
          >> >> > I have been exploring helm-bibtex a bit today and have some questions.
          >> >> btw
          >> >> > is this the preferred way to make requests/ask questions or is
          >> >> > github preferred?
          >> >>
          >> >> Helm-bibtex is not part of org (although it tries to work well with
          >> >> org).  So I’m not sure whether this list is the best place for
          >> >> discussing it.  For now the issue tracker on Github might be a better
          >> >> option:
          >> >>
          >> >>   https://github.com/tmalsburg/helm-bibtex/issues
          >> >>
          >> >> > in any case i was wondering a few things:
          >> >> >
          >> >> > 1. is it possible to have custom sorting? i want all views to sort by
          >> >> > Author, year, month
          >> >>
          >> >> I prefer to see the entries in the (inverse) order in which they appear
          >> >> in the BibTeX file.  This way, recent additions show up at the
          >> >> top.  However, I agree that sorting would be useful (see issues #5 and
          >> >> #21); it just doesn’t have high priority for me.  Pull requests welcome.
          >> >>
          >> >> > 2. i would really like a way to have stored smart groups (like the
          >> jabref
          >> >> > dynamic groups if your aware of that). that is for example create a
          >> group
          >> >> > that auto selects all publications i have (by my first/last name) and
          >> >> shows
          >> >> > the count (in numbers) of these publications.
          >> >>
          >> >> I’m not familiar with smart groups but it seems that all helm-bibtex is
          >> >> doing is giving you very flexible smart groups defined by your search
          >> >> expressions.  For example, if you want a list of your publications, you
          >> >> can simple enter your name.  And if you want a list of your articles,
          >> >> you can enter your name + “article”.  If you want all your articles from
          >> >> 2010, enter your name + “articles 2010”.  And so on.  The number of
          >> >> matches will be displayed in the mode line.  If you don’t want to type
          >> >> these search expressions, you could create a command that invokes
          >> >> helm-bibtex with a default search expression and that command could be
          >> >> bound to a keyboard shortcut.
          >> >>
          >> >> > Another example is a group to keep track of all the papers im working
          >> on
          >> >> or
          >> >> > invloved with by matching keyword author and prep/*other key word
          >> >>
          >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
          >> >> describing the content of the paper (as usual) and “tags” for meta
          >> >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
          >> >> “talk”, … So if I want a list of all articles in progress, I search for
          >> >> “own manuscript”.  Since the tags field is non-standard, it has to be
          >> >> added to `helm-bibtex-additional-search-fields`.
          >> >>
          >> >> Another solution would be to use the pubstate field and to search for
          >> >> your name and “forthcoming” (add pubstate to
          >> >> helm-bibtex-additional-search-fields for this to work).
          >> >>
          >> >> > 3.is it possible to ass an option to auto generate a bibkey for a
          >> >> selected
          >> >> > citation based on user criteria such as author(date)short-title?
          >> >>
          >> >> Maintaining the content of the BibTeX file not really in the scope of
          >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
          >> >> org-ref or ebib can help here?  Once you have a function that generates
          >> >> a new key and inserts it in the BibTeX file, you can easily add it to
          >> >> the list of actions in helm-bibtex.
          >> >>
          >> >> Hope that helps.
          >> >>
          >> >>   Titus
          >> >>
          >> >> > thx so much in advance, you and john have given me confidence to
          >> finally
          >> >> > dive into the whole latex/bibteX world
          >> >> >
          >> >> > best
          >> >> >
          >> >> > Z
          >> >>
          >> >>
          >>
          >>
          
          
          [-- Attachment #2: signature.asc --]
          [-- Type: application/pgp-signature, Size: 472 bytes --]
          
          ^ permalink raw reply	[flat|nested] 26+ messages in thread

        • • * Re: helm-bibtex questions
              2015-06-21 18:29         ` Titus von der Malsburg
            @ 2015-06-21 18:40           ` John Kitchin
              2015-06-22 14:28             ` Xebar Saram
              0 siblings, 1 reply; 26+ messages in thread
            From: John Kitchin @ 2015-06-21 18:40 UTC (permalink / raw)
              To: Titus von der Malsburg; +Cc: Xebar Saram, org mode
            
            [-- Attachment #1: Type: text/plain, Size: 8321 bytes --]
            
            sweet! I did not know you could do that! I will be refactoring org-ref soon
            to do that instead of redefining the commands!
            
            John
            
            -----------------------------------
            Professor John Kitchin
            Doherty Hall A207F
            Department of Chemical Engineering
            Carnegie Mellon University
            Pittsburgh, PA 15213
            412-268-7803
            @johnkitchin
            http://kitchingroup.cheme.cmu.edu
            
            
            On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <malsburg@posteo.de>
            wrote:
            
            >
            > On 2015-06-19 Fri 03:56, Xebar Saram wrote:
            > > Hi again Titus
            > >
            > > 2 quick questions that arose from using helm-bitex today extensively:
            > >
            > > how does one exclude in the search items? for example i want to search
            > for
            > > xebar without keyword "progress" (I want to exclude in progress articles
            > > not published yet)
            > >
            > > is it possible to define default enter command in helm-bibtex ?
            >
            > Yes.  Helm uses the first action as the default action.  To move an
            > action to the top of the list you can use the following code:
            >
            >   (helm-delete-action-from-source "Insert BibTeX key" helm-source-bibtex)
            >   (helm-add-action-to-source "Insert BibTeX key" 'helm-bibtex-insert-key
            > helm-source-bibtex 0)
            >
            > The second argument in the second line is the function that executes the
            > action.  Here is a list of all actions and their functions:
            >
            >   Open PDF file (if present): helm-bibtex-open-pdf
            >   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
            >   Insert citation: helm-bibtex-insert-citation
            >   Insert reference: helm-bibtex-insert-reference
            >   Insert BibTeX key: helm-bibtex-insert-key
            >   Insert BibTeX entry: helm-bibtex-insert-bibtex
            >   Attach PDF to email: helm-bibtex-add-PDF-attachment
            >   Edit notes: helm-bibtex-edit-notes
            >   Show entry: helm-bibtex-show-entry
            >
            > Best,
            >
            >   Titus
            >
            > >
            > > best
            > >
            > > Z
            > >
            > > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
            > malsburg@posteo.de>
            > > wrote:
            > >
            > >>
            > >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
            > >> > Hi Titus and thx so much for the answers!
            > >> >
            > >> > i will in the future use the github page to make requests.
            > >> >
            > >> > "The number of matches will be displayed in the mode line. "
            > >> >
            > >> > i see that now thx! :) the problem was(is) that its colored black on
            > my
            > >> > black modline BG which makes it invisible ;-) i assume thats an helm
            > >> config
            > >> > i need to change
            > >> >
            > >> >
            > >> > "If you don’t want to type these search expressions, you could create
            > a
            > >> > command that invokes helm-bibtex with a default search expression and
            > >> that
            > >> > command could be bound to a keyboard shortcut."
            > >> >
            > >> > that would be prefect for me and a solution to my issue. would you
            > mind
            > >> > giving an example of such a code chunk. unfortunately i dont know
            > elisp
            > >> though
            > >> > as john recommended i will do my best this summer when the semester
            > ends
            > >> to
            > >> > try and pick it up :)
            > >>
            > >> Sure, here you go:
            > >>
            > >> #+BEGIN_SRC elisp
            > >> ;; Define helm-search with predefined search expression:
            > >> (defun helm-bibtex-my-publications ()
            > >>   "Search BibTeX entries authored by Xebar Saram."
            > >>   (interactive)
            > >>   (helm :sources '(helm-source-bibtex)
            > >>         :full-frame t
            > >>         :input "xebar saram"
            > >>         :candidate-number-limit 500))
            > >>
            > >> ;; Bind this search function to Ctrl-x p:
            > >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
            > >> #+END_SRC
            > >>
            > >> > i will definitely use your tag system as you recommended, sounds
            > perfect
            > >> > for me
            > >>
            > >> The tag system also comes in handy when generating publication lists for
            > >> CVs and web pages because BibTeX does not distinguish between conference
            > >> papers, posters, and talks.  If you have tags for that, it’s relatively
            > >> easy to create separate sections for these types of publications using
            > >> biblatex or bib2bib and bibtex2html in the case of web pages.
            > >>
            > >> > thanks again for your kind help and the amazing app ;-)
            > >>
            > >> You are welcome.
            > >>
            > >>   Titus
            > >>
            > >> >
            > >> > best
            > >> >
            > >> > Z
            > >> >
            > >> >
            > >> >
            > >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
            > >> malsburg@posteo.de
            > >> >> wrote:
            > >> >
            > >> >>
            > >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
            > >> >> > Hi Titus
            > >> >> >
            > >> >> > I have been exploring helm-bibtex a bit today and have some
            > questions.
            > >> >> btw
            > >> >> > is this the preferred way to make requests/ask questions or is
            > >> >> > github preferred?
            > >> >>
            > >> >> Helm-bibtex is not part of org (although it tries to work well with
            > >> >> org).  So I’m not sure whether this list is the best place for
            > >> >> discussing it.  For now the issue tracker on Github might be a better
            > >> >> option:
            > >> >>
            > >> >>   https://github.com/tmalsburg/helm-bibtex/issues
            > >> >>
            > >> >> > in any case i was wondering a few things:
            > >> >> >
            > >> >> > 1. is it possible to have custom sorting? i want all views to sort
            > by
            > >> >> > Author, year, month
            > >> >>
            > >> >> I prefer to see the entries in the (inverse) order in which they
            > appear
            > >> >> in the BibTeX file.  This way, recent additions show up at the
            > >> >> top.  However, I agree that sorting would be useful (see issues #5
            > and
            > >> >> #21); it just doesn’t have high priority for me.  Pull requests
            > welcome.
            > >> >>
            > >> >> > 2. i would really like a way to have stored smart groups (like the
            > >> jabref
            > >> >> > dynamic groups if your aware of that). that is for example create a
            > >> group
            > >> >> > that auto selects all publications i have (by my first/last name)
            > and
            > >> >> shows
            > >> >> > the count (in numbers) of these publications.
            > >> >>
            > >> >> I’m not familiar with smart groups but it seems that all helm-bibtex
            > is
            > >> >> doing is giving you very flexible smart groups defined by your search
            > >> >> expressions.  For example, if you want a list of your publications,
            > you
            > >> >> can simple enter your name.  And if you want a list of your articles,
            > >> >> you can enter your name + “article”.  If you want all your articles
            > from
            > >> >> 2010, enter your name + “articles 2010”.  And so on.  The number of
            > >> >> matches will be displayed in the mode line.  If you don’t want to
            > type
            > >> >> these search expressions, you could create a command that invokes
            > >> >> helm-bibtex with a default search expression and that command could
            > be
            > >> >> bound to a keyboard shortcut.
            > >> >>
            > >> >> > Another example is a group to keep track of all the papers im
            > working
            > >> on
            > >> >> or
            > >> >> > invloved with by matching keyword author and prep/*other key word
            > >> >>
            > >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
            > >> >> describing the content of the paper (as usual) and “tags” for meta
            > >> >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
            > >> >> “talk”, … So if I want a list of all articles in progress, I search
            > for
            > >> >> “own manuscript”.  Since the tags field is non-standard, it has to be
            > >> >> added to `helm-bibtex-additional-search-fields`.
            > >> >>
            > >> >> Another solution would be to use the pubstate field and to search for
            > >> >> your name and “forthcoming” (add pubstate to
            > >> >> helm-bibtex-additional-search-fields for this to work).
            > >> >>
            > >> >> > 3.is it possible to ass an option to auto generate a bibkey for a
            > >> >> selected
            > >> >> > citation based on user criteria such as author(date)short-title?
            > >> >>
            > >> >> Maintaining the content of the BibTeX file not really in the scope of
            > >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
            > >> >> org-ref or ebib can help here?  Once you have a function that
            > generates
            > >> >> a new key and inserts it in the BibTeX file, you can easily add it to
            > >> >> the list of actions in helm-bibtex.
            > >> >>
            > >> >> Hope that helps.
            > >> >>
            > >> >>   Titus
            > >> >>
            > >> >> > thx so much in advance, you and john have given me confidence to
            > >> finally
            > >> >> > dive into the whole latex/bibteX world
            > >> >> >
            > >> >> > best
            > >> >> >
            > >> >> > Z
            > >> >>
            > >> >>
            > >>
            > >>
            >
            >
            
            [-- Attachment #2: Type: text/html, Size: 11248 bytes --]
            
            ^ permalink raw reply	[flat|nested] 26+ messages in thread

          • • * Re: helm-bibtex questions
                2015-06-21 18:40           ` John Kitchin
              @ 2015-06-22 14:28             ` Xebar Saram
                2015-06-22 15:12               ` Titus von der Malsburg
                0 siblings, 1 reply; 26+ messages in thread
              From: Xebar Saram @ 2015-06-22 14:28 UTC (permalink / raw)
                To: John Kitchin; +Cc: org mode
              
              [-- Attachment #1: Type: text/plain, Size: 8975 bytes --]
              
              Hi John
              
              a bit off topic, but do you also write your academic CV in orgmode or
              lateX? in anycase would you mind sharing your org/latex CV template? it
              would be helpful as a starting point for me if thats possible.
              
              kind regards and thanks so much in advance
              
              Z
              
              On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
              wrote:
              
              > sweet! I did not know you could do that! I will be refactoring org-ref
              > soon to do that instead of redefining the commands!
              >
              > John
              >
              > -----------------------------------
              > Professor John Kitchin
              > Doherty Hall A207F
              > Department of Chemical Engineering
              > Carnegie Mellon University
              > Pittsburgh, PA 15213
              > 412-268-7803
              > @johnkitchin
              > http://kitchingroup.cheme.cmu.edu
              >
              >
              > On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
              > malsburg@posteo.de> wrote:
              >
              >>
              >> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
              >> > Hi again Titus
              >> >
              >> > 2 quick questions that arose from using helm-bitex today extensively:
              >> >
              >> > how does one exclude in the search items? for example i want to search
              >> for
              >> > xebar without keyword "progress" (I want to exclude in progress articles
              >> > not published yet)
              >> >
              >> > is it possible to define default enter command in helm-bibtex ?
              >>
              >> Yes.  Helm uses the first action as the default action.  To move an
              >> action to the top of the list you can use the following code:
              >>
              >>   (helm-delete-action-from-source "Insert BibTeX key" helm-source-bibtex)
              >>   (helm-add-action-to-source "Insert BibTeX key" 'helm-bibtex-insert-key
              >> helm-source-bibtex 0)
              >>
              >> The second argument in the second line is the function that executes the
              >> action.  Here is a list of all actions and their functions:
              >>
              >>   Open PDF file (if present): helm-bibtex-open-pdf
              >>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
              >>   Insert citation: helm-bibtex-insert-citation
              >>   Insert reference: helm-bibtex-insert-reference
              >>   Insert BibTeX key: helm-bibtex-insert-key
              >>   Insert BibTeX entry: helm-bibtex-insert-bibtex
              >>   Attach PDF to email: helm-bibtex-add-PDF-attachment
              >>   Edit notes: helm-bibtex-edit-notes
              >>   Show entry: helm-bibtex-show-entry
              >>
              >> Best,
              >>
              >>   Titus
              >>
              >> >
              >> > best
              >> >
              >> > Z
              >> >
              >> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
              >> malsburg@posteo.de>
              >> > wrote:
              >> >
              >> >>
              >> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
              >> >> > Hi Titus and thx so much for the answers!
              >> >> >
              >> >> > i will in the future use the github page to make requests.
              >> >> >
              >> >> > "The number of matches will be displayed in the mode line. "
              >> >> >
              >> >> > i see that now thx! :) the problem was(is) that its colored black on
              >> my
              >> >> > black modline BG which makes it invisible ;-) i assume thats an helm
              >> >> config
              >> >> > i need to change
              >> >> >
              >> >> >
              >> >> > "If you don’t want to type these search expressions, you could
              >> create a
              >> >> > command that invokes helm-bibtex with a default search expression and
              >> >> that
              >> >> > command could be bound to a keyboard shortcut."
              >> >> >
              >> >> > that would be prefect for me and a solution to my issue. would you
              >> mind
              >> >> > giving an example of such a code chunk. unfortunately i dont know
              >> elisp
              >> >> though
              >> >> > as john recommended i will do my best this summer when the semester
              >> ends
              >> >> to
              >> >> > try and pick it up :)
              >> >>
              >> >> Sure, here you go:
              >> >>
              >> >> #+BEGIN_SRC elisp
              >> >> ;; Define helm-search with predefined search expression:
              >> >> (defun helm-bibtex-my-publications ()
              >> >>   "Search BibTeX entries authored by Xebar Saram."
              >> >>   (interactive)
              >> >>   (helm :sources '(helm-source-bibtex)
              >> >>         :full-frame t
              >> >>         :input "xebar saram"
              >> >>         :candidate-number-limit 500))
              >> >>
              >> >> ;; Bind this search function to Ctrl-x p:
              >> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
              >> >> #+END_SRC
              >> >>
              >> >> > i will definitely use your tag system as you recommended, sounds
              >> perfect
              >> >> > for me
              >> >>
              >> >> The tag system also comes in handy when generating publication lists
              >> for
              >> >> CVs and web pages because BibTeX does not distinguish between
              >> conference
              >> >> papers, posters, and talks.  If you have tags for that, it’s relatively
              >> >> easy to create separate sections for these types of publications using
              >> >> biblatex or bib2bib and bibtex2html in the case of web pages.
              >> >>
              >> >> > thanks again for your kind help and the amazing app ;-)
              >> >>
              >> >> You are welcome.
              >> >>
              >> >>   Titus
              >> >>
              >> >> >
              >> >> > best
              >> >> >
              >> >> > Z
              >> >> >
              >> >> >
              >> >> >
              >> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
              >> >> malsburg@posteo.de
              >> >> >> wrote:
              >> >> >
              >> >> >>
              >> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
              >> >> >> > Hi Titus
              >> >> >> >
              >> >> >> > I have been exploring helm-bibtex a bit today and have some
              >> questions.
              >> >> >> btw
              >> >> >> > is this the preferred way to make requests/ask questions or is
              >> >> >> > github preferred?
              >> >> >>
              >> >> >> Helm-bibtex is not part of org (although it tries to work well with
              >> >> >> org).  So I’m not sure whether this list is the best place for
              >> >> >> discussing it.  For now the issue tracker on Github might be a
              >> better
              >> >> >> option:
              >> >> >>
              >> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
              >> >> >>
              >> >> >> > in any case i was wondering a few things:
              >> >> >> >
              >> >> >> > 1. is it possible to have custom sorting? i want all views to
              >> sort by
              >> >> >> > Author, year, month
              >> >> >>
              >> >> >> I prefer to see the entries in the (inverse) order in which they
              >> appear
              >> >> >> in the BibTeX file.  This way, recent additions show up at the
              >> >> >> top.  However, I agree that sorting would be useful (see issues #5
              >> and
              >> >> >> #21); it just doesn’t have high priority for me.  Pull requests
              >> welcome.
              >> >> >>
              >> >> >> > 2. i would really like a way to have stored smart groups (like the
              >> >> jabref
              >> >> >> > dynamic groups if your aware of that). that is for example create
              >> a
              >> >> group
              >> >> >> > that auto selects all publications i have (by my first/last name)
              >> and
              >> >> >> shows
              >> >> >> > the count (in numbers) of these publications.
              >> >> >>
              >> >> >> I’m not familiar with smart groups but it seems that all
              >> helm-bibtex is
              >> >> >> doing is giving you very flexible smart groups defined by your
              >> search
              >> >> >> expressions.  For example, if you want a list of your publications,
              >> you
              >> >> >> can simple enter your name.  And if you want a list of your
              >> articles,
              >> >> >> you can enter your name + “article”.  If you want all your articles
              >> from
              >> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number of
              >> >> >> matches will be displayed in the mode line.  If you don’t want to
              >> type
              >> >> >> these search expressions, you could create a command that invokes
              >> >> >> helm-bibtex with a default search expression and that command could
              >> be
              >> >> >> bound to a keyboard shortcut.
              >> >> >>
              >> >> >> > Another example is a group to keep track of all the papers im
              >> working
              >> >> on
              >> >> >> or
              >> >> >> > invloved with by matching keyword author and prep/*other key word
              >> >> >>
              >> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
              >> >> >> describing the content of the paper (as usual) and “tags” for meta
              >> >> >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
              >> >> >> “talk”, … So if I want a list of all articles in progress, I search
              >> for
              >> >> >> “own manuscript”.  Since the tags field is non-standard, it has to
              >> be
              >> >> >> added to `helm-bibtex-additional-search-fields`.
              >> >> >>
              >> >> >> Another solution would be to use the pubstate field and to search
              >> for
              >> >> >> your name and “forthcoming” (add pubstate to
              >> >> >> helm-bibtex-additional-search-fields for this to work).
              >> >> >>
              >> >> >> > 3.is it possible to ass an option to auto generate a bibkey for a
              >> >> >> selected
              >> >> >> > citation based on user criteria such as author(date)short-title?
              >> >> >>
              >> >> >> Maintaining the content of the BibTeX file not really in the scope
              >> of
              >> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
              >> >> >> org-ref or ebib can help here?  Once you have a function that
              >> generates
              >> >> >> a new key and inserts it in the BibTeX file, you can easily add it
              >> to
              >> >> >> the list of actions in helm-bibtex.
              >> >> >>
              >> >> >> Hope that helps.
              >> >> >>
              >> >> >>   Titus
              >> >> >>
              >> >> >> > thx so much in advance, you and john have given me confidence to
              >> >> finally
              >> >> >> > dive into the whole latex/bibteX world
              >> >> >> >
              >> >> >> > best
              >> >> >> >
              >> >> >> > Z
              >> >> >>
              >> >> >>
              >> >>
              >> >>
              >>
              >>
              >
              
              [-- Attachment #2: Type: text/html, Size: 12056 bytes --]
              
              ^ permalink raw reply	[flat|nested] 26+ messages in thread

            • • * Re: helm-bibtex questions
                  2015-06-22 14:28             ` Xebar Saram
                @ 2015-06-22 15:12               ` Titus von der Malsburg
                  2015-06-24 19:54                 ` Xebar Saram
                  2015-06-26  7:21                 ` Xebar Saram
                  0 siblings, 2 replies; 26+ messages in thread
                From: Titus von der Malsburg @ 2015-06-22 15:12 UTC (permalink / raw)
                  To: Xebar Saram; +Cc: org mode, John Kitchin
                
                [-- Attachment #1: Type: text/plain, Size: 9926 bytes --]
                
                
                
                Here is my CV in org-mode:
                
                  https://gist.github.com/tmalsburg/96084ba82281937c26b7
                
                It’s a pretty straightforward org document except for one thing: the key
                to making this work was biblatex which can be used to create several
                lists of references filtered according to keywords, author, etc.  This
                allowed me to have separate sections for journal articles, conference
                presentations, etc.  I store the relevant keywords in the tags field of
                the BibTeX entries and since biblatex doesn’t know this field, I copy
                the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                LaTeX headers).
                
                  Titus
                
                On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                > Hi John
                >
                > a bit off topic, but do you also write your academic CV in orgmode or
                > lateX? in anycase would you mind sharing your org/latex CV template? it
                > would be helpful as a starting point for me if thats possible.
                >
                > kind regards and thanks so much in advance
                >
                > Z
                >
                > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                > wrote:
                >
                >> sweet! I did not know you could do that! I will be refactoring org-ref
                >> soon to do that instead of redefining the commands!
                >>
                >> John
                >>
                >> -----------------------------------
                >> Professor John Kitchin
                >> Doherty Hall A207F
                >> Department of Chemical Engineering
                >> Carnegie Mellon University
                >> Pittsburgh, PA 15213
                >> 412-268-7803
                >> @johnkitchin
                >> http://kitchingroup.cheme.cmu.edu
                >>
                >>
                >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                >> malsburg@posteo.de> wrote:
                >>
                >>>
                >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                >>> > Hi again Titus
                >>> >
                >>> > 2 quick questions that arose from using helm-bitex today extensively:
                >>> >
                >>> > how does one exclude in the search items? for example i want to search
                >>> for
                >>> > xebar without keyword "progress" (I want to exclude in progress articles
                >>> > not published yet)
                >>> >
                >>> > is it possible to define default enter command in helm-bibtex ?
                >>>
                >>> Yes.  Helm uses the first action as the default action.  To move an
                >>> action to the top of the list you can use the following code:
                >>>
                >>>   (helm-delete-action-from-source "Insert BibTeX key" helm-source-bibtex)
                >>>   (helm-add-action-to-source "Insert BibTeX key" 'helm-bibtex-insert-key
                >>> helm-source-bibtex 0)
                >>>
                >>> The second argument in the second line is the function that executes the
                >>> action.  Here is a list of all actions and their functions:
                >>>
                >>>   Open PDF file (if present): helm-bibtex-open-pdf
                >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                >>>   Insert citation: helm-bibtex-insert-citation
                >>>   Insert reference: helm-bibtex-insert-reference
                >>>   Insert BibTeX key: helm-bibtex-insert-key
                >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                >>>   Edit notes: helm-bibtex-edit-notes
                >>>   Show entry: helm-bibtex-show-entry
                >>>
                >>> Best,
                >>>
                >>>   Titus
                >>>
                >>> >
                >>> > best
                >>> >
                >>> > Z
                >>> >
                >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                >>> malsburg@posteo.de>
                >>> > wrote:
                >>> >
                >>> >>
                >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                >>> >> > Hi Titus and thx so much for the answers!
                >>> >> >
                >>> >> > i will in the future use the github page to make requests.
                >>> >> >
                >>> >> > "The number of matches will be displayed in the mode line. "
                >>> >> >
                >>> >> > i see that now thx! :) the problem was(is) that its colored black on
                >>> my
                >>> >> > black modline BG which makes it invisible ;-) i assume thats an helm
                >>> >> config
                >>> >> > i need to change
                >>> >> >
                >>> >> >
                >>> >> > "If you don’t want to type these search expressions, you could
                >>> create a
                >>> >> > command that invokes helm-bibtex with a default search expression and
                >>> >> that
                >>> >> > command could be bound to a keyboard shortcut."
                >>> >> >
                >>> >> > that would be prefect for me and a solution to my issue. would you
                >>> mind
                >>> >> > giving an example of such a code chunk. unfortunately i dont know
                >>> elisp
                >>> >> though
                >>> >> > as john recommended i will do my best this summer when the semester
                >>> ends
                >>> >> to
                >>> >> > try and pick it up :)
                >>> >>
                >>> >> Sure, here you go:
                >>> >>
                >>> >> #+BEGIN_SRC elisp
                >>> >> ;; Define helm-search with predefined search expression:
                >>> >> (defun helm-bibtex-my-publications ()
                >>> >>   "Search BibTeX entries authored by Xebar Saram."
                >>> >>   (interactive)
                >>> >>   (helm :sources '(helm-source-bibtex)
                >>> >>         :full-frame t
                >>> >>         :input "xebar saram"
                >>> >>         :candidate-number-limit 500))
                >>> >>
                >>> >> ;; Bind this search function to Ctrl-x p:
                >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                >>> >> #+END_SRC
                >>> >>
                >>> >> > i will definitely use your tag system as you recommended, sounds
                >>> perfect
                >>> >> > for me
                >>> >>
                >>> >> The tag system also comes in handy when generating publication lists
                >>> for
                >>> >> CVs and web pages because BibTeX does not distinguish between
                >>> conference
                >>> >> papers, posters, and talks.  If you have tags for that, it’s relatively
                >>> >> easy to create separate sections for these types of publications using
                >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                >>> >>
                >>> >> > thanks again for your kind help and the amazing app ;-)
                >>> >>
                >>> >> You are welcome.
                >>> >>
                >>> >>   Titus
                >>> >>
                >>> >> >
                >>> >> > best
                >>> >> >
                >>> >> > Z
                >>> >> >
                >>> >> >
                >>> >> >
                >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                >>> >> malsburg@posteo.de
                >>> >> >> wrote:
                >>> >> >
                >>> >> >>
                >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                >>> >> >> > Hi Titus
                >>> >> >> >
                >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                >>> questions.
                >>> >> >> btw
                >>> >> >> > is this the preferred way to make requests/ask questions or is
                >>> >> >> > github preferred?
                >>> >> >>
                >>> >> >> Helm-bibtex is not part of org (although it tries to work well with
                >>> >> >> org).  So I’m not sure whether this list is the best place for
                >>> >> >> discussing it.  For now the issue tracker on Github might be a
                >>> better
                >>> >> >> option:
                >>> >> >>
                >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                >>> >> >>
                >>> >> >> > in any case i was wondering a few things:
                >>> >> >> >
                >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                >>> sort by
                >>> >> >> > Author, year, month
                >>> >> >>
                >>> >> >> I prefer to see the entries in the (inverse) order in which they
                >>> appear
                >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                >>> >> >> top.  However, I agree that sorting would be useful (see issues #5
                >>> and
                >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                >>> welcome.
                >>> >> >>
                >>> >> >> > 2. i would really like a way to have stored smart groups (like the
                >>> >> jabref
                >>> >> >> > dynamic groups if your aware of that). that is for example create
                >>> a
                >>> >> group
                >>> >> >> > that auto selects all publications i have (by my first/last name)
                >>> and
                >>> >> >> shows
                >>> >> >> > the count (in numbers) of these publications.
                >>> >> >>
                >>> >> >> I’m not familiar with smart groups but it seems that all
                >>> helm-bibtex is
                >>> >> >> doing is giving you very flexible smart groups defined by your
                >>> search
                >>> >> >> expressions.  For example, if you want a list of your publications,
                >>> you
                >>> >> >> can simple enter your name.  And if you want a list of your
                >>> articles,
                >>> >> >> you can enter your name + “article”.  If you want all your articles
                >>> from
                >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number of
                >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                >>> type
                >>> >> >> these search expressions, you could create a command that invokes
                >>> >> >> helm-bibtex with a default search expression and that command could
                >>> be
                >>> >> >> bound to a keyboard shortcut.
                >>> >> >>
                >>> >> >> > Another example is a group to keep track of all the papers im
                >>> working
                >>> >> on
                >>> >> >> or
                >>> >> >> > invloved with by matching keyword author and prep/*other key word
                >>> >> >>
                >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                >>> >> >> describing the content of the paper (as usual) and “tags” for meta
                >>> >> >> data.  Values that I use in tags are “own”, “manuscript”, “poster”,
                >>> >> >> “talk”, … So if I want a list of all articles in progress, I search
                >>> for
                >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has to
                >>> be
                >>> >> >> added to `helm-bibtex-additional-search-fields`.
                >>> >> >>
                >>> >> >> Another solution would be to use the pubstate field and to search
                >>> for
                >>> >> >> your name and “forthcoming” (add pubstate to
                >>> >> >> helm-bibtex-additional-search-fields for this to work).
                >>> >> >>
                >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey for a
                >>> >> >> selected
                >>> >> >> > citation based on user criteria such as author(date)short-title?
                >>> >> >>
                >>> >> >> Maintaining the content of the BibTeX file not really in the scope
                >>> of
                >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
                >>> >> >> org-ref or ebib can help here?  Once you have a function that
                >>> generates
                >>> >> >> a new key and inserts it in the BibTeX file, you can easily add it
                >>> to
                >>> >> >> the list of actions in helm-bibtex.
                >>> >> >>
                >>> >> >> Hope that helps.
                >>> >> >>
                >>> >> >>   Titus
                >>> >> >>
                >>> >> >> > thx so much in advance, you and john have given me confidence to
                >>> >> finally
                >>> >> >> > dive into the whole latex/bibteX world
                >>> >> >> >
                >>> >> >> > best
                >>> >> >> >
                >>> >> >> > Z
                >>> >> >>
                >>> >> >>
                >>> >>
                >>> >>
                >>>
                >>>
                >>
                
                
                [-- Attachment #2: signature.asc --]
                [-- Type: application/pgp-signature, Size: 472 bytes --]
                
                ^ permalink raw reply	[flat|nested] 26+ messages in thread

              • • * Re: helm-bibtex questions
                    2015-06-22 15:12               ` Titus von der Malsburg
                  @ 2015-06-24 19:54                 ` Xebar Saram
                    2015-06-24 21:03                   ` John Kitchin
                    2015-06-26  7:21                 ` Xebar Saram
                    1 sibling, 1 reply; 26+ messages in thread
                  From: Xebar Saram @ 2015-06-24 19:54 UTC (permalink / raw)
                    To: Titus von der Malsburg; +Cc: org mode, John Kitchin
                  
                  [-- Attachment #1: Type: text/plain, Size: 11016 bytes --]
                  
                  John
                  
                  First of all thanks so much for the excellent org-ref-clean-bibtex-entry
                  function i love it!
                  also your blog post on cleaning the bib file is a life saver
                  
                  i have 800 references, is there a way to auto
                  make org-ref-clean-bibtex-entry go thorough my whole bib file instead of me
                  going and cleaning it 1 by 1?
                  
                  kind regards
                  
                  Z.
                  
                  On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de>
                  wrote:
                  
                  >
                  >
                  > Here is my CV in org-mode:
                  >
                  >   https://gist.github.com/tmalsburg/96084ba82281937c26b7
                  >
                  > It’s a pretty straightforward org document except for one thing: the key
                  > to making this work was biblatex which can be used to create several
                  > lists of references filtered according to keywords, author, etc.  This
                  > allowed me to have separate sections for journal articles, conference
                  > presentations, etc.  I store the relevant keywords in the tags field of
                  > the BibTeX entries and since biblatex doesn’t know this field, I copy
                  > the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                  > LaTeX headers).
                  >
                  >   Titus
                  >
                  > On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                  > > Hi John
                  > >
                  > > a bit off topic, but do you also write your academic CV in orgmode or
                  > > lateX? in anycase would you mind sharing your org/latex CV template? it
                  > > would be helpful as a starting point for me if thats possible.
                  > >
                  > > kind regards and thanks so much in advance
                  > >
                  > > Z
                  > >
                  > > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                  > > wrote:
                  > >
                  > >> sweet! I did not know you could do that! I will be refactoring org-ref
                  > >> soon to do that instead of redefining the commands!
                  > >>
                  > >> John
                  > >>
                  > >> -----------------------------------
                  > >> Professor John Kitchin
                  > >> Doherty Hall A207F
                  > >> Department of Chemical Engineering
                  > >> Carnegie Mellon University
                  > >> Pittsburgh, PA 15213
                  > >> 412-268-7803
                  > >> @johnkitchin
                  > >> http://kitchingroup.cheme.cmu.edu
                  > >>
                  > >>
                  > >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                  > >> malsburg@posteo.de> wrote:
                  > >>
                  > >>>
                  > >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                  > >>> > Hi again Titus
                  > >>> >
                  > >>> > 2 quick questions that arose from using helm-bitex today extensively:
                  > >>> >
                  > >>> > how does one exclude in the search items? for example i want to
                  > search
                  > >>> for
                  > >>> > xebar without keyword "progress" (I want to exclude in progress
                  > articles
                  > >>> > not published yet)
                  > >>> >
                  > >>> > is it possible to define default enter command in helm-bibtex ?
                  > >>>
                  > >>> Yes.  Helm uses the first action as the default action.  To move an
                  > >>> action to the top of the list you can use the following code:
                  > >>>
                  > >>>   (helm-delete-action-from-source "Insert BibTeX key"
                  > helm-source-bibtex)
                  > >>>   (helm-add-action-to-source "Insert BibTeX key"
                  > 'helm-bibtex-insert-key
                  > >>> helm-source-bibtex 0)
                  > >>>
                  > >>> The second argument in the second line is the function that executes
                  > the
                  > >>> action.  Here is a list of all actions and their functions:
                  > >>>
                  > >>>   Open PDF file (if present): helm-bibtex-open-pdf
                  > >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                  > >>>   Insert citation: helm-bibtex-insert-citation
                  > >>>   Insert reference: helm-bibtex-insert-reference
                  > >>>   Insert BibTeX key: helm-bibtex-insert-key
                  > >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                  > >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                  > >>>   Edit notes: helm-bibtex-edit-notes
                  > >>>   Show entry: helm-bibtex-show-entry
                  > >>>
                  > >>> Best,
                  > >>>
                  > >>>   Titus
                  > >>>
                  > >>> >
                  > >>> > best
                  > >>> >
                  > >>> > Z
                  > >>> >
                  > >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                  > >>> malsburg@posteo.de>
                  > >>> > wrote:
                  > >>> >
                  > >>> >>
                  > >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                  > >>> >> > Hi Titus and thx so much for the answers!
                  > >>> >> >
                  > >>> >> > i will in the future use the github page to make requests.
                  > >>> >> >
                  > >>> >> > "The number of matches will be displayed in the mode line. "
                  > >>> >> >
                  > >>> >> > i see that now thx! :) the problem was(is) that its colored black
                  > on
                  > >>> my
                  > >>> >> > black modline BG which makes it invisible ;-) i assume thats an
                  > helm
                  > >>> >> config
                  > >>> >> > i need to change
                  > >>> >> >
                  > >>> >> >
                  > >>> >> > "If you don’t want to type these search expressions, you could
                  > >>> create a
                  > >>> >> > command that invokes helm-bibtex with a default search expression
                  > and
                  > >>> >> that
                  > >>> >> > command could be bound to a keyboard shortcut."
                  > >>> >> >
                  > >>> >> > that would be prefect for me and a solution to my issue. would you
                  > >>> mind
                  > >>> >> > giving an example of such a code chunk. unfortunately i dont know
                  > >>> elisp
                  > >>> >> though
                  > >>> >> > as john recommended i will do my best this summer when the
                  > semester
                  > >>> ends
                  > >>> >> to
                  > >>> >> > try and pick it up :)
                  > >>> >>
                  > >>> >> Sure, here you go:
                  > >>> >>
                  > >>> >> #+BEGIN_SRC elisp
                  > >>> >> ;; Define helm-search with predefined search expression:
                  > >>> >> (defun helm-bibtex-my-publications ()
                  > >>> >>   "Search BibTeX entries authored by Xebar Saram."
                  > >>> >>   (interactive)
                  > >>> >>   (helm :sources '(helm-source-bibtex)
                  > >>> >>         :full-frame t
                  > >>> >>         :input "xebar saram"
                  > >>> >>         :candidate-number-limit 500))
                  > >>> >>
                  > >>> >> ;; Bind this search function to Ctrl-x p:
                  > >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                  > >>> >> #+END_SRC
                  > >>> >>
                  > >>> >> > i will definitely use your tag system as you recommended, sounds
                  > >>> perfect
                  > >>> >> > for me
                  > >>> >>
                  > >>> >> The tag system also comes in handy when generating publication lists
                  > >>> for
                  > >>> >> CVs and web pages because BibTeX does not distinguish between
                  > >>> conference
                  > >>> >> papers, posters, and talks.  If you have tags for that, it’s
                  > relatively
                  > >>> >> easy to create separate sections for these types of publications
                  > using
                  > >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                  > >>> >>
                  > >>> >> > thanks again for your kind help and the amazing app ;-)
                  > >>> >>
                  > >>> >> You are welcome.
                  > >>> >>
                  > >>> >>   Titus
                  > >>> >>
                  > >>> >> >
                  > >>> >> > best
                  > >>> >> >
                  > >>> >> > Z
                  > >>> >> >
                  > >>> >> >
                  > >>> >> >
                  > >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                  > >>> >> malsburg@posteo.de
                  > >>> >> >> wrote:
                  > >>> >> >
                  > >>> >> >>
                  > >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                  > >>> >> >> > Hi Titus
                  > >>> >> >> >
                  > >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                  > >>> questions.
                  > >>> >> >> btw
                  > >>> >> >> > is this the preferred way to make requests/ask questions or is
                  > >>> >> >> > github preferred?
                  > >>> >> >>
                  > >>> >> >> Helm-bibtex is not part of org (although it tries to work well
                  > with
                  > >>> >> >> org).  So I’m not sure whether this list is the best place for
                  > >>> >> >> discussing it.  For now the issue tracker on Github might be a
                  > >>> better
                  > >>> >> >> option:
                  > >>> >> >>
                  > >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                  > >>> >> >>
                  > >>> >> >> > in any case i was wondering a few things:
                  > >>> >> >> >
                  > >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                  > >>> sort by
                  > >>> >> >> > Author, year, month
                  > >>> >> >>
                  > >>> >> >> I prefer to see the entries in the (inverse) order in which they
                  > >>> appear
                  > >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                  > >>> >> >> top.  However, I agree that sorting would be useful (see issues
                  > #5
                  > >>> and
                  > >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                  > >>> welcome.
                  > >>> >> >>
                  > >>> >> >> > 2. i would really like a way to have stored smart groups (like
                  > the
                  > >>> >> jabref
                  > >>> >> >> > dynamic groups if your aware of that). that is for example
                  > create
                  > >>> a
                  > >>> >> group
                  > >>> >> >> > that auto selects all publications i have (by my first/last
                  > name)
                  > >>> and
                  > >>> >> >> shows
                  > >>> >> >> > the count (in numbers) of these publications.
                  > >>> >> >>
                  > >>> >> >> I’m not familiar with smart groups but it seems that all
                  > >>> helm-bibtex is
                  > >>> >> >> doing is giving you very flexible smart groups defined by your
                  > >>> search
                  > >>> >> >> expressions.  For example, if you want a list of your
                  > publications,
                  > >>> you
                  > >>> >> >> can simple enter your name.  And if you want a list of your
                  > >>> articles,
                  > >>> >> >> you can enter your name + “article”.  If you want all your
                  > articles
                  > >>> from
                  > >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
                  > of
                  > >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                  > >>> type
                  > >>> >> >> these search expressions, you could create a command that invokes
                  > >>> >> >> helm-bibtex with a default search expression and that command
                  > could
                  > >>> be
                  > >>> >> >> bound to a keyboard shortcut.
                  > >>> >> >>
                  > >>> >> >> > Another example is a group to keep track of all the papers im
                  > >>> working
                  > >>> >> on
                  > >>> >> >> or
                  > >>> >> >> > invloved with by matching keyword author and prep/*other key
                  > word
                  > >>> >> >>
                  > >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                  > >>> >> >> describing the content of the paper (as usual) and “tags” for
                  > meta
                  > >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
                  > “poster”,
                  > >>> >> >> “talk”, … So if I want a list of all articles in progress, I
                  > search
                  > >>> for
                  > >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
                  > to
                  > >>> be
                  > >>> >> >> added to `helm-bibtex-additional-search-fields`.
                  > >>> >> >>
                  > >>> >> >> Another solution would be to use the pubstate field and to search
                  > >>> for
                  > >>> >> >> your name and “forthcoming” (add pubstate to
                  > >>> >> >> helm-bibtex-additional-search-fields for this to work).
                  > >>> >> >>
                  > >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
                  > for a
                  > >>> >> >> selected
                  > >>> >> >> > citation based on user criteria such as
                  > author(date)short-title?
                  > >>> >> >>
                  > >>> >> >> Maintaining the content of the BibTeX file not really in the
                  > scope
                  > >>> of
                  > >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
                  > Perhaps
                  > >>> >> >> org-ref or ebib can help here?  Once you have a function that
                  > >>> generates
                  > >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
                  > it
                  > >>> to
                  > >>> >> >> the list of actions in helm-bibtex.
                  > >>> >> >>
                  > >>> >> >> Hope that helps.
                  > >>> >> >>
                  > >>> >> >>   Titus
                  > >>> >> >>
                  > >>> >> >> > thx so much in advance, you and john have given me confidence
                  > to
                  > >>> >> finally
                  > >>> >> >> > dive into the whole latex/bibteX world
                  > >>> >> >> >
                  > >>> >> >> > best
                  > >>> >> >> >
                  > >>> >> >> > Z
                  > >>> >> >>
                  > >>> >> >>
                  > >>> >>
                  > >>> >>
                  > >>>
                  > >>>
                  > >>
                  >
                  >
                  
                  [-- Attachment #2: Type: text/html, Size: 16596 bytes --]
                  
                  ^ permalink raw reply	[flat|nested] 26+ messages in thread

                • • * Re: helm-bibtex questions
                      2015-06-24 19:54                 ` Xebar Saram
                    @ 2015-06-24 21:03                   ` John Kitchin
                      0 siblings, 0 replies; 26+ messages in thread
                    From: John Kitchin @ 2015-06-24 21:03 UTC (permalink / raw)
                      To: Xebar Saram; +Cc: org mode, Titus von der Malsburg
                    
                    yes, there is a way ;)
                    
                    First. Make sure you have a backup of the references. I like to keep
                    mine in a local git repo so you can undo any mistakes that get made.
                    
                    I suggest you run these first:
                    %% (bibtex-validate-globally)   ; checks for duplicate keys
                    %% (bibtex-validate)
                    
                    I also recommend you run bibtex-sort (it is easier to spot duplicates in
                    a sorted list).
                    
                    and (org-ref-build-full-bibliography) <- makes a pdf of all references.
                    
                    to make sure everything is compliant and functional.
                    
                    Then, put this next line at the top of your bibtex file. The t argument to
                    org-ref-clean-bibtex-entry will preserve your existing keys.
                    
                    % (bibtex-map-entries (lambda (key start end) (org-ref-clean-bibtex-entry t)))
                    
                    Put your cursor at the end of that line, and type C-x C-e to run the function, and
                    wait patiently. It took a few minutes on my 1300 entries, and I had to
                    restart it once on some entry.
                    
                    when it is done, run (org-ref-build-full-bibliography) again to make
                    sure it works and review the ~200 page pdf ;). fix errors and repeat until it builds ;)
                    
                    Note if you want to change title cases in all entries you can use
                    
                    % (bibtex-map-entries 'jmax-title-case-article)
                    % (bibtex-map-entries 'jmax-sentence-case-article)
                    
                    I hope that helps!
                    
                    Xebar Saram writes:
                    
                    > John
                    >
                    > First of all thanks so much for the excellent org-ref-clean-bibtex-entry
                    > function i love it!
                    > also your blog post on cleaning the bib file is a life saver
                    >
                    > i have 800 references, is there a way to auto
                    > make org-ref-clean-bibtex-entry go thorough my whole bib file instead of me
                    > going and cleaning it 1 by 1?
                    >
                    > kind regards
                    >
                    > Z.
                    >
                    > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de>
                    > wrote:
                    >
                    >>
                    >>
                    >> Here is my CV in org-mode:
                    >>
                    >>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
                    >>
                    >> It’s a pretty straightforward org document except for one thing: the key
                    >> to making this work was biblatex which can be used to create several
                    >> lists of references filtered according to keywords, author, etc.  This
                    >> allowed me to have separate sections for journal articles, conference
                    >> presentations, etc.  I store the relevant keywords in the tags field of
                    >> the BibTeX entries and since biblatex doesn’t know this field, I copy
                    >> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                    >> LaTeX headers).
                    >>
                    >>   Titus
                    >>
                    >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                    >> > Hi John
                    >> >
                    >> > a bit off topic, but do you also write your academic CV in orgmode or
                    >> > lateX? in anycase would you mind sharing your org/latex CV template? it
                    >> > would be helpful as a starting point for me if thats possible.
                    >> >
                    >> > kind regards and thanks so much in advance
                    >> >
                    >> > Z
                    >> >
                    >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                    >> > wrote:
                    >> >
                    >> >> sweet! I did not know you could do that! I will be refactoring org-ref
                    >> >> soon to do that instead of redefining the commands!
                    >> >>
                    >> >> John
                    >> >>
                    >> >> -----------------------------------
                    >> >> Professor John Kitchin
                    >> >> Doherty Hall A207F
                    >> >> Department of Chemical Engineering
                    >> >> Carnegie Mellon University
                    >> >> Pittsburgh, PA 15213
                    >> >> 412-268-7803
                    >> >> @johnkitchin
                    >> >> http://kitchingroup.cheme.cmu.edu
                    >> >>
                    >> >>
                    >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                    >> >> malsburg@posteo.de> wrote:
                    >> >>
                    >> >>>
                    >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                    >> >>> > Hi again Titus
                    >> >>> >
                    >> >>> > 2 quick questions that arose from using helm-bitex today extensively:
                    >> >>> >
                    >> >>> > how does one exclude in the search items? for example i want to
                    >> search
                    >> >>> for
                    >> >>> > xebar without keyword "progress" (I want to exclude in progress
                    >> articles
                    >> >>> > not published yet)
                    >> >>> >
                    >> >>> > is it possible to define default enter command in helm-bibtex ?
                    >> >>>
                    >> >>> Yes.  Helm uses the first action as the default action.  To move an
                    >> >>> action to the top of the list you can use the following code:
                    >> >>>
                    >> >>>   (helm-delete-action-from-source "Insert BibTeX key"
                    >> helm-source-bibtex)
                    >> >>>   (helm-add-action-to-source "Insert BibTeX key"
                    >> 'helm-bibtex-insert-key
                    >> >>> helm-source-bibtex 0)
                    >> >>>
                    >> >>> The second argument in the second line is the function that executes
                    >> the
                    >> >>> action.  Here is a list of all actions and their functions:
                    >> >>>
                    >> >>>   Open PDF file (if present): helm-bibtex-open-pdf
                    >> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                    >> >>>   Insert citation: helm-bibtex-insert-citation
                    >> >>>   Insert reference: helm-bibtex-insert-reference
                    >> >>>   Insert BibTeX key: helm-bibtex-insert-key
                    >> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                    >> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                    >> >>>   Edit notes: helm-bibtex-edit-notes
                    >> >>>   Show entry: helm-bibtex-show-entry
                    >> >>>
                    >> >>> Best,
                    >> >>>
                    >> >>>   Titus
                    >> >>>
                    >> >>> >
                    >> >>> > best
                    >> >>> >
                    >> >>> > Z
                    >> >>> >
                    >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                    >> >>> malsburg@posteo.de>
                    >> >>> > wrote:
                    >> >>> >
                    >> >>> >>
                    >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                    >> >>> >> > Hi Titus and thx so much for the answers!
                    >> >>> >> >
                    >> >>> >> > i will in the future use the github page to make requests.
                    >> >>> >> >
                    >> >>> >> > "The number of matches will be displayed in the mode line. "
                    >> >>> >> >
                    >> >>> >> > i see that now thx! :) the problem was(is) that its colored black
                    >> on
                    >> >>> my
                    >> >>> >> > black modline BG which makes it invisible ;-) i assume thats an
                    >> helm
                    >> >>> >> config
                    >> >>> >> > i need to change
                    >> >>> >> >
                    >> >>> >> >
                    >> >>> >> > "If you don’t want to type these search expressions, you could
                    >> >>> create a
                    >> >>> >> > command that invokes helm-bibtex with a default search expression
                    >> and
                    >> >>> >> that
                    >> >>> >> > command could be bound to a keyboard shortcut."
                    >> >>> >> >
                    >> >>> >> > that would be prefect for me and a solution to my issue. would you
                    >> >>> mind
                    >> >>> >> > giving an example of such a code chunk. unfortunately i dont know
                    >> >>> elisp
                    >> >>> >> though
                    >> >>> >> > as john recommended i will do my best this summer when the
                    >> semester
                    >> >>> ends
                    >> >>> >> to
                    >> >>> >> > try and pick it up :)
                    >> >>> >>
                    >> >>> >> Sure, here you go:
                    >> >>> >>
                    >> >>> >> #+BEGIN_SRC elisp
                    >> >>> >> ;; Define helm-search with predefined search expression:
                    >> >>> >> (defun helm-bibtex-my-publications ()
                    >> >>> >>   "Search BibTeX entries authored by Xebar Saram."
                    >> >>> >>   (interactive)
                    >> >>> >>   (helm :sources '(helm-source-bibtex)
                    >> >>> >>         :full-frame t
                    >> >>> >>         :input "xebar saram"
                    >> >>> >>         :candidate-number-limit 500))
                    >> >>> >>
                    >> >>> >> ;; Bind this search function to Ctrl-x p:
                    >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                    >> >>> >> #+END_SRC
                    >> >>> >>
                    >> >>> >> > i will definitely use your tag system as you recommended, sounds
                    >> >>> perfect
                    >> >>> >> > for me
                    >> >>> >>
                    >> >>> >> The tag system also comes in handy when generating publication lists
                    >> >>> for
                    >> >>> >> CVs and web pages because BibTeX does not distinguish between
                    >> >>> conference
                    >> >>> >> papers, posters, and talks.  If you have tags for that, it’s
                    >> relatively
                    >> >>> >> easy to create separate sections for these types of publications
                    >> using
                    >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                    >> >>> >>
                    >> >>> >> > thanks again for your kind help and the amazing app ;-)
                    >> >>> >>
                    >> >>> >> You are welcome.
                    >> >>> >>
                    >> >>> >>   Titus
                    >> >>> >>
                    >> >>> >> >
                    >> >>> >> > best
                    >> >>> >> >
                    >> >>> >> > Z
                    >> >>> >> >
                    >> >>> >> >
                    >> >>> >> >
                    >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                    >> >>> >> malsburg@posteo.de
                    >> >>> >> >> wrote:
                    >> >>> >> >
                    >> >>> >> >>
                    >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                    >> >>> >> >> > Hi Titus
                    >> >>> >> >> >
                    >> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                    >> >>> questions.
                    >> >>> >> >> btw
                    >> >>> >> >> > is this the preferred way to make requests/ask questions or is
                    >> >>> >> >> > github preferred?
                    >> >>> >> >>
                    >> >>> >> >> Helm-bibtex is not part of org (although it tries to work well
                    >> with
                    >> >>> >> >> org).  So I’m not sure whether this list is the best place for
                    >> >>> >> >> discussing it.  For now the issue tracker on Github might be a
                    >> >>> better
                    >> >>> >> >> option:
                    >> >>> >> >>
                    >> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                    >> >>> >> >>
                    >> >>> >> >> > in any case i was wondering a few things:
                    >> >>> >> >> >
                    >> >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                    >> >>> sort by
                    >> >>> >> >> > Author, year, month
                    >> >>> >> >>
                    >> >>> >> >> I prefer to see the entries in the (inverse) order in which they
                    >> >>> appear
                    >> >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                    >> >>> >> >> top.  However, I agree that sorting would be useful (see issues
                    >> #5
                    >> >>> and
                    >> >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                    >> >>> welcome.
                    >> >>> >> >>
                    >> >>> >> >> > 2. i would really like a way to have stored smart groups (like
                    >> the
                    >> >>> >> jabref
                    >> >>> >> >> > dynamic groups if your aware of that). that is for example
                    >> create
                    >> >>> a
                    >> >>> >> group
                    >> >>> >> >> > that auto selects all publications i have (by my first/last
                    >> name)
                    >> >>> and
                    >> >>> >> >> shows
                    >> >>> >> >> > the count (in numbers) of these publications.
                    >> >>> >> >>
                    >> >>> >> >> I’m not familiar with smart groups but it seems that all
                    >> >>> helm-bibtex is
                    >> >>> >> >> doing is giving you very flexible smart groups defined by your
                    >> >>> search
                    >> >>> >> >> expressions.  For example, if you want a list of your
                    >> publications,
                    >> >>> you
                    >> >>> >> >> can simple enter your name.  And if you want a list of your
                    >> >>> articles,
                    >> >>> >> >> you can enter your name + “article”.  If you want all your
                    >> articles
                    >> >>> from
                    >> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
                    >> of
                    >> >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                    >> >>> type
                    >> >>> >> >> these search expressions, you could create a command that invokes
                    >> >>> >> >> helm-bibtex with a default search expression and that command
                    >> could
                    >> >>> be
                    >> >>> >> >> bound to a keyboard shortcut.
                    >> >>> >> >>
                    >> >>> >> >> > Another example is a group to keep track of all the papers im
                    >> >>> working
                    >> >>> >> on
                    >> >>> >> >> or
                    >> >>> >> >> > invloved with by matching keyword author and prep/*other key
                    >> word
                    >> >>> >> >>
                    >> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                    >> >>> >> >> describing the content of the paper (as usual) and “tags” for
                    >> meta
                    >> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
                    >> “poster”,
                    >> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
                    >> search
                    >> >>> for
                    >> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
                    >> to
                    >> >>> be
                    >> >>> >> >> added to `helm-bibtex-additional-search-fields`.
                    >> >>> >> >>
                    >> >>> >> >> Another solution would be to use the pubstate field and to search
                    >> >>> for
                    >> >>> >> >> your name and “forthcoming” (add pubstate to
                    >> >>> >> >> helm-bibtex-additional-search-fields for this to work).
                    >> >>> >> >>
                    >> >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
                    >> for a
                    >> >>> >> >> selected
                    >> >>> >> >> > citation based on user criteria such as
                    >> author(date)short-title?
                    >> >>> >> >>
                    >> >>> >> >> Maintaining the content of the BibTeX file not really in the
                    >> scope
                    >> >>> of
                    >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
                    >> Perhaps
                    >> >>> >> >> org-ref or ebib can help here?  Once you have a function that
                    >> >>> generates
                    >> >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
                    >> it
                    >> >>> to
                    >> >>> >> >> the list of actions in helm-bibtex.
                    >> >>> >> >>
                    >> >>> >> >> Hope that helps.
                    >> >>> >> >>
                    >> >>> >> >>   Titus
                    >> >>> >> >>
                    >> >>> >> >> > thx so much in advance, you and john have given me confidence
                    >> to
                    >> >>> >> finally
                    >> >>> >> >> > dive into the whole latex/bibteX world
                    >> >>> >> >> >
                    >> >>> >> >> > best
                    >> >>> >> >> >
                    >> >>> >> >> > Z
                    >> >>> >> >>
                    >> >>> >> >>
                    >> >>> >>
                    >> >>> >>
                    >> >>>
                    >> >>>
                    >> >>
                    >>
                    >>
                    
                    --
                    Professor John Kitchin
                    Doherty Hall A207F
                    Department of Chemical Engineering
                    Carnegie Mellon University
                    Pittsburgh, PA 15213
                    412-268-7803
                    @johnkitchin
                    http://kitchingroup.cheme.cmu.edu
                    
                    ^ permalink raw reply	[flat|nested] 26+ messages in thread

                • * Re: helm-bibtex questions
                    2015-06-22 15:12               ` Titus von der Malsburg
                    2015-06-24 19:54                 ` Xebar Saram
                  @ 2015-06-26  7:21                 ` Xebar Saram
                    2015-06-26 17:21                   ` Titus von der Malsburg
                    1 sibling, 1 reply; 26+ messages in thread
                  From: Xebar Saram @ 2015-06-26  7:21 UTC (permalink / raw)
                    To: Titus von der Malsburg; +Cc: org mode
                  
                  [-- Attachment #1: Type: text/plain, Size: 11812 bytes --]
                  
                  Hi Titus
                  
                  Another round of helm-bibtex questions if you dont mind (question come
                  since i use it 50 times a day now ;-))
                  
                  1. is there a way (or a keybind) to select all entries filtered? now to
                  select all my publications for example i have to use C-space repeatedly.
                  
                  2. what is the syntax for greater then? for example all articles > 2012
                  (year)
                  
                  4. i cant get helm-bibtex to search the biblatex field of pubstate. are
                  biblatex (biber) supported/ i have this in my config?
                  
                  (setq helm-bibtex-additional-search-fields '(pubstate))
                  
                  also on a related issue i assume one can define many fields in the above
                  example. since my elisp sucks would the syntax be this
                  
                  (setq helm-bibtex-additional-search-fields '(pubstate tags))
                  
                  or do you need to qoute them or use a , symbol?
                  
                  5. i love the insert formatted reference (f5) option and use it often
                  sending people references:
                  a. does it also auto send that to the clipboard?
                  b. it cuts most of the authors name and leaves only the first few. is there
                  a switch to get it to print all authors. is that a latex cite formatting
                  issue?
                  
                  best and thanks so much again
                  
                  Z
                  
                  On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de>
                  wrote:
                  
                  >
                  >
                  > Here is my CV in org-mode:
                  >
                  >   https://gist.github.com/tmalsburg/96084ba82281937c26b7
                  >
                  > It’s a pretty straightforward org document except for one thing: the key
                  > to making this work was biblatex which can be used to create several
                  > lists of references filtered according to keywords, author, etc.  This
                  > allowed me to have separate sections for journal articles, conference
                  > presentations, etc.  I store the relevant keywords in the tags field of
                  > the BibTeX entries and since biblatex doesn’t know this field, I copy
                  > the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                  > LaTeX headers).
                  >
                  >   Titus
                  >
                  > On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                  > > Hi John
                  > >
                  > > a bit off topic, but do you also write your academic CV in orgmode or
                  > > lateX? in anycase would you mind sharing your org/latex CV template? it
                  > > would be helpful as a starting point for me if thats possible.
                  > >
                  > > kind regards and thanks so much in advance
                  > >
                  > > Z
                  > >
                  > > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                  > > wrote:
                  > >
                  > >> sweet! I did not know you could do that! I will be refactoring org-ref
                  > >> soon to do that instead of redefining the commands!
                  > >>
                  > >> John
                  > >>
                  > >> -----------------------------------
                  > >> Professor John Kitchin
                  > >> Doherty Hall A207F
                  > >> Department of Chemical Engineering
                  > >> Carnegie Mellon University
                  > >> Pittsburgh, PA 15213
                  > >> 412-268-7803
                  > >> @johnkitchin
                  > >> http://kitchingroup.cheme.cmu.edu
                  > >>
                  > >>
                  > >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                  > >> malsburg@posteo.de> wrote:
                  > >>
                  > >>>
                  > >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                  > >>> > Hi again Titus
                  > >>> >
                  > >>> > 2 quick questions that arose from using helm-bitex today extensively:
                  > >>> >
                  > >>> > how does one exclude in the search items? for example i want to
                  > search
                  > >>> for
                  > >>> > xebar without keyword "progress" (I want to exclude in progress
                  > articles
                  > >>> > not published yet)
                  > >>> >
                  > >>> > is it possible to define default enter command in helm-bibtex ?
                  > >>>
                  > >>> Yes.  Helm uses the first action as the default action.  To move an
                  > >>> action to the top of the list you can use the following code:
                  > >>>
                  > >>>   (helm-delete-action-from-source "Insert BibTeX key"
                  > helm-source-bibtex)
                  > >>>   (helm-add-action-to-source "Insert BibTeX key"
                  > 'helm-bibtex-insert-key
                  > >>> helm-source-bibtex 0)
                  > >>>
                  > >>> The second argument in the second line is the function that executes
                  > the
                  > >>> action.  Here is a list of all actions and their functions:
                  > >>>
                  > >>>   Open PDF file (if present): helm-bibtex-open-pdf
                  > >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                  > >>>   Insert citation: helm-bibtex-insert-citation
                  > >>>   Insert reference: helm-bibtex-insert-reference
                  > >>>   Insert BibTeX key: helm-bibtex-insert-key
                  > >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                  > >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                  > >>>   Edit notes: helm-bibtex-edit-notes
                  > >>>   Show entry: helm-bibtex-show-entry
                  > >>>
                  > >>> Best,
                  > >>>
                  > >>>   Titus
                  > >>>
                  > >>> >
                  > >>> > best
                  > >>> >
                  > >>> > Z
                  > >>> >
                  > >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                  > >>> malsburg@posteo.de>
                  > >>> > wrote:
                  > >>> >
                  > >>> >>
                  > >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                  > >>> >> > Hi Titus and thx so much for the answers!
                  > >>> >> >
                  > >>> >> > i will in the future use the github page to make requests.
                  > >>> >> >
                  > >>> >> > "The number of matches will be displayed in the mode line. "
                  > >>> >> >
                  > >>> >> > i see that now thx! :) the problem was(is) that its colored black
                  > on
                  > >>> my
                  > >>> >> > black modline BG which makes it invisible ;-) i assume thats an
                  > helm
                  > >>> >> config
                  > >>> >> > i need to change
                  > >>> >> >
                  > >>> >> >
                  > >>> >> > "If you don’t want to type these search expressions, you could
                  > >>> create a
                  > >>> >> > command that invokes helm-bibtex with a default search expression
                  > and
                  > >>> >> that
                  > >>> >> > command could be bound to a keyboard shortcut."
                  > >>> >> >
                  > >>> >> > that would be prefect for me and a solution to my issue. would you
                  > >>> mind
                  > >>> >> > giving an example of such a code chunk. unfortunately i dont know
                  > >>> elisp
                  > >>> >> though
                  > >>> >> > as john recommended i will do my best this summer when the
                  > semester
                  > >>> ends
                  > >>> >> to
                  > >>> >> > try and pick it up :)
                  > >>> >>
                  > >>> >> Sure, here you go:
                  > >>> >>
                  > >>> >> #+BEGIN_SRC elisp
                  > >>> >> ;; Define helm-search with predefined search expression:
                  > >>> >> (defun helm-bibtex-my-publications ()
                  > >>> >>   "Search BibTeX entries authored by Xebar Saram."
                  > >>> >>   (interactive)
                  > >>> >>   (helm :sources '(helm-source-bibtex)
                  > >>> >>         :full-frame t
                  > >>> >>         :input "xebar saram"
                  > >>> >>         :candidate-number-limit 500))
                  > >>> >>
                  > >>> >> ;; Bind this search function to Ctrl-x p:
                  > >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                  > >>> >> #+END_SRC
                  > >>> >>
                  > >>> >> > i will definitely use your tag system as you recommended, sounds
                  > >>> perfect
                  > >>> >> > for me
                  > >>> >>
                  > >>> >> The tag system also comes in handy when generating publication lists
                  > >>> for
                  > >>> >> CVs and web pages because BibTeX does not distinguish between
                  > >>> conference
                  > >>> >> papers, posters, and talks.  If you have tags for that, it’s
                  > relatively
                  > >>> >> easy to create separate sections for these types of publications
                  > using
                  > >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                  > >>> >>
                  > >>> >> > thanks again for your kind help and the amazing app ;-)
                  > >>> >>
                  > >>> >> You are welcome.
                  > >>> >>
                  > >>> >>   Titus
                  > >>> >>
                  > >>> >> >
                  > >>> >> > best
                  > >>> >> >
                  > >>> >> > Z
                  > >>> >> >
                  > >>> >> >
                  > >>> >> >
                  > >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                  > >>> >> malsburg@posteo.de
                  > >>> >> >> wrote:
                  > >>> >> >
                  > >>> >> >>
                  > >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                  > >>> >> >> > Hi Titus
                  > >>> >> >> >
                  > >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                  > >>> questions.
                  > >>> >> >> btw
                  > >>> >> >> > is this the preferred way to make requests/ask questions or is
                  > >>> >> >> > github preferred?
                  > >>> >> >>
                  > >>> >> >> Helm-bibtex is not part of org (although it tries to work well
                  > with
                  > >>> >> >> org).  So I’m not sure whether this list is the best place for
                  > >>> >> >> discussing it.  For now the issue tracker on Github might be a
                  > >>> better
                  > >>> >> >> option:
                  > >>> >> >>
                  > >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                  > >>> >> >>
                  > >>> >> >> > in any case i was wondering a few things:
                  > >>> >> >> >
                  > >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                  > >>> sort by
                  > >>> >> >> > Author, year, month
                  > >>> >> >>
                  > >>> >> >> I prefer to see the entries in the (inverse) order in which they
                  > >>> appear
                  > >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                  > >>> >> >> top.  However, I agree that sorting would be useful (see issues
                  > #5
                  > >>> and
                  > >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                  > >>> welcome.
                  > >>> >> >>
                  > >>> >> >> > 2. i would really like a way to have stored smart groups (like
                  > the
                  > >>> >> jabref
                  > >>> >> >> > dynamic groups if your aware of that). that is for example
                  > create
                  > >>> a
                  > >>> >> group
                  > >>> >> >> > that auto selects all publications i have (by my first/last
                  > name)
                  > >>> and
                  > >>> >> >> shows
                  > >>> >> >> > the count (in numbers) of these publications.
                  > >>> >> >>
                  > >>> >> >> I’m not familiar with smart groups but it seems that all
                  > >>> helm-bibtex is
                  > >>> >> >> doing is giving you very flexible smart groups defined by your
                  > >>> search
                  > >>> >> >> expressions.  For example, if you want a list of your
                  > publications,
                  > >>> you
                  > >>> >> >> can simple enter your name.  And if you want a list of your
                  > >>> articles,
                  > >>> >> >> you can enter your name + “article”.  If you want all your
                  > articles
                  > >>> from
                  > >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
                  > of
                  > >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                  > >>> type
                  > >>> >> >> these search expressions, you could create a command that invokes
                  > >>> >> >> helm-bibtex with a default search expression and that command
                  > could
                  > >>> be
                  > >>> >> >> bound to a keyboard shortcut.
                  > >>> >> >>
                  > >>> >> >> > Another example is a group to keep track of all the papers im
                  > >>> working
                  > >>> >> on
                  > >>> >> >> or
                  > >>> >> >> > invloved with by matching keyword author and prep/*other key
                  > word
                  > >>> >> >>
                  > >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                  > >>> >> >> describing the content of the paper (as usual) and “tags” for
                  > meta
                  > >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
                  > “poster”,
                  > >>> >> >> “talk”, … So if I want a list of all articles in progress, I
                  > search
                  > >>> for
                  > >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
                  > to
                  > >>> be
                  > >>> >> >> added to `helm-bibtex-additional-search-fields`.
                  > >>> >> >>
                  > >>> >> >> Another solution would be to use the pubstate field and to search
                  > >>> for
                  > >>> >> >> your name and “forthcoming” (add pubstate to
                  > >>> >> >> helm-bibtex-additional-search-fields for this to work).
                  > >>> >> >>
                  > >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
                  > for a
                  > >>> >> >> selected
                  > >>> >> >> > citation based on user criteria such as
                  > author(date)short-title?
                  > >>> >> >>
                  > >>> >> >> Maintaining the content of the BibTeX file not really in the
                  > scope
                  > >>> of
                  > >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
                  > Perhaps
                  > >>> >> >> org-ref or ebib can help here?  Once you have a function that
                  > >>> generates
                  > >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
                  > it
                  > >>> to
                  > >>> >> >> the list of actions in helm-bibtex.
                  > >>> >> >>
                  > >>> >> >> Hope that helps.
                  > >>> >> >>
                  > >>> >> >>   Titus
                  > >>> >> >>
                  > >>> >> >> > thx so much in advance, you and john have given me confidence
                  > to
                  > >>> >> finally
                  > >>> >> >> > dive into the whole latex/bibteX world
                  > >>> >> >> >
                  > >>> >> >> > best
                  > >>> >> >> >
                  > >>> >> >> > Z
                  > >>> >> >>
                  > >>> >> >>
                  > >>> >>
                  > >>> >>
                  > >>>
                  > >>>
                  > >>
                  >
                  >
                  
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                  ^ permalink raw reply	[flat|nested] 26+ messages in thread

                • • * Re: helm-bibtex questions
                      2015-06-26  7:21                 ` Xebar Saram
                    @ 2015-06-26 17:21                   ` Titus von der Malsburg
                      2015-06-26 17:35                     ` Titus von der Malsburg
                      2015-06-26 17:54                     ` John Kitchin
                      0 siblings, 2 replies; 26+ messages in thread
                    From: Titus von der Malsburg @ 2015-06-26 17:21 UTC (permalink / raw)
                      To: Xebar Saram; +Cc: org mode
                    
                    [-- Attachment #1: Type: text/plain, Size: 13545 bytes --]
                    
                    
                    On 2015-06-26 Fri 00:21, Xebar Saram wrote:
                    > Hi Titus
                    >
                    > Another round of helm-bibtex questions if you dont mind (question come
                    > since i use it 50 times a day now ;-))
                    
                    No problem.  I’ve also learned a couple of things though this exchange.
                    
                    > 1. is there a way (or a keybind) to select all entries filtered? now to
                    > select all my publications for example i have to use C-space
                    > repeatedly.
                    
                    Key bindings are inherited from Helm so it’s useful to consult Helm’s
                    documentation for question of that type.  I just checked and found that
                    M-a selects all candidates.
                    
                    > 2. what is the syntax for greater then? for example all articles > 2012
                    > (year)
                    
                    I’m afraid that’s not possible because 2012 is just another string for
                    the purposes of matching.  But you may want to check Helm’s
                    documentation and mailing lists.  Helm is full of surprises.
                    
                    > 4. i cant get helm-bibtex to search the biblatex field of pubstate. are
                    > biblatex (biber) supported/ i have this in my config?
                    >
                    > (setq helm-bibtex-additional-search-fields '(pubstate))
                    
                    This works on my setup.  Helm-bibtex doesn’t really care whether
                    something is a BibTeX or a Biblatex field.  You should be able to use
                    any kind of field whether standard or not.  Note that additional search
                    fields are not displayed in the results list (they are only used for
                    matching).  Perhaps that’s why you thought it doesn’t work?
                    
                    > also on a related issue i assume one can define many fields in the above
                    > example. since my elisp sucks would the syntax be this
                    >
                    > (setq helm-bibtex-additional-search-fields '(pubstate tags))
                    
                    This is correct.
                    
                    > or do you need to qoute them or use a , symbol?
                    >
                    > 5. i love the insert formatted reference (f5) option and use it often
                    > sending people references:
                    > a. does it also auto send that to the clipboard?
                    
                    There is currently no way to copy references directly to the
                    clipboard.  My recommendation is to use one of Emacs’ mail clients, then
                    you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
                    when combined with helm-mu).
                    
                    > b. it cuts most of the authors name and leaves only the first few. is there
                    > a switch to get it to print all authors. is that a latex cite formatting
                    > issue?
                    
                    Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
                    anything in my setup.  Could you please provide an example?  (Perhaps
                    this is something for the issue tracker on Github.)
                    
                    Best wishes,
                    
                      Titus
                    
                    
                    >
                    > best and thanks so much again
                    >
                    > Z
                    >
                    > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de>
                    > wrote:
                    >
                    >>
                    >>
                    >> Here is my CV in org-mode:
                    >>
                    >>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
                    >>
                    >> It’s a pretty straightforward org document except for one thing: the key
                    >> to making this work was biblatex which can be used to create several
                    >> lists of references filtered according to keywords, author, etc.  This
                    >> allowed me to have separate sections for journal articles, conference
                    >> presentations, etc.  I store the relevant keywords in the tags field of
                    >> the BibTeX entries and since biblatex doesn’t know this field, I copy
                    >> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                    >> LaTeX headers).
                    >>
                    >>   Titus
                    >>
                    >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                    >> > Hi John
                    >> >
                    >> > a bit off topic, but do you also write your academic CV in orgmode or
                    >> > lateX? in anycase would you mind sharing your org/latex CV template? it
                    >> > would be helpful as a starting point for me if thats possible.
                    >> >
                    >> > kind regards and thanks so much in advance
                    >> >
                    >> > Z
                    >> >
                    >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                    >> > wrote:
                    >> >
                    >> >> sweet! I did not know you could do that! I will be refactoring org-ref
                    >> >> soon to do that instead of redefining the commands!
                    >> >>
                    >> >> John
                    >> >>
                    >> >> -----------------------------------
                    >> >> Professor John Kitchin
                    >> >> Doherty Hall A207F
                    >> >> Department of Chemical Engineering
                    >> >> Carnegie Mellon University
                    >> >> Pittsburgh, PA 15213
                    >> >> 412-268-7803
                    >> >> @johnkitchin
                    >> >> http://kitchingroup.cheme.cmu.edu
                    >> >>
                    >> >>
                    >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                    >> >> malsburg@posteo.de> wrote:
                    >> >>
                    >> >>>
                    >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                    >> >>> > Hi again Titus
                    >> >>> >
                    >> >>> > 2 quick questions that arose from using helm-bitex today extensively:
                    >> >>> >
                    >> >>> > how does one exclude in the search items? for example i want to
                    >> search
                    >> >>> for
                    >> >>> > xebar without keyword "progress" (I want to exclude in progress
                    >> articles
                    >> >>> > not published yet)
                    >> >>> >
                    >> >>> > is it possible to define default enter command in helm-bibtex ?
                    >> >>>
                    >> >>> Yes.  Helm uses the first action as the default action.  To move an
                    >> >>> action to the top of the list you can use the following code:
                    >> >>>
                    >> >>>   (helm-delete-action-from-source "Insert BibTeX key"
                    >> helm-source-bibtex)
                    >> >>>   (helm-add-action-to-source "Insert BibTeX key"
                    >> 'helm-bibtex-insert-key
                    >> >>> helm-source-bibtex 0)
                    >> >>>
                    >> >>> The second argument in the second line is the function that executes
                    >> the
                    >> >>> action.  Here is a list of all actions and their functions:
                    >> >>>
                    >> >>>   Open PDF file (if present): helm-bibtex-open-pdf
                    >> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                    >> >>>   Insert citation: helm-bibtex-insert-citation
                    >> >>>   Insert reference: helm-bibtex-insert-reference
                    >> >>>   Insert BibTeX key: helm-bibtex-insert-key
                    >> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                    >> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                    >> >>>   Edit notes: helm-bibtex-edit-notes
                    >> >>>   Show entry: helm-bibtex-show-entry
                    >> >>>
                    >> >>> Best,
                    >> >>>
                    >> >>>   Titus
                    >> >>>
                    >> >>> >
                    >> >>> > best
                    >> >>> >
                    >> >>> > Z
                    >> >>> >
                    >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                    >> >>> malsburg@posteo.de>
                    >> >>> > wrote:
                    >> >>> >
                    >> >>> >>
                    >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                    >> >>> >> > Hi Titus and thx so much for the answers!
                    >> >>> >> >
                    >> >>> >> > i will in the future use the github page to make requests.
                    >> >>> >> >
                    >> >>> >> > "The number of matches will be displayed in the mode line. "
                    >> >>> >> >
                    >> >>> >> > i see that now thx! :) the problem was(is) that its colored black
                    >> on
                    >> >>> my
                    >> >>> >> > black modline BG which makes it invisible ;-) i assume thats an
                    >> helm
                    >> >>> >> config
                    >> >>> >> > i need to change
                    >> >>> >> >
                    >> >>> >> >
                    >> >>> >> > "If you don’t want to type these search expressions, you could
                    >> >>> create a
                    >> >>> >> > command that invokes helm-bibtex with a default search expression
                    >> and
                    >> >>> >> that
                    >> >>> >> > command could be bound to a keyboard shortcut."
                    >> >>> >> >
                    >> >>> >> > that would be prefect for me and a solution to my issue. would you
                    >> >>> mind
                    >> >>> >> > giving an example of such a code chunk. unfortunately i dont know
                    >> >>> elisp
                    >> >>> >> though
                    >> >>> >> > as john recommended i will do my best this summer when the
                    >> semester
                    >> >>> ends
                    >> >>> >> to
                    >> >>> >> > try and pick it up :)
                    >> >>> >>
                    >> >>> >> Sure, here you go:
                    >> >>> >>
                    >> >>> >> #+BEGIN_SRC elisp
                    >> >>> >> ;; Define helm-search with predefined search expression:
                    >> >>> >> (defun helm-bibtex-my-publications ()
                    >> >>> >>   "Search BibTeX entries authored by Xebar Saram."
                    >> >>> >>   (interactive)
                    >> >>> >>   (helm :sources '(helm-source-bibtex)
                    >> >>> >>         :full-frame t
                    >> >>> >>         :input "xebar saram"
                    >> >>> >>         :candidate-number-limit 500))
                    >> >>> >>
                    >> >>> >> ;; Bind this search function to Ctrl-x p:
                    >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                    >> >>> >> #+END_SRC
                    >> >>> >>
                    >> >>> >> > i will definitely use your tag system as you recommended, sounds
                    >> >>> perfect
                    >> >>> >> > for me
                    >> >>> >>
                    >> >>> >> The tag system also comes in handy when generating publication lists
                    >> >>> for
                    >> >>> >> CVs and web pages because BibTeX does not distinguish between
                    >> >>> conference
                    >> >>> >> papers, posters, and talks.  If you have tags for that, it’s
                    >> relatively
                    >> >>> >> easy to create separate sections for these types of publications
                    >> using
                    >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                    >> >>> >>
                    >> >>> >> > thanks again for your kind help and the amazing app ;-)
                    >> >>> >>
                    >> >>> >> You are welcome.
                    >> >>> >>
                    >> >>> >>   Titus
                    >> >>> >>
                    >> >>> >> >
                    >> >>> >> > best
                    >> >>> >> >
                    >> >>> >> > Z
                    >> >>> >> >
                    >> >>> >> >
                    >> >>> >> >
                    >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                    >> >>> >> malsburg@posteo.de
                    >> >>> >> >> wrote:
                    >> >>> >> >
                    >> >>> >> >>
                    >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                    >> >>> >> >> > Hi Titus
                    >> >>> >> >> >
                    >> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                    >> >>> questions.
                    >> >>> >> >> btw
                    >> >>> >> >> > is this the preferred way to make requests/ask questions or is
                    >> >>> >> >> > github preferred?
                    >> >>> >> >>
                    >> >>> >> >> Helm-bibtex is not part of org (although it tries to work well
                    >> with
                    >> >>> >> >> org).  So I’m not sure whether this list is the best place for
                    >> >>> >> >> discussing it.  For now the issue tracker on Github might be a
                    >> >>> better
                    >> >>> >> >> option:
                    >> >>> >> >>
                    >> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                    >> >>> >> >>
                    >> >>> >> >> > in any case i was wondering a few things:
                    >> >>> >> >> >
                    >> >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                    >> >>> sort by
                    >> >>> >> >> > Author, year, month
                    >> >>> >> >>
                    >> >>> >> >> I prefer to see the entries in the (inverse) order in which they
                    >> >>> appear
                    >> >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                    >> >>> >> >> top.  However, I agree that sorting would be useful (see issues
                    >> #5
                    >> >>> and
                    >> >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                    >> >>> welcome.
                    >> >>> >> >>
                    >> >>> >> >> > 2. i would really like a way to have stored smart groups (like
                    >> the
                    >> >>> >> jabref
                    >> >>> >> >> > dynamic groups if your aware of that). that is for example
                    >> create
                    >> >>> a
                    >> >>> >> group
                    >> >>> >> >> > that auto selects all publications i have (by my first/last
                    >> name)
                    >> >>> and
                    >> >>> >> >> shows
                    >> >>> >> >> > the count (in numbers) of these publications.
                    >> >>> >> >>
                    >> >>> >> >> I’m not familiar with smart groups but it seems that all
                    >> >>> helm-bibtex is
                    >> >>> >> >> doing is giving you very flexible smart groups defined by your
                    >> >>> search
                    >> >>> >> >> expressions.  For example, if you want a list of your
                    >> publications,
                    >> >>> you
                    >> >>> >> >> can simple enter your name.  And if you want a list of your
                    >> >>> articles,
                    >> >>> >> >> you can enter your name + “article”.  If you want all your
                    >> articles
                    >> >>> from
                    >> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
                    >> of
                    >> >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                    >> >>> type
                    >> >>> >> >> these search expressions, you could create a command that invokes
                    >> >>> >> >> helm-bibtex with a default search expression and that command
                    >> could
                    >> >>> be
                    >> >>> >> >> bound to a keyboard shortcut.
                    >> >>> >> >>
                    >> >>> >> >> > Another example is a group to keep track of all the papers im
                    >> >>> working
                    >> >>> >> on
                    >> >>> >> >> or
                    >> >>> >> >> > invloved with by matching keyword author and prep/*other key
                    >> word
                    >> >>> >> >>
                    >> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                    >> >>> >> >> describing the content of the paper (as usual) and “tags” for
                    >> meta
                    >> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
                    >> “poster”,
                    >> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
                    >> search
                    >> >>> for
                    >> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
                    >> to
                    >> >>> be
                    >> >>> >> >> added to `helm-bibtex-additional-search-fields`.
                    >> >>> >> >>
                    >> >>> >> >> Another solution would be to use the pubstate field and to search
                    >> >>> for
                    >> >>> >> >> your name and “forthcoming” (add pubstate to
                    >> >>> >> >> helm-bibtex-additional-search-fields for this to work).
                    >> >>> >> >>
                    >> >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
                    >> for a
                    >> >>> >> >> selected
                    >> >>> >> >> > citation based on user criteria such as
                    >> author(date)short-title?
                    >> >>> >> >>
                    >> >>> >> >> Maintaining the content of the BibTeX file not really in the
                    >> scope
                    >> >>> of
                    >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
                    >> Perhaps
                    >> >>> >> >> org-ref or ebib can help here?  Once you have a function that
                    >> >>> generates
                    >> >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
                    >> it
                    >> >>> to
                    >> >>> >> >> the list of actions in helm-bibtex.
                    >> >>> >> >>
                    >> >>> >> >> Hope that helps.
                    >> >>> >> >>
                    >> >>> >> >>   Titus
                    >> >>> >> >>
                    >> >>> >> >> > thx so much in advance, you and john have given me confidence
                    >> to
                    >> >>> >> finally
                    >> >>> >> >> > dive into the whole latex/bibteX world
                    >> >>> >> >> >
                    >> >>> >> >> > best
                    >> >>> >> >> >
                    >> >>> >> >> > Z
                    >> >>> >> >>
                    >> >>> >> >>
                    >> >>> >>
                    >> >>> >>
                    >> >>>
                    >> >>>
                    >> >>
                    >>
                    >>
                    
                    
                    [-- Attachment #2: signature.asc --]
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                    ^ permalink raw reply	[flat|nested] 26+ messages in thread

                  • • * Re: helm-bibtex questions
                        2015-06-26 17:21                   ` Titus von der Malsburg
                      @ 2015-06-26 17:35                     ` Titus von der Malsburg
                        2015-06-26 17:54                     ` John Kitchin
                        1 sibling, 0 replies; 26+ messages in thread
                      From: Titus von der Malsburg @ 2015-06-26 17:35 UTC (permalink / raw)
                        To: Xebar Saram; +Cc: org mode
                      
                      [-- Attachment #1: Type: text/plain, Size: 14135 bytes --]
                      
                      
                      On 2015-06-26 Fri 10:21, Titus von der Malsburg wrote:
                      > On 2015-06-26 Fri 00:21, Xebar Saram wrote:
                      >> Hi Titus
                      >>
                      >> Another round of helm-bibtex questions if you dont mind (question come
                      >> since i use it 50 times a day now ;-))
                      >
                      > No problem.  I’ve also learned a couple of things though this exchange.
                      >
                      >> 1. is there a way (or a keybind) to select all entries filtered? now to
                      >> select all my publications for example i have to use C-space
                      >> repeatedly.
                      >
                      > Key bindings are inherited from Helm so it’s useful to consult Helm’s
                      > documentation for question of that type.  I just checked and found that
                      > M-a selects all candidates.
                      >
                      >> 2. what is the syntax for greater then? for example all articles > 2012
                      >> (year)
                      >
                      > I’m afraid that’s not possible because 2012 is just another string for
                      > the purposes of matching.  But you may want to check Helm’s
                      > documentation and mailing lists.  Helm is full of surprises.
                      
                      Of course you can use regular expressions to search for a range of
                      years:
                      
                        201[2-5]
                      
                      Almost as good as >2012.
                      
                      >
                      >> 4. i cant get helm-bibtex to search the biblatex field of pubstate. are
                      >> biblatex (biber) supported/ i have this in my config?
                      >>
                      >> (setq helm-bibtex-additional-search-fields '(pubstate))
                      >
                      > This works on my setup.  Helm-bibtex doesn’t really care whether
                      > something is a BibTeX or a Biblatex field.  You should be able to use
                      > any kind of field whether standard or not.  Note that additional search
                      > fields are not displayed in the results list (they are only used for
                      > matching).  Perhaps that’s why you thought it doesn’t work?
                      >
                      >> also on a related issue i assume one can define many fields in the above
                      >> example. since my elisp sucks would the syntax be this
                      >>
                      >> (setq helm-bibtex-additional-search-fields '(pubstate tags))
                      >
                      > This is correct.
                      >
                      >> or do you need to qoute them or use a , symbol?
                      >>
                      >> 5. i love the insert formatted reference (f5) option and use it often
                      >> sending people references:
                      >> a. does it also auto send that to the clipboard?
                      >
                      > There is currently no way to copy references directly to the
                      > clipboard.  My recommendation is to use one of Emacs’ mail clients, then
                      > you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
                      > when combined with helm-mu).
                      >
                      >> b. it cuts most of the authors name and leaves only the first few. is there
                      >> a switch to get it to print all authors. is that a latex cite formatting
                      >> issue?
                      >
                      > Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
                      > anything in my setup.  Could you please provide an example?  (Perhaps
                      > this is something for the issue tracker on Github.)
                      >
                      > Best wishes,
                      >
                      >   Titus
                      >
                      >
                      >>
                      >> best and thanks so much again
                      >>
                      >> Z
                      >>
                      >> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de>
                      >> wrote:
                      >>
                      >>>
                      >>>
                      >>> Here is my CV in org-mode:
                      >>>
                      >>>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
                      >>>
                      >>> It’s a pretty straightforward org document except for one thing: the key
                      >>> to making this work was biblatex which can be used to create several
                      >>> lists of references filtered according to keywords, author, etc.  This
                      >>> allowed me to have separate sections for journal articles, conference
                      >>> presentations, etc.  I store the relevant keywords in the tags field of
                      >>> the BibTeX entries and since biblatex doesn’t know this field, I copy
                      >>> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                      >>> LaTeX headers).
                      >>>
                      >>>   Titus
                      >>>
                      >>> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                      >>> > Hi John
                      >>> >
                      >>> > a bit off topic, but do you also write your academic CV in orgmode or
                      >>> > lateX? in anycase would you mind sharing your org/latex CV template? it
                      >>> > would be helpful as a starting point for me if thats possible.
                      >>> >
                      >>> > kind regards and thanks so much in advance
                      >>> >
                      >>> > Z
                      >>> >
                      >>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                      >>> > wrote:
                      >>> >
                      >>> >> sweet! I did not know you could do that! I will be refactoring org-ref
                      >>> >> soon to do that instead of redefining the commands!
                      >>> >>
                      >>> >> John
                      >>> >>
                      >>> >> -----------------------------------
                      >>> >> Professor John Kitchin
                      >>> >> Doherty Hall A207F
                      >>> >> Department of Chemical Engineering
                      >>> >> Carnegie Mellon University
                      >>> >> Pittsburgh, PA 15213
                      >>> >> 412-268-7803
                      >>> >> @johnkitchin
                      >>> >> http://kitchingroup.cheme.cmu.edu
                      >>> >>
                      >>> >>
                      >>> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                      >>> >> malsburg@posteo.de> wrote:
                      >>> >>
                      >>> >>>
                      >>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                      >>> >>> > Hi again Titus
                      >>> >>> >
                      >>> >>> > 2 quick questions that arose from using helm-bitex today extensively:
                      >>> >>> >
                      >>> >>> > how does one exclude in the search items? for example i want to
                      >>> search
                      >>> >>> for
                      >>> >>> > xebar without keyword "progress" (I want to exclude in progress
                      >>> articles
                      >>> >>> > not published yet)
                      >>> >>> >
                      >>> >>> > is it possible to define default enter command in helm-bibtex ?
                      >>> >>>
                      >>> >>> Yes.  Helm uses the first action as the default action.  To move an
                      >>> >>> action to the top of the list you can use the following code:
                      >>> >>>
                      >>> >>>   (helm-delete-action-from-source "Insert BibTeX key"
                      >>> helm-source-bibtex)
                      >>> >>>   (helm-add-action-to-source "Insert BibTeX key"
                      >>> 'helm-bibtex-insert-key
                      >>> >>> helm-source-bibtex 0)
                      >>> >>>
                      >>> >>> The second argument in the second line is the function that executes
                      >>> the
                      >>> >>> action.  Here is a list of all actions and their functions:
                      >>> >>>
                      >>> >>>   Open PDF file (if present): helm-bibtex-open-pdf
                      >>> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                      >>> >>>   Insert citation: helm-bibtex-insert-citation
                      >>> >>>   Insert reference: helm-bibtex-insert-reference
                      >>> >>>   Insert BibTeX key: helm-bibtex-insert-key
                      >>> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                      >>> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                      >>> >>>   Edit notes: helm-bibtex-edit-notes
                      >>> >>>   Show entry: helm-bibtex-show-entry
                      >>> >>>
                      >>> >>> Best,
                      >>> >>>
                      >>> >>>   Titus
                      >>> >>>
                      >>> >>> >
                      >>> >>> > best
                      >>> >>> >
                      >>> >>> > Z
                      >>> >>> >
                      >>> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                      >>> >>> malsburg@posteo.de>
                      >>> >>> > wrote:
                      >>> >>> >
                      >>> >>> >>
                      >>> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                      >>> >>> >> > Hi Titus and thx so much for the answers!
                      >>> >>> >> >
                      >>> >>> >> > i will in the future use the github page to make requests.
                      >>> >>> >> >
                      >>> >>> >> > "The number of matches will be displayed in the mode line. "
                      >>> >>> >> >
                      >>> >>> >> > i see that now thx! :) the problem was(is) that its colored black
                      >>> on
                      >>> >>> my
                      >>> >>> >> > black modline BG which makes it invisible ;-) i assume thats an
                      >>> helm
                      >>> >>> >> config
                      >>> >>> >> > i need to change
                      >>> >>> >> >
                      >>> >>> >> >
                      >>> >>> >> > "If you don’t want to type these search expressions, you could
                      >>> >>> create a
                      >>> >>> >> > command that invokes helm-bibtex with a default search expression
                      >>> and
                      >>> >>> >> that
                      >>> >>> >> > command could be bound to a keyboard shortcut."
                      >>> >>> >> >
                      >>> >>> >> > that would be prefect for me and a solution to my issue. would you
                      >>> >>> mind
                      >>> >>> >> > giving an example of such a code chunk. unfortunately i dont know
                      >>> >>> elisp
                      >>> >>> >> though
                      >>> >>> >> > as john recommended i will do my best this summer when the
                      >>> semester
                      >>> >>> ends
                      >>> >>> >> to
                      >>> >>> >> > try and pick it up :)
                      >>> >>> >>
                      >>> >>> >> Sure, here you go:
                      >>> >>> >>
                      >>> >>> >> #+BEGIN_SRC elisp
                      >>> >>> >> ;; Define helm-search with predefined search expression:
                      >>> >>> >> (defun helm-bibtex-my-publications ()
                      >>> >>> >>   "Search BibTeX entries authored by Xebar Saram."
                      >>> >>> >>   (interactive)
                      >>> >>> >>   (helm :sources '(helm-source-bibtex)
                      >>> >>> >>         :full-frame t
                      >>> >>> >>         :input "xebar saram"
                      >>> >>> >>         :candidate-number-limit 500))
                      >>> >>> >>
                      >>> >>> >> ;; Bind this search function to Ctrl-x p:
                      >>> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                      >>> >>> >> #+END_SRC
                      >>> >>> >>
                      >>> >>> >> > i will definitely use your tag system as you recommended, sounds
                      >>> >>> perfect
                      >>> >>> >> > for me
                      >>> >>> >>
                      >>> >>> >> The tag system also comes in handy when generating publication lists
                      >>> >>> for
                      >>> >>> >> CVs and web pages because BibTeX does not distinguish between
                      >>> >>> conference
                      >>> >>> >> papers, posters, and talks.  If you have tags for that, it’s
                      >>> relatively
                      >>> >>> >> easy to create separate sections for these types of publications
                      >>> using
                      >>> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                      >>> >>> >>
                      >>> >>> >> > thanks again for your kind help and the amazing app ;-)
                      >>> >>> >>
                      >>> >>> >> You are welcome.
                      >>> >>> >>
                      >>> >>> >>   Titus
                      >>> >>> >>
                      >>> >>> >> >
                      >>> >>> >> > best
                      >>> >>> >> >
                      >>> >>> >> > Z
                      >>> >>> >> >
                      >>> >>> >> >
                      >>> >>> >> >
                      >>> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                      >>> >>> >> malsburg@posteo.de
                      >>> >>> >> >> wrote:
                      >>> >>> >> >
                      >>> >>> >> >>
                      >>> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                      >>> >>> >> >> > Hi Titus
                      >>> >>> >> >> >
                      >>> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                      >>> >>> questions.
                      >>> >>> >> >> btw
                      >>> >>> >> >> > is this the preferred way to make requests/ask questions or is
                      >>> >>> >> >> > github preferred?
                      >>> >>> >> >>
                      >>> >>> >> >> Helm-bibtex is not part of org (although it tries to work well
                      >>> with
                      >>> >>> >> >> org).  So I’m not sure whether this list is the best place for
                      >>> >>> >> >> discussing it.  For now the issue tracker on Github might be a
                      >>> >>> better
                      >>> >>> >> >> option:
                      >>> >>> >> >>
                      >>> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                      >>> >>> >> >>
                      >>> >>> >> >> > in any case i was wondering a few things:
                      >>> >>> >> >> >
                      >>> >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                      >>> >>> sort by
                      >>> >>> >> >> > Author, year, month
                      >>> >>> >> >>
                      >>> >>> >> >> I prefer to see the entries in the (inverse) order in which they
                      >>> >>> appear
                      >>> >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                      >>> >>> >> >> top.  However, I agree that sorting would be useful (see issues
                      >>> #5
                      >>> >>> and
                      >>> >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                      >>> >>> welcome.
                      >>> >>> >> >>
                      >>> >>> >> >> > 2. i would really like a way to have stored smart groups (like
                      >>> the
                      >>> >>> >> jabref
                      >>> >>> >> >> > dynamic groups if your aware of that). that is for example
                      >>> create
                      >>> >>> a
                      >>> >>> >> group
                      >>> >>> >> >> > that auto selects all publications i have (by my first/last
                      >>> name)
                      >>> >>> and
                      >>> >>> >> >> shows
                      >>> >>> >> >> > the count (in numbers) of these publications.
                      >>> >>> >> >>
                      >>> >>> >> >> I’m not familiar with smart groups but it seems that all
                      >>> >>> helm-bibtex is
                      >>> >>> >> >> doing is giving you very flexible smart groups defined by your
                      >>> >>> search
                      >>> >>> >> >> expressions.  For example, if you want a list of your
                      >>> publications,
                      >>> >>> you
                      >>> >>> >> >> can simple enter your name.  And if you want a list of your
                      >>> >>> articles,
                      >>> >>> >> >> you can enter your name + “article”.  If you want all your
                      >>> articles
                      >>> >>> from
                      >>> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
                      >>> of
                      >>> >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                      >>> >>> type
                      >>> >>> >> >> these search expressions, you could create a command that invokes
                      >>> >>> >> >> helm-bibtex with a default search expression and that command
                      >>> could
                      >>> >>> be
                      >>> >>> >> >> bound to a keyboard shortcut.
                      >>> >>> >> >>
                      >>> >>> >> >> > Another example is a group to keep track of all the papers im
                      >>> >>> working
                      >>> >>> >> on
                      >>> >>> >> >> or
                      >>> >>> >> >> > invloved with by matching keyword author and prep/*other key
                      >>> word
                      >>> >>> >> >>
                      >>> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                      >>> >>> >> >> describing the content of the paper (as usual) and “tags” for
                      >>> meta
                      >>> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
                      >>> “poster”,
                      >>> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
                      >>> search
                      >>> >>> for
                      >>> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
                      >>> to
                      >>> >>> be
                      >>> >>> >> >> added to `helm-bibtex-additional-search-fields`.
                      >>> >>> >> >>
                      >>> >>> >> >> Another solution would be to use the pubstate field and to search
                      >>> >>> for
                      >>> >>> >> >> your name and “forthcoming” (add pubstate to
                      >>> >>> >> >> helm-bibtex-additional-search-fields for this to work).
                      >>> >>> >> >>
                      >>> >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
                      >>> for a
                      >>> >>> >> >> selected
                      >>> >>> >> >> > citation based on user criteria such as
                      >>> author(date)short-title?
                      >>> >>> >> >>
                      >>> >>> >> >> Maintaining the content of the BibTeX file not really in the
                      >>> scope
                      >>> >>> of
                      >>> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
                      >>> Perhaps
                      >>> >>> >> >> org-ref or ebib can help here?  Once you have a function that
                      >>> >>> generates
                      >>> >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
                      >>> it
                      >>> >>> to
                      >>> >>> >> >> the list of actions in helm-bibtex.
                      >>> >>> >> >>
                      >>> >>> >> >> Hope that helps.
                      >>> >>> >> >>
                      >>> >>> >> >>   Titus
                      >>> >>> >> >>
                      >>> >>> >> >> > thx so much in advance, you and john have given me confidence
                      >>> to
                      >>> >>> >> finally
                      >>> >>> >> >> > dive into the whole latex/bibteX world
                      >>> >>> >> >> >
                      >>> >>> >> >> > best
                      >>> >>> >> >> >
                      >>> >>> >> >> > Z
                      >>> >>> >> >>
                      >>> >>> >> >>
                      >>> >>> >>
                      >>> >>> >>
                      >>> >>>
                      >>> >>>
                      >>> >>
                      >>>
                      >>>
                      
                      
                      [-- Attachment #2: signature.asc --]
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                      ^ permalink raw reply	[flat|nested] 26+ messages in thread

                    • * Re: helm-bibtex questions
                        2015-06-26 17:21                   ` Titus von der Malsburg
                        2015-06-26 17:35                     ` Titus von der Malsburg
                      @ 2015-06-26 17:54                     ` John Kitchin
                        1 sibling, 0 replies; 26+ messages in thread
                      From: John Kitchin @ 2015-06-26 17:54 UTC (permalink / raw)
                        To: Titus von der Malsburg; +Cc: Xebar Saram, org mode
                      
                      In org-ref, I have a function that will copy a bibtex entry to the
                      clipboard in the helm menu for the cite link actions:
                      
                      https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3363
                      
                      And here a menu item to insert a bibtex entry and attach its pdf to an
                      email:
                      
                      https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3382
                      
                      exactly for those purposes!
                      
                      >> 5. i love the insert formatted reference (f5) option and use it often
                      >> sending people references:
                      >> a. does it also auto send that to the clipboard?
                      >
                      > There is currently no way to copy references directly to the
                      > clipboard.  My recommendation is to use one of Emacs’ mail clients, then
                      > you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
                      > when combined with helm-mu).
                      >
                      >> b. it cuts most of the authors name and leaves only the first few. is there
                      >> a switch to get it to print all authors. is that a latex cite formatting
                      >> issue?
                      >
                      > Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
                      > anything in my setup.  Could you please provide an example?  (Perhaps
                      > this is something for the issue tracker on Github.)
                      >
                      > Best wishes,
                      >
                      >   Titus
                      >
                      >
                      >>
                      >> best and thanks so much again
                      >>
                      >> Z
                      >>
                      >> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <malsburg@posteo.de>
                      >> wrote:
                      >>
                      >>>
                      >>>
                      >>> Here is my CV in org-mode:
                      >>>
                      >>>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
                      >>>
                      >>> It’s a pretty straightforward org document except for one thing: the key
                      >>> to making this work was biblatex which can be used to create several
                      >>> lists of references filtered according to keywords, author, etc.  This
                      >>> allowed me to have separate sections for journal articles, conference
                      >>> presentations, etc.  I store the relevant keywords in the tags field of
                      >>> the BibTeX entries and since biblatex doesn’t know this field, I copy
                      >>> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
                      >>> LaTeX headers).
                      >>>
                      >>>   Titus
                      >>>
                      >>> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
                      >>> > Hi John
                      >>> >
                      >>> > a bit off topic, but do you also write your academic CV in orgmode or
                      >>> > lateX? in anycase would you mind sharing your org/latex CV template? it
                      >>> > would be helpful as a starting point for me if thats possible.
                      >>> >
                      >>> > kind regards and thanks so much in advance
                      >>> >
                      >>> > Z
                      >>> >
                      >>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <jkitchin@andrew.cmu.edu>
                      >>> > wrote:
                      >>> >
                      >>> >> sweet! I did not know you could do that! I will be refactoring org-ref
                      >>> >> soon to do that instead of redefining the commands!
                      >>> >>
                      >>> >> John
                      >>> >>
                      >>> >> -----------------------------------
                      >>> >> Professor John Kitchin
                      >>> >> Doherty Hall A207F
                      >>> >> Department of Chemical Engineering
                      >>> >> Carnegie Mellon University
                      >>> >> Pittsburgh, PA 15213
                      >>> >> 412-268-7803
                      >>> >> @johnkitchin
                      >>> >> http://kitchingroup.cheme.cmu.edu
                      >>> >>
                      >>> >>
                      >>> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
                      >>> >> malsburg@posteo.de> wrote:
                      >>> >>
                      >>> >>>
                      >>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
                      >>> >>> > Hi again Titus
                      >>> >>> >
                      >>> >>> > 2 quick questions that arose from using helm-bitex today extensively:
                      >>> >>> >
                      >>> >>> > how does one exclude in the search items? for example i want to
                      >>> search
                      >>> >>> for
                      >>> >>> > xebar without keyword "progress" (I want to exclude in progress
                      >>> articles
                      >>> >>> > not published yet)
                      >>> >>> >
                      >>> >>> > is it possible to define default enter command in helm-bibtex ?
                      >>> >>>
                      >>> >>> Yes.  Helm uses the first action as the default action.  To move an
                      >>> >>> action to the top of the list you can use the following code:
                      >>> >>>
                      >>> >>>   (helm-delete-action-from-source "Insert BibTeX key"
                      >>> helm-source-bibtex)
                      >>> >>>   (helm-add-action-to-source "Insert BibTeX key"
                      >>> 'helm-bibtex-insert-key
                      >>> >>> helm-source-bibtex 0)
                      >>> >>>
                      >>> >>> The second argument in the second line is the function that executes
                      >>> the
                      >>> >>> action.  Here is a list of all actions and their functions:
                      >>> >>>
                      >>> >>>   Open PDF file (if present): helm-bibtex-open-pdf
                      >>> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
                      >>> >>>   Insert citation: helm-bibtex-insert-citation
                      >>> >>>   Insert reference: helm-bibtex-insert-reference
                      >>> >>>   Insert BibTeX key: helm-bibtex-insert-key
                      >>> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
                      >>> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
                      >>> >>>   Edit notes: helm-bibtex-edit-notes
                      >>> >>>   Show entry: helm-bibtex-show-entry
                      >>> >>>
                      >>> >>> Best,
                      >>> >>>
                      >>> >>>   Titus
                      >>> >>>
                      >>> >>> >
                      >>> >>> > best
                      >>> >>> >
                      >>> >>> > Z
                      >>> >>> >
                      >>> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
                      >>> >>> malsburg@posteo.de>
                      >>> >>> > wrote:
                      >>> >>> >
                      >>> >>> >>
                      >>> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
                      >>> >>> >> > Hi Titus and thx so much for the answers!
                      >>> >>> >> >
                      >>> >>> >> > i will in the future use the github page to make requests.
                      >>> >>> >> >
                      >>> >>> >> > "The number of matches will be displayed in the mode line. "
                      >>> >>> >> >
                      >>> >>> >> > i see that now thx! :) the problem was(is) that its colored black
                      >>> on
                      >>> >>> my
                      >>> >>> >> > black modline BG which makes it invisible ;-) i assume thats an
                      >>> helm
                      >>> >>> >> config
                      >>> >>> >> > i need to change
                      >>> >>> >> >
                      >>> >>> >> >
                      >>> >>> >> > "If you don’t want to type these search expressions, you could
                      >>> >>> create a
                      >>> >>> >> > command that invokes helm-bibtex with a default search expression
                      >>> and
                      >>> >>> >> that
                      >>> >>> >> > command could be bound to a keyboard shortcut."
                      >>> >>> >> >
                      >>> >>> >> > that would be prefect for me and a solution to my issue. would you
                      >>> >>> mind
                      >>> >>> >> > giving an example of such a code chunk. unfortunately i dont know
                      >>> >>> elisp
                      >>> >>> >> though
                      >>> >>> >> > as john recommended i will do my best this summer when the
                      >>> semester
                      >>> >>> ends
                      >>> >>> >> to
                      >>> >>> >> > try and pick it up :)
                      >>> >>> >>
                      >>> >>> >> Sure, here you go:
                      >>> >>> >>
                      >>> >>> >> #+BEGIN_SRC elisp
                      >>> >>> >> ;; Define helm-search with predefined search expression:
                      >>> >>> >> (defun helm-bibtex-my-publications ()
                      >>> >>> >>   "Search BibTeX entries authored by Xebar Saram."
                      >>> >>> >>   (interactive)
                      >>> >>> >>   (helm :sources '(helm-source-bibtex)
                      >>> >>> >>         :full-frame t
                      >>> >>> >>         :input "xebar saram"
                      >>> >>> >>         :candidate-number-limit 500))
                      >>> >>> >>
                      >>> >>> >> ;; Bind this search function to Ctrl-x p:
                      >>> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
                      >>> >>> >> #+END_SRC
                      >>> >>> >>
                      >>> >>> >> > i will definitely use your tag system as you recommended, sounds
                      >>> >>> perfect
                      >>> >>> >> > for me
                      >>> >>> >>
                      >>> >>> >> The tag system also comes in handy when generating publication lists
                      >>> >>> for
                      >>> >>> >> CVs and web pages because BibTeX does not distinguish between
                      >>> >>> conference
                      >>> >>> >> papers, posters, and talks.  If you have tags for that, it’s
                      >>> relatively
                      >>> >>> >> easy to create separate sections for these types of publications
                      >>> using
                      >>> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
                      >>> >>> >>
                      >>> >>> >> > thanks again for your kind help and the amazing app ;-)
                      >>> >>> >>
                      >>> >>> >> You are welcome.
                      >>> >>> >>
                      >>> >>> >>   Titus
                      >>> >>> >>
                      >>> >>> >> >
                      >>> >>> >> > best
                      >>> >>> >> >
                      >>> >>> >> > Z
                      >>> >>> >> >
                      >>> >>> >> >
                      >>> >>> >> >
                      >>> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
                      >>> >>> >> malsburg@posteo.de
                      >>> >>> >> >> wrote:
                      >>> >>> >> >
                      >>> >>> >> >>
                      >>> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
                      >>> >>> >> >> > Hi Titus
                      >>> >>> >> >> >
                      >>> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
                      >>> >>> questions.
                      >>> >>> >> >> btw
                      >>> >>> >> >> > is this the preferred way to make requests/ask questions or is
                      >>> >>> >> >> > github preferred?
                      >>> >>> >> >>
                      >>> >>> >> >> Helm-bibtex is not part of org (although it tries to work well
                      >>> with
                      >>> >>> >> >> org).  So I’m not sure whether this list is the best place for
                      >>> >>> >> >> discussing it.  For now the issue tracker on Github might be a
                      >>> >>> better
                      >>> >>> >> >> option:
                      >>> >>> >> >>
                      >>> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
                      >>> >>> >> >>
                      >>> >>> >> >> > in any case i was wondering a few things:
                      >>> >>> >> >> >
                      >>> >>> >> >> > 1. is it possible to have custom sorting? i want all views to
                      >>> >>> sort by
                      >>> >>> >> >> > Author, year, month
                      >>> >>> >> >>
                      >>> >>> >> >> I prefer to see the entries in the (inverse) order in which they
                      >>> >>> appear
                      >>> >>> >> >> in the BibTeX file.  This way, recent additions show up at the
                      >>> >>> >> >> top.  However, I agree that sorting would be useful (see issues
                      >>> #5
                      >>> >>> and
                      >>> >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
                      >>> >>> welcome.
                      >>> >>> >> >>
                      >>> >>> >> >> > 2. i would really like a way to have stored smart groups (like
                      >>> the
                      >>> >>> >> jabref
                      >>> >>> >> >> > dynamic groups if your aware of that). that is for example
                      >>> create
                      >>> >>> a
                      >>> >>> >> group
                      >>> >>> >> >> > that auto selects all publications i have (by my first/last
                      >>> name)
                      >>> >>> and
                      >>> >>> >> >> shows
                      >>> >>> >> >> > the count (in numbers) of these publications.
                      >>> >>> >> >>
                      >>> >>> >> >> I’m not familiar with smart groups but it seems that all
                      >>> >>> helm-bibtex is
                      >>> >>> >> >> doing is giving you very flexible smart groups defined by your
                      >>> >>> search
                      >>> >>> >> >> expressions.  For example, if you want a list of your
                      >>> publications,
                      >>> >>> you
                      >>> >>> >> >> can simple enter your name.  And if you want a list of your
                      >>> >>> articles,
                      >>> >>> >> >> you can enter your name + “article”.  If you want all your
                      >>> articles
                      >>> >>> from
                      >>> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
                      >>> of
                      >>> >>> >> >> matches will be displayed in the mode line.  If you don’t want to
                      >>> >>> type
                      >>> >>> >> >> these search expressions, you could create a command that invokes
                      >>> >>> >> >> helm-bibtex with a default search expression and that command
                      >>> could
                      >>> >>> be
                      >>> >>> >> >> bound to a keyboard shortcut.
                      >>> >>> >> >>
                      >>> >>> >> >> > Another example is a group to keep track of all the papers im
                      >>> >>> working
                      >>> >>> >> on
                      >>> >>> >> >> or
                      >>> >>> >> >> > invloved with by matching keyword author and prep/*other key
                      >>> word
                      >>> >>> >> >>
                      >>> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
                      >>> >>> >> >> describing the content of the paper (as usual) and “tags” for
                      >>> meta
                      >>> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
                      >>> “poster”,
                      >>> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
                      >>> search
                      >>> >>> for
                      >>> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
                      >>> to
                      >>> >>> be
                      >>> >>> >> >> added to `helm-bibtex-additional-search-fields`.
                      >>> >>> >> >>
                      >>> >>> >> >> Another solution would be to use the pubstate field and to search
                      >>> >>> for
                      >>> >>> >> >> your name and “forthcoming” (add pubstate to
                      >>> >>> >> >> helm-bibtex-additional-search-fields for this to work).
                      >>> >>> >> >>
                      >>> >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
                      >>> for a
                      >>> >>> >> >> selected
                      >>> >>> >> >> > citation based on user criteria such as
                      >>> author(date)short-title?
                      >>> >>> >> >>
                      >>> >>> >> >> Maintaining the content of the BibTeX file not really in the
                      >>> scope
                      >>> >>> of
                      >>> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
                      >>> Perhaps
                      >>> >>> >> >> org-ref or ebib can help here?  Once you have a function that
                      >>> >>> generates
                      >>> >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
                      >>> it
                      >>> >>> to
                      >>> >>> >> >> the list of actions in helm-bibtex.
                      >>> >>> >> >>
                      >>> >>> >> >> Hope that helps.
                      >>> >>> >> >>
                      >>> >>> >> >>   Titus
                      >>> >>> >> >>
                      >>> >>> >> >> > thx so much in advance, you and john have given me confidence
                      >>> to
                      >>> >>> >> finally
                      >>> >>> >> >> > dive into the whole latex/bibteX world
                      >>> >>> >> >> >
                      >>> >>> >> >> > best
                      >>> >>> >> >> >
                      >>> >>> >> >> > Z
                      >>> >>> >> >>
                      >>> >>> >> >>
                      >>> >>> >>
                      >>> >>> >>
                      >>> >>>
                      >>> >>>
                      >>> >>
                      >>>
                      >>>
                      
                      --
                      Professor John Kitchin
                      Doherty Hall A207F
                      Department of Chemical Engineering
                      Carnegie Mellon University
                      Pittsburgh, PA 15213
                      412-268-7803
                      @johnkitchin
                      http://kitchingroup.cheme.cmu.edu
                      
                      ^ permalink raw reply	[flat|nested] 26+ messages in thread

  • * Re: helm-bibtex questions
      2015-06-17 20:02 ` Titus von der Malsburg
      2015-06-18 11:32   ` Xebar Saram
    @ 2015-06-19 21:08   ` John Kitchin
      1 sibling, 0 replies; 26+ messages in thread
    From: John Kitchin @ 2015-06-19 21:08 UTC (permalink / raw)
      To: Titus von der Malsburg; +Cc: Xebar Saram, org mode
    
    >
    >> 3.is it possible to ass an option to auto generate a bibkey for a selected
    >> citation based on user criteria such as author(date)short-title?
    >
    > Maintaining the content of the BibTeX file not really in the scope of
    > helm-bibtex (I prefer to write my BibTeX entries by hand).  Perhaps
    > org-ref or ebib can help here?  Once you have a function that generates
    > a new key and inserts it in the BibTeX file, you can easily add it to
    > the list of actions in helm-bibtex.
    
    Indeed. See org-ref-clean-bibtex-entry
    
    This adds a key according to some rules, and cleans up the entries in a
    lot of ways. We try to always get bibtex entries from a doi (using
    doi-utils.el), and they almost always need some "cleaning".
    
    >
    > Hope that helps.
    >
    >   Titus
    >
    >> thx so much in advance, you and john have given me confidence to finally
    >> dive into the whole latex/bibteX world
    >>
    >> best
    >>
    >> Z
    
    --
    Professor John Kitchin
    Doherty Hall A207F
    Department of Chemical Engineering
    Carnegie Mellon University
    Pittsburgh, PA 15213
    412-268-7803
    @johnkitchin
    http://kitchingroup.cheme.cmu.edu
    
    ^ permalink raw reply	[flat|nested] 26+ messages in thread

[parent not found: <s7xudwyj5ehe8r98klrf3034.1435230561139@email.android.com>]

• * Re: helm-bibtex questions
         [not found] <s7xudwyj5ehe8r98klrf3034.1435230561139@email.android.com>
  @ 2015-06-26  7:14 ` Xebar Saram
    2015-06-26 14:28   ` John Kitchin
    0 siblings, 1 reply; 26+ messages in thread
  From: Xebar Saram @ 2015-06-26  7:14 UTC (permalink / raw)
    To: John Kitchin, org mode
  
  [-- Attachment #1: Type: text/plain, Size: 15312 bytes --]
  
  thanks so much again John
  
  i did add this line
  (bibtex-set-dialect 'biblatex)
  in my init but that dosent seem to do much as i still get the "journal
  mandatory field missing" error. anything else i can try?
  
  best
  
  Z
  
  
  On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin <johnrkitchin@gmail.com>
  wrote:
  
  > I believe that is an emacs bibtex issue. You need some kind of line in
  > your bibtex file to specify it is the biblatex dialect.
  >
  >
  > On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> wrote:
  >
  >
  > Great, works well. one question though (and this may very well be due to
  > my inexperience). the jabref export i had used 'journaltitle' instead of
  > journal to be (to my understanding) compatible with the newer .bib files
  > used by biblatex (and biber). when i ran org-ref clean it gave an error on"
  > journal mandatory field missing". i had to replace all 'journaltitle'  to
  > 'journal' to get it to work.
  > is this by design? does org-ref not support the new biblatex/biber .bib
  > file format?
  >
  > kind regards
  >
  > Itai
  >
  > On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin <jkitchin@andrew.cmu.edu>
  > wrote:
  >
  >> yes, there is a way ;)
  >>
  >> First. Make sure you have a backup of the references. I like to keep
  >> mine in a local git repo so you can undo any mistakes that get made.
  >>
  >> I suggest you run these first:
  >> %% (bibtex-validate-globally)   ; checks for duplicate keys
  >> %% (bibtex-validate)
  >>
  >> I also recommend you run bibtex-sort (it is easier to spot duplicates in
  >> a sorted list).
  >>
  >> and (org-ref-build-full-bibliography) <- makes a pdf of all references.
  >>
  >> to make sure everything is compliant and functional.
  >>
  >> Then, put this next line at the top of your bibtex file. The t argument to
  >> org-ref-clean-bibtex-entry will preserve your existing keys.
  >>
  >> % (bibtex-map-entries (lambda (key start end) (org-ref-clean-bibtex-entry
  >> t)))
  >>
  >> Put your cursor at the end of that line, and type C-x C-e to run the
  >> function, and
  >> wait patiently. It took a few minutes on my 1300 entries, and I had to
  >> restart it once on some entry.
  >>
  >> when it is done, run (org-ref-build-full-bibliography) again to make
  >> sure it works and review the ~200 page pdf ;). fix errors and repeat
  >> until it builds ;)
  >>
  >> Note if you want to change title cases in all entries you can use
  >>
  >> % (bibtex-map-entries 'jmax-title-case-article)
  >> % (bibtex-map-entries 'jmax-sentence-case-article)
  >>
  >> I hope that helps!
  >>
  >> Xebar Saram writes:
  >>
  >> > John
  >> >
  >> > First of all thanks so much for the excellent org-ref-clean-bibtex-entry
  >> > function i love it!
  >> > also your blog post on cleaning the bib file is a life saver
  >> >
  >> > i have 800 references, is there a way to auto
  >> > make org-ref-clean-bibtex-entry go thorough my whole bib file instead
  >> of me
  >> > going and cleaning it 1 by 1?
  >> >
  >> > kind regards
  >> >
  >> > Z.
  >> >
  >> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <
  >> malsburg@posteo.de>
  >> > wrote:
  >> >
  >> >>
  >> >>
  >> >> Here is my CV in org-mode:
  >> >>
  >> >>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
  >> >>
  >> >> It’s a pretty straightforward org document except for one thing: the
  >> key
  >> >> to making this work was biblatex which can be used to create several
  >> >> lists of references filtered according to keywords, author, etc.  This
  >> >> allowed me to have separate sections for journal articles, conference
  >> >> presentations, etc.  I store the relevant keywords in the tags field of
  >> >> the BibTeX entries and since biblatex doesn’t know this field, I copy
  >> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
  >> >> LaTeX headers).
  >> >>
  >> >>   Titus
  >> >>
  >> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
  >> >> > Hi John
  >> >> >
  >> >> > a bit off topic, but do you also write your academic CV in orgmode or
  >> >> > lateX? in anycase would you mind sharing your org/latex CV template?
  >> it
  >> >> > would be helpful as a starting point for me if thats possible.
  >> >> >
  >> >> > kind regards and thanks so much in advance
  >> >> >
  >> >> > Z
  >> >> >
  >> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <
  >> jkitchin@andrew.cmu.edu>
  >> >> > wrote:
  >> >> >
  >> >> >> sweet! I did not know you could do that! I will be refactoring
  >> org-ref
  >> >> >> soon to do that instead of redefining the commands!
  >> >> >>
  >> >> >> John
  >> >> >>
  >> >> >> -----------------------------------
  >> >> >> Professor John Kitchin
  >> >> >> Doherty Hall A207F
  >> >> >> Department of Chemical Engineering
  >> >> >> Carnegie Mellon University
  >> >> >> Pittsburgh, PA 15213
  >> >> >> 412-268-7803
  >> >> >> @johnkitchin
  >> >> >> http://kitchingroup.cheme.cmu.edu
  >> >> >>
  >> >> >>
  >> >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
  >> >> >> malsburg@posteo.de> wrote:
  >> >> >>
  >> >> >>>
  >> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
  >> >> >>> > Hi again Titus
  >> >> >>> >
  >> >> >>> > 2 quick questions that arose from using helm-bitex today
  >> extensively:
  >> >> >>> >
  >> >> >>> > how does one exclude in the search items? for example i want to
  >> >> search
  >> >> >>> for
  >> >> >>> > xebar without keyword "progress" (I want to exclude in progress
  >> >> articles
  >> >> >>> > not published yet)
  >> >> >>> >
  >> >> >>> > is it possible to define default enter command in helm-bibtex ?
  >> >> >>>
  >> >> >>> Yes.  Helm uses the first action as the default action.  To move an
  >> >> >>> action to the top of the list you can use the following code:
  >> >> >>>
  >> >> >>>   (helm-delete-action-from-source "Insert BibTeX key"
  >> >> helm-source-bibtex)
  >> >> >>>   (helm-add-action-to-source "Insert BibTeX key"
  >> >> 'helm-bibtex-insert-key
  >> >> >>> helm-source-bibtex 0)
  >> >> >>>
  >> >> >>> The second argument in the second line is the function that
  >> executes
  >> >> the
  >> >> >>> action.  Here is a list of all actions and their functions:
  >> >> >>>
  >> >> >>>   Open PDF file (if present): helm-bibtex-open-pdf
  >> >> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
  >> >> >>>   Insert citation: helm-bibtex-insert-citation
  >> >> >>>   Insert reference: helm-bibtex-insert-reference
  >> >> >>>   Insert BibTeX key: helm-bibtex-insert-key
  >> >> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
  >> >> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
  >> >> >>>   Edit notes: helm-bibtex-edit-notes
  >> >> >>>   Show entry: helm-bibtex-show-entry
  >> >> >>>
  >> >> >>> Best,
  >> >> >>>
  >> >> >>>   Titus
  >> >> >>>
  >> >> >>> >
  >> >> >>> > best
  >> >> >>> >
  >> >> >>> > Z
  >> >> >>> >
  >> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
  >> >> >>> malsburg@posteo.de>
  >> >> >>> > wrote:
  >> >> >>> >
  >> >> >>> >>
  >> >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
  >> >> >>> >> > Hi Titus and thx so much for the answers!
  >> >> >>> >> >
  >> >> >>> >> > i will in the future use the github page to make requests.
  >> >> >>> >> >
  >> >> >>> >> > "The number of matches will be displayed in the mode line. "
  >> >> >>> >> >
  >> >> >>> >> > i see that now thx! :) the problem was(is) that its colored
  >> black
  >> >> on
  >> >> >>> my
  >> >> >>> >> > black modline BG which makes it invisible ;-) i assume thats
  >> an
  >> >> helm
  >> >> >>> >> config
  >> >> >>> >> > i need to change
  >> >> >>> >> >
  >> >> >>> >> >
  >> >> >>> >> > "If you don’t want to type these search expressions, you could
  >> >> >>> create a
  >> >> >>> >> > command that invokes helm-bibtex with a default search
  >> expression
  >> >> and
  >> >> >>> >> that
  >> >> >>> >> > command could be bound to a keyboard shortcut."
  >> >> >>> >> >
  >> >> >>> >> > that would be prefect for me and a solution to my issue.
  >> would you
  >> >> >>> mind
  >> >> >>> >> > giving an example of such a code chunk. unfortunately i dont
  >> know
  >> >> >>> elisp
  >> >> >>> >> though
  >> >> >>> >> > as john recommended i will do my best this summer when the
  >> >> semester
  >> >> >>> ends
  >> >> >>> >> to
  >> >> >>> >> > try and pick it up :)
  >> >> >>> >>
  >> >> >>> >> Sure, here you go:
  >> >> >>> >>
  >> >> >>> >> #+BEGIN_SRC elisp
  >> >> >>> >> ;; Define helm-search with predefined search expression:
  >> >> >>> >> (defun helm-bibtex-my-publications ()
  >> >> >>> >>   "Search BibTeX entries authored by Xebar Saram."
  >> >> >>> >>   (interactive)
  >> >> >>> >>   (helm :sources '(helm-source-bibtex)
  >> >> >>> >>         :full-frame t
  >> >> >>> >>         :input "xebar saram"
  >> >> >>> >>         :candidate-number-limit 500))
  >> >> >>> >>
  >> >> >>> >> ;; Bind this search function to Ctrl-x p:
  >> >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
  >> >> >>> >> #+END_SRC
  >> >> >>> >>
  >> >> >>> >> > i will definitely use your tag system as you recommended,
  >> sounds
  >> >> >>> perfect
  >> >> >>> >> > for me
  >> >> >>> >>
  >> >> >>> >> The tag system also comes in handy when generating publication
  >> lists
  >> >> >>> for
  >> >> >>> >> CVs and web pages because BibTeX does not distinguish between
  >> >> >>> conference
  >> >> >>> >> papers, posters, and talks.  If you have tags for that, it’s
  >> >> relatively
  >> >> >>> >> easy to create separate sections for these types of publications
  >> >> using
  >> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
  >> >> >>> >>
  >> >> >>> >> > thanks again for your kind help and the amazing app ;-)
  >> >> >>> >>
  >> >> >>> >> You are welcome.
  >> >> >>> >>
  >> >> >>> >>   Titus
  >> >> >>> >>
  >> >> >>> >> >
  >> >> >>> >> > best
  >> >> >>> >> >
  >> >> >>> >> > Z
  >> >> >>> >> >
  >> >> >>> >> >
  >> >> >>> >> >
  >> >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
  >> >> >>> >> malsburg@posteo.de
  >> >> >>> >> >> wrote:
  >> >> >>> >> >
  >> >> >>> >> >>
  >> >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
  >> >> >>> >> >> > Hi Titus
  >> >> >>> >> >> >
  >> >> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
  >> >> >>> questions.
  >> >> >>> >> >> btw
  >> >> >>> >> >> > is this the preferred way to make requests/ask questions
  >> or is
  >> >> >>> >> >> > github preferred?
  >> >> >>> >> >>
  >> >> >>> >> >> Helm-bibtex is not part of org (although it tries to work
  >> well
  >> >> with
  >> >> >>> >> >> org).  So I’m not sure whether this list is the best place
  >> for
  >> >> >>> >> >> discussing it.  For now the issue tracker on Github might be
  >> a
  >> >> >>> better
  >> >> >>> >> >> option:
  >> >> >>> >> >>
  >> >> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
  >> >> >>> >> >>
  >> >> >>> >> >> > in any case i was wondering a few things:
  >> >> >>> >> >> >
  >> >> >>> >> >> > 1. is it possible to have custom sorting? i want all views
  >> to
  >> >> >>> sort by
  >> >> >>> >> >> > Author, year, month
  >> >> >>> >> >>
  >> >> >>> >> >> I prefer to see the entries in the (inverse) order in which
  >> they
  >> >> >>> appear
  >> >> >>> >> >> in the BibTeX file.  This way, recent additions show up at
  >> the
  >> >> >>> >> >> top.  However, I agree that sorting would be useful (see
  >> issues
  >> >> #5
  >> >> >>> and
  >> >> >>> >> >> #21); it just doesn’t have high priority for me.  Pull
  >> requests
  >> >> >>> welcome.
  >> >> >>> >> >>
  >> >> >>> >> >> > 2. i would really like a way to have stored smart groups
  >> (like
  >> >> the
  >> >> >>> >> jabref
  >> >> >>> >> >> > dynamic groups if your aware of that). that is for example
  >> >> create
  >> >> >>> a
  >> >> >>> >> group
  >> >> >>> >> >> > that auto selects all publications i have (by my first/last
  >> >> name)
  >> >> >>> and
  >> >> >>> >> >> shows
  >> >> >>> >> >> > the count (in numbers) of these publications.
  >> >> >>> >> >>
  >> >> >>> >> >> I’m not familiar with smart groups but it seems that all
  >> >> >>> helm-bibtex is
  >> >> >>> >> >> doing is giving you very flexible smart groups defined by
  >> your
  >> >> >>> search
  >> >> >>> >> >> expressions.  For example, if you want a list of your
  >> >> publications,
  >> >> >>> you
  >> >> >>> >> >> can simple enter your name.  And if you want a list of your
  >> >> >>> articles,
  >> >> >>> >> >> you can enter your name + “article”.  If you want all your
  >> >> articles
  >> >> >>> from
  >> >> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The
  >> number
  >> >> of
  >> >> >>> >> >> matches will be displayed in the mode line.  If you don’t
  >> want to
  >> >> >>> type
  >> >> >>> >> >> these search expressions, you could create a command that
  >> invokes
  >> >> >>> >> >> helm-bibtex with a default search expression and that command
  >> >> could
  >> >> >>> be
  >> >> >>> >> >> bound to a keyboard shortcut.
  >> >> >>> >> >>
  >> >> >>> >> >> > Another example is a group to keep track of all the papers
  >> im
  >> >> >>> working
  >> >> >>> >> on
  >> >> >>> >> >> or
  >> >> >>> >> >> > invloved with by matching keyword author and prep/*other
  >> key
  >> >> word
  >> >> >>> >> >>
  >> >> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for
  >> keywords
  >> >> >>> >> >> describing the content of the paper (as usual) and “tags” for
  >> >> meta
  >> >> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
  >> >> “poster”,
  >> >> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
  >> >> search
  >> >> >>> for
  >> >> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it
  >> has
  >> >> to
  >> >> >>> be
  >> >> >>> >> >> added to `helm-bibtex-additional-search-fields`.
  >> >> >>> >> >>
  >> >> >>> >> >> Another solution would be to use the pubstate field and to
  >> search
  >> >> >>> for
  >> >> >>> >> >> your name and “forthcoming” (add pubstate to
  >> >> >>> >> >> helm-bibtex-additional-search-fields for this to work).
  >> >> >>> >> >>
  >> >> >>> >> >> > 3.is it possible to ass an option to auto generate a
  >> bibkey
  >> >> for a
  >> >> >>> >> >> selected
  >> >> >>> >> >> > citation based on user criteria such as
  >> >> author(date)short-title?
  >> >> >>> >> >>
  >> >> >>> >> >> Maintaining the content of the BibTeX file not really in the
  >> >> scope
  >> >> >>> of
  >> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
  >> >> Perhaps
  >> >> >>> >> >> org-ref or ebib can help here?  Once you have a function that
  >> >> >>> generates
  >> >> >>> >> >> a new key and inserts it in the BibTeX file, you can easily
  >> add
  >> >> it
  >> >> >>> to
  >> >> >>> >> >> the list of actions in helm-bibtex.
  >> >> >>> >> >>
  >> >> >>> >> >> Hope that helps.
  >> >> >>> >> >>
  >> >> >>> >> >>   Titus
  >> >> >>> >> >>
  >> >> >>> >> >> > thx so much in advance, you and john have given me
  >> confidence
  >> >> to
  >> >> >>> >> finally
  >> >> >>> >> >> > dive into the whole latex/bibteX world
  >> >> >>> >> >> >
  >> >> >>> >> >> > best
  >> >> >>> >> >> >
  >> >> >>> >> >> > Z
  >> >> >>> >> >>
  >> >> >>> >> >>
  >> >> >>> >>
  >> >> >>> >>
  >> >> >>>
  >> >> >>>
  >> >> >>
  >> >>
  >> >>
  >>
  >> --
  >> Professor John Kitchin
  >> Doherty Hall A207F
  >> Department of Chemical Engineering
  >> Carnegie Mellon University
  >> Pittsburgh, PA 15213
  >> 412-268-7803
  >> @johnkitchin
  >> http://kitchingroup.cheme.cmu.edu
  >>
  >
  >
  
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  ^ permalink raw reply	[flat|nested] 26+ messages in thread

• • * Re: helm-bibtex questions
      2015-06-26  7:14 ` Xebar Saram
    @ 2015-06-26 14:28   ` John Kitchin
      2015-06-27  6:11     ` Xebar Saram
      0 siblings, 1 reply; 26+ messages in thread
    From: John Kitchin @ 2015-06-26 14:28 UTC (permalink / raw)
      To: Xebar Saram; +Cc: org mode
    
    http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bibliography-files-for-biblatex
    
    I think you need this in your bibtex file:
    
    -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
    
    
    Xebar Saram writes:
    
    > thanks so much again John
    >
    > i did add this line
    > (bibtex-set-dialect 'biblatex)
    > in my init but that dosent seem to do much as i still get the "journal
    > mandatory field missing" error. anything else i can try?
    >
    > best
    >
    > Z
    >
    >
    > On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin <johnrkitchin@gmail.com>
    > wrote:
    >
    >> I believe that is an emacs bibtex issue. You need some kind of line in
    >> your bibtex file to specify it is the biblatex dialect.
    >>
    >>
    >> On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> wrote:
    >>
    >>
    >> Great, works well. one question though (and this may very well be due to
    >> my inexperience). the jabref export i had used 'journaltitle' instead of
    >> journal to be (to my understanding) compatible with the newer .bib files
    >> used by biblatex (and biber). when i ran org-ref clean it gave an error on"
    >> journal mandatory field missing". i had to replace all 'journaltitle'  to
    >> 'journal' to get it to work.
    >> is this by design? does org-ref not support the new biblatex/biber .bib
    >> file format?
    >>
    >> kind regards
    >>
    >> Itai
    >>
    >> On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin <jkitchin@andrew.cmu.edu>
    >> wrote:
    >>
    >>> yes, there is a way ;)
    >>>
    >>> First. Make sure you have a backup of the references. I like to keep
    >>> mine in a local git repo so you can undo any mistakes that get made.
    >>>
    >>> I suggest you run these first:
    >>> %% (bibtex-validate-globally)   ; checks for duplicate keys
    >>> %% (bibtex-validate)
    >>>
    >>> I also recommend you run bibtex-sort (it is easier to spot duplicates in
    >>> a sorted list).
    >>>
    >>> and (org-ref-build-full-bibliography) <- makes a pdf of all references.
    >>>
    >>> to make sure everything is compliant and functional.
    >>>
    >>> Then, put this next line at the top of your bibtex file. The t argument to
    >>> org-ref-clean-bibtex-entry will preserve your existing keys.
    >>>
    >>> % (bibtex-map-entries (lambda (key start end) (org-ref-clean-bibtex-entry
    >>> t)))
    >>>
    >>> Put your cursor at the end of that line, and type C-x C-e to run the
    >>> function, and
    >>> wait patiently. It took a few minutes on my 1300 entries, and I had to
    >>> restart it once on some entry.
    >>>
    >>> when it is done, run (org-ref-build-full-bibliography) again to make
    >>> sure it works and review the ~200 page pdf ;). fix errors and repeat
    >>> until it builds ;)
    >>>
    >>> Note if you want to change title cases in all entries you can use
    >>>
    >>> % (bibtex-map-entries 'jmax-title-case-article)
    >>> % (bibtex-map-entries 'jmax-sentence-case-article)
    >>>
    >>> I hope that helps!
    >>>
    >>> Xebar Saram writes:
    >>>
    >>> > John
    >>> >
    >>> > First of all thanks so much for the excellent org-ref-clean-bibtex-entry
    >>> > function i love it!
    >>> > also your blog post on cleaning the bib file is a life saver
    >>> >
    >>> > i have 800 references, is there a way to auto
    >>> > make org-ref-clean-bibtex-entry go thorough my whole bib file instead
    >>> of me
    >>> > going and cleaning it 1 by 1?
    >>> >
    >>> > kind regards
    >>> >
    >>> > Z.
    >>> >
    >>> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <
    >>> malsburg@posteo.de>
    >>> > wrote:
    >>> >
    >>> >>
    >>> >>
    >>> >> Here is my CV in org-mode:
    >>> >>
    >>> >>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
    >>> >>
    >>> >> It’s a pretty straightforward org document except for one thing: the
    >>> key
    >>> >> to making this work was biblatex which can be used to create several
    >>> >> lists of references filtered according to keywords, author, etc.  This
    >>> >> allowed me to have separate sections for journal articles, conference
    >>> >> presentations, etc.  I store the relevant keywords in the tags field of
    >>> >> the BibTeX entries and since biblatex doesn’t know this field, I copy
    >>> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
    >>> >> LaTeX headers).
    >>> >>
    >>> >>   Titus
    >>> >>
    >>> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
    >>> >> > Hi John
    >>> >> >
    >>> >> > a bit off topic, but do you also write your academic CV in orgmode or
    >>> >> > lateX? in anycase would you mind sharing your org/latex CV template?
    >>> it
    >>> >> > would be helpful as a starting point for me if thats possible.
    >>> >> >
    >>> >> > kind regards and thanks so much in advance
    >>> >> >
    >>> >> > Z
    >>> >> >
    >>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <
    >>> jkitchin@andrew.cmu.edu>
    >>> >> > wrote:
    >>> >> >
    >>> >> >> sweet! I did not know you could do that! I will be refactoring
    >>> org-ref
    >>> >> >> soon to do that instead of redefining the commands!
    >>> >> >>
    >>> >> >> John
    >>> >> >>
    >>> >> >> -----------------------------------
    >>> >> >> Professor John Kitchin
    >>> >> >> Doherty Hall A207F
    >>> >> >> Department of Chemical Engineering
    >>> >> >> Carnegie Mellon University
    >>> >> >> Pittsburgh, PA 15213
    >>> >> >> 412-268-7803
    >>> >> >> @johnkitchin
    >>> >> >> http://kitchingroup.cheme.cmu.edu
    >>> >> >>
    >>> >> >>
    >>> >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
    >>> >> >> malsburg@posteo.de> wrote:
    >>> >> >>
    >>> >> >>>
    >>> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
    >>> >> >>> > Hi again Titus
    >>> >> >>> >
    >>> >> >>> > 2 quick questions that arose from using helm-bitex today
    >>> extensively:
    >>> >> >>> >
    >>> >> >>> > how does one exclude in the search items? for example i want to
    >>> >> search
    >>> >> >>> for
    >>> >> >>> > xebar without keyword "progress" (I want to exclude in progress
    >>> >> articles
    >>> >> >>> > not published yet)
    >>> >> >>> >
    >>> >> >>> > is it possible to define default enter command in helm-bibtex ?
    >>> >> >>>
    >>> >> >>> Yes.  Helm uses the first action as the default action.  To move an
    >>> >> >>> action to the top of the list you can use the following code:
    >>> >> >>>
    >>> >> >>>   (helm-delete-action-from-source "Insert BibTeX key"
    >>> >> helm-source-bibtex)
    >>> >> >>>   (helm-add-action-to-source "Insert BibTeX key"
    >>> >> 'helm-bibtex-insert-key
    >>> >> >>> helm-source-bibtex 0)
    >>> >> >>>
    >>> >> >>> The second argument in the second line is the function that
    >>> executes
    >>> >> the
    >>> >> >>> action.  Here is a list of all actions and their functions:
    >>> >> >>>
    >>> >> >>>   Open PDF file (if present): helm-bibtex-open-pdf
    >>> >> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
    >>> >> >>>   Insert citation: helm-bibtex-insert-citation
    >>> >> >>>   Insert reference: helm-bibtex-insert-reference
    >>> >> >>>   Insert BibTeX key: helm-bibtex-insert-key
    >>> >> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
    >>> >> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
    >>> >> >>>   Edit notes: helm-bibtex-edit-notes
    >>> >> >>>   Show entry: helm-bibtex-show-entry
    >>> >> >>>
    >>> >> >>> Best,
    >>> >> >>>
    >>> >> >>>   Titus
    >>> >> >>>
    >>> >> >>> >
    >>> >> >>> > best
    >>> >> >>> >
    >>> >> >>> > Z
    >>> >> >>> >
    >>> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
    >>> >> >>> malsburg@posteo.de>
    >>> >> >>> > wrote:
    >>> >> >>> >
    >>> >> >>> >>
    >>> >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
    >>> >> >>> >> > Hi Titus and thx so much for the answers!
    >>> >> >>> >> >
    >>> >> >>> >> > i will in the future use the github page to make requests.
    >>> >> >>> >> >
    >>> >> >>> >> > "The number of matches will be displayed in the mode line. "
    >>> >> >>> >> >
    >>> >> >>> >> > i see that now thx! :) the problem was(is) that its colored
    >>> black
    >>> >> on
    >>> >> >>> my
    >>> >> >>> >> > black modline BG which makes it invisible ;-) i assume thats
    >>> an
    >>> >> helm
    >>> >> >>> >> config
    >>> >> >>> >> > i need to change
    >>> >> >>> >> >
    >>> >> >>> >> >
    >>> >> >>> >> > "If you don’t want to type these search expressions, you could
    >>> >> >>> create a
    >>> >> >>> >> > command that invokes helm-bibtex with a default search
    >>> expression
    >>> >> and
    >>> >> >>> >> that
    >>> >> >>> >> > command could be bound to a keyboard shortcut."
    >>> >> >>> >> >
    >>> >> >>> >> > that would be prefect for me and a solution to my issue.
    >>> would you
    >>> >> >>> mind
    >>> >> >>> >> > giving an example of such a code chunk. unfortunately i dont
    >>> know
    >>> >> >>> elisp
    >>> >> >>> >> though
    >>> >> >>> >> > as john recommended i will do my best this summer when the
    >>> >> semester
    >>> >> >>> ends
    >>> >> >>> >> to
    >>> >> >>> >> > try and pick it up :)
    >>> >> >>> >>
    >>> >> >>> >> Sure, here you go:
    >>> >> >>> >>
    >>> >> >>> >> #+BEGIN_SRC elisp
    >>> >> >>> >> ;; Define helm-search with predefined search expression:
    >>> >> >>> >> (defun helm-bibtex-my-publications ()
    >>> >> >>> >>   "Search BibTeX entries authored by Xebar Saram."
    >>> >> >>> >>   (interactive)
    >>> >> >>> >>   (helm :sources '(helm-source-bibtex)
    >>> >> >>> >>         :full-frame t
    >>> >> >>> >>         :input "xebar saram"
    >>> >> >>> >>         :candidate-number-limit 500))
    >>> >> >>> >>
    >>> >> >>> >> ;; Bind this search function to Ctrl-x p:
    >>> >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
    >>> >> >>> >> #+END_SRC
    >>> >> >>> >>
    >>> >> >>> >> > i will definitely use your tag system as you recommended,
    >>> sounds
    >>> >> >>> perfect
    >>> >> >>> >> > for me
    >>> >> >>> >>
    >>> >> >>> >> The tag system also comes in handy when generating publication
    >>> lists
    >>> >> >>> for
    >>> >> >>> >> CVs and web pages because BibTeX does not distinguish between
    >>> >> >>> conference
    >>> >> >>> >> papers, posters, and talks.  If you have tags for that, it’s
    >>> >> relatively
    >>> >> >>> >> easy to create separate sections for these types of publications
    >>> >> using
    >>> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
    >>> >> >>> >>
    >>> >> >>> >> > thanks again for your kind help and the amazing app ;-)
    >>> >> >>> >>
    >>> >> >>> >> You are welcome.
    >>> >> >>> >>
    >>> >> >>> >>   Titus
    >>> >> >>> >>
    >>> >> >>> >> >
    >>> >> >>> >> > best
    >>> >> >>> >> >
    >>> >> >>> >> > Z
    >>> >> >>> >> >
    >>> >> >>> >> >
    >>> >> >>> >> >
    >>> >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
    >>> >> >>> >> malsburg@posteo.de
    >>> >> >>> >> >> wrote:
    >>> >> >>> >> >
    >>> >> >>> >> >>
    >>> >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
    >>> >> >>> >> >> > Hi Titus
    >>> >> >>> >> >> >
    >>> >> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
    >>> >> >>> questions.
    >>> >> >>> >> >> btw
    >>> >> >>> >> >> > is this the preferred way to make requests/ask questions
    >>> or is
    >>> >> >>> >> >> > github preferred?
    >>> >> >>> >> >>
    >>> >> >>> >> >> Helm-bibtex is not part of org (although it tries to work
    >>> well
    >>> >> with
    >>> >> >>> >> >> org).  So I’m not sure whether this list is the best place
    >>> for
    >>> >> >>> >> >> discussing it.  For now the issue tracker on Github might be
    >>> a
    >>> >> >>> better
    >>> >> >>> >> >> option:
    >>> >> >>> >> >>
    >>> >> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
    >>> >> >>> >> >>
    >>> >> >>> >> >> > in any case i was wondering a few things:
    >>> >> >>> >> >> >
    >>> >> >>> >> >> > 1. is it possible to have custom sorting? i want all views
    >>> to
    >>> >> >>> sort by
    >>> >> >>> >> >> > Author, year, month
    >>> >> >>> >> >>
    >>> >> >>> >> >> I prefer to see the entries in the (inverse) order in which
    >>> they
    >>> >> >>> appear
    >>> >> >>> >> >> in the BibTeX file.  This way, recent additions show up at
    >>> the
    >>> >> >>> >> >> top.  However, I agree that sorting would be useful (see
    >>> issues
    >>> >> #5
    >>> >> >>> and
    >>> >> >>> >> >> #21); it just doesn’t have high priority for me.  Pull
    >>> requests
    >>> >> >>> welcome.
    >>> >> >>> >> >>
    >>> >> >>> >> >> > 2. i would really like a way to have stored smart groups
    >>> (like
    >>> >> the
    >>> >> >>> >> jabref
    >>> >> >>> >> >> > dynamic groups if your aware of that). that is for example
    >>> >> create
    >>> >> >>> a
    >>> >> >>> >> group
    >>> >> >>> >> >> > that auto selects all publications i have (by my first/last
    >>> >> name)
    >>> >> >>> and
    >>> >> >>> >> >> shows
    >>> >> >>> >> >> > the count (in numbers) of these publications.
    >>> >> >>> >> >>
    >>> >> >>> >> >> I’m not familiar with smart groups but it seems that all
    >>> >> >>> helm-bibtex is
    >>> >> >>> >> >> doing is giving you very flexible smart groups defined by
    >>> your
    >>> >> >>> search
    >>> >> >>> >> >> expressions.  For example, if you want a list of your
    >>> >> publications,
    >>> >> >>> you
    >>> >> >>> >> >> can simple enter your name.  And if you want a list of your
    >>> >> >>> articles,
    >>> >> >>> >> >> you can enter your name + “article”.  If you want all your
    >>> >> articles
    >>> >> >>> from
    >>> >> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The
    >>> number
    >>> >> of
    >>> >> >>> >> >> matches will be displayed in the mode line.  If you don’t
    >>> want to
    >>> >> >>> type
    >>> >> >>> >> >> these search expressions, you could create a command that
    >>> invokes
    >>> >> >>> >> >> helm-bibtex with a default search expression and that command
    >>> >> could
    >>> >> >>> be
    >>> >> >>> >> >> bound to a keyboard shortcut.
    >>> >> >>> >> >>
    >>> >> >>> >> >> > Another example is a group to keep track of all the papers
    >>> im
    >>> >> >>> working
    >>> >> >>> >> on
    >>> >> >>> >> >> or
    >>> >> >>> >> >> > invloved with by matching keyword author and prep/*other
    >>> key
    >>> >> word
    >>> >> >>> >> >>
    >>> >> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for
    >>> keywords
    >>> >> >>> >> >> describing the content of the paper (as usual) and “tags” for
    >>> >> meta
    >>> >> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
    >>> >> “poster”,
    >>> >> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
    >>> >> search
    >>> >> >>> for
    >>> >> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it
    >>> has
    >>> >> to
    >>> >> >>> be
    >>> >> >>> >> >> added to `helm-bibtex-additional-search-fields`.
    >>> >> >>> >> >>
    >>> >> >>> >> >> Another solution would be to use the pubstate field and to
    >>> search
    >>> >> >>> for
    >>> >> >>> >> >> your name and “forthcoming” (add pubstate to
    >>> >> >>> >> >> helm-bibtex-additional-search-fields for this to work).
    >>> >> >>> >> >>
    >>> >> >>> >> >> > 3.is it possible to ass an option to auto generate a
    >>> bibkey
    >>> >> for a
    >>> >> >>> >> >> selected
    >>> >> >>> >> >> > citation based on user criteria such as
    >>> >> author(date)short-title?
    >>> >> >>> >> >>
    >>> >> >>> >> >> Maintaining the content of the BibTeX file not really in the
    >>> >> scope
    >>> >> >>> of
    >>> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
    >>> >> Perhaps
    >>> >> >>> >> >> org-ref or ebib can help here?  Once you have a function that
    >>> >> >>> generates
    >>> >> >>> >> >> a new key and inserts it in the BibTeX file, you can easily
    >>> add
    >>> >> it
    >>> >> >>> to
    >>> >> >>> >> >> the list of actions in helm-bibtex.
    >>> >> >>> >> >>
    >>> >> >>> >> >> Hope that helps.
    >>> >> >>> >> >>
    >>> >> >>> >> >>   Titus
    >>> >> >>> >> >>
    >>> >> >>> >> >> > thx so much in advance, you and john have given me
    >>> confidence
    >>> >> to
    >>> >> >>> >> finally
    >>> >> >>> >> >> > dive into the whole latex/bibteX world
    >>> >> >>> >> >> >
    >>> >> >>> >> >> > best
    >>> >> >>> >> >> >
    >>> >> >>> >> >> > Z
    >>> >> >>> >> >>
    >>> >> >>> >> >>
    >>> >> >>> >>
    >>> >> >>> >>
    >>> >> >>>
    >>> >> >>>
    >>> >> >>
    >>> >>
    >>> >>
    >>>
    >>> --
    >>> Professor John Kitchin
    >>> Doherty Hall A207F
    >>> Department of Chemical Engineering
    >>> Carnegie Mellon University
    >>> Pittsburgh, PA 15213
    >>> 412-268-7803
    >>> @johnkitchin
    >>> http://kitchingroup.cheme.cmu.edu
    >>>
    >>
    >>
    
    --
    Professor John Kitchin
    Doherty Hall A207F
    Department of Chemical Engineering
    Carnegie Mellon University
    Pittsburgh, PA 15213
    412-268-7803
    @johnkitchin
    http://kitchingroup.cheme.cmu.edu
    
    ^ permalink raw reply	[flat|nested] 26+ messages in thread

  • • * Re: helm-bibtex questions
        2015-06-26 14:28   ` John Kitchin
      @ 2015-06-27  6:11     ` Xebar Saram
        2015-06-27 11:44       ` John Kitchin
        2015-06-30  9:15       ` Eric S Fraga
        0 siblings, 2 replies; 26+ messages in thread
      From: Xebar Saram @ 2015-06-27  6:11 UTC (permalink / raw)
        To: John Kitchin; +Cc: org mode
      
      [-- Attachment #1: Type: text/plain, Size: 18304 bytes --]
      
      hmm strange still dosent work for me. here is the top section of my bib file
      
      -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
      
      @article{ackerman-1998-discr-clear,
        author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
                        {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
                        Gumley, {L.E.}},
        title = {Discriminating Clear Sky From Clouds With Modis},
        journal = {Journal of Geophysical Research},
        volume = 103,
        number = {D24},
        pages = {32,141--32,157},
        year = 1998,
        shorttitle = {Discriminating clear sky from clouds with {MODIS}},
      }
      
      
      when i use the org ref clean i still get
      
      bibtex-format-entry: Mandatory field `journal' is missing
      
      
      also in the emacs menu the entry type is still bibtex. i tried restarting
      emacs and still no go.
      
      any clue? also do you prefer I continue this discussion on the github
      org-ref site?
      
      best!
      
      Z
      
      
      On Fri, Jun 26, 2015 at 5:28 PM, John Kitchin <jkitchin@andrew.cmu.edu>
      wrote:
      
      >
      > http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bibliography-files-for-biblatex
      >
      > I think you need this in your bibtex file:
      >
      > -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
      >
      >
      > Xebar Saram writes:
      >
      > > thanks so much again John
      > >
      > > i did add this line
      > > (bibtex-set-dialect 'biblatex)
      > > in my init but that dosent seem to do much as i still get the "journal
      > > mandatory field missing" error. anything else i can try?
      > >
      > > best
      > >
      > > Z
      > >
      > >
      > > On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin <johnrkitchin@gmail.com>
      > > wrote:
      > >
      > >> I believe that is an emacs bibtex issue. You need some kind of line in
      > >> your bibtex file to specify it is the biblatex dialect.
      > >>
      > >>
      > >> On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> wrote:
      > >>
      > >>
      > >> Great, works well. one question though (and this may very well be due to
      > >> my inexperience). the jabref export i had used 'journaltitle' instead of
      > >> journal to be (to my understanding) compatible with the newer .bib files
      > >> used by biblatex (and biber). when i ran org-ref clean it gave an error
      > on"
      > >> journal mandatory field missing". i had to replace all 'journaltitle'
      > to
      > >> 'journal' to get it to work.
      > >> is this by design? does org-ref not support the new biblatex/biber .bib
      > >> file format?
      > >>
      > >> kind regards
      > >>
      > >> Itai
      > >>
      > >> On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin <jkitchin@andrew.cmu.edu
      > >
      > >> wrote:
      > >>
      > >>> yes, there is a way ;)
      > >>>
      > >>> First. Make sure you have a backup of the references. I like to keep
      > >>> mine in a local git repo so you can undo any mistakes that get made.
      > >>>
      > >>> I suggest you run these first:
      > >>> %% (bibtex-validate-globally)   ; checks for duplicate keys
      > >>> %% (bibtex-validate)
      > >>>
      > >>> I also recommend you run bibtex-sort (it is easier to spot duplicates
      > in
      > >>> a sorted list).
      > >>>
      > >>> and (org-ref-build-full-bibliography) <- makes a pdf of all references.
      > >>>
      > >>> to make sure everything is compliant and functional.
      > >>>
      > >>> Then, put this next line at the top of your bibtex file. The t
      > argument to
      > >>> org-ref-clean-bibtex-entry will preserve your existing keys.
      > >>>
      > >>> % (bibtex-map-entries (lambda (key start end)
      > (org-ref-clean-bibtex-entry
      > >>> t)))
      > >>>
      > >>> Put your cursor at the end of that line, and type C-x C-e to run the
      > >>> function, and
      > >>> wait patiently. It took a few minutes on my 1300 entries, and I had to
      > >>> restart it once on some entry.
      > >>>
      > >>> when it is done, run (org-ref-build-full-bibliography) again to make
      > >>> sure it works and review the ~200 page pdf ;). fix errors and repeat
      > >>> until it builds ;)
      > >>>
      > >>> Note if you want to change title cases in all entries you can use
      > >>>
      > >>> % (bibtex-map-entries 'jmax-title-case-article)
      > >>> % (bibtex-map-entries 'jmax-sentence-case-article)
      > >>>
      > >>> I hope that helps!
      > >>>
      > >>> Xebar Saram writes:
      > >>>
      > >>> > John
      > >>> >
      > >>> > First of all thanks so much for the excellent
      > org-ref-clean-bibtex-entry
      > >>> > function i love it!
      > >>> > also your blog post on cleaning the bib file is a life saver
      > >>> >
      > >>> > i have 800 references, is there a way to auto
      > >>> > make org-ref-clean-bibtex-entry go thorough my whole bib file instead
      > >>> of me
      > >>> > going and cleaning it 1 by 1?
      > >>> >
      > >>> > kind regards
      > >>> >
      > >>> > Z.
      > >>> >
      > >>> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <
      > >>> malsburg@posteo.de>
      > >>> > wrote:
      > >>> >
      > >>> >>
      > >>> >>
      > >>> >> Here is my CV in org-mode:
      > >>> >>
      > >>> >>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
      > >>> >>
      > >>> >> It’s a pretty straightforward org document except for one thing: the
      > >>> key
      > >>> >> to making this work was biblatex which can be used to create several
      > >>> >> lists of references filtered according to keywords, author, etc.
      > This
      > >>> >> allowed me to have separate sections for journal articles,
      > conference
      > >>> >> presentations, etc.  I store the relevant keywords in the tags
      > field of
      > >>> >> the BibTeX entries and since biblatex doesn’t know this field, I
      > copy
      > >>> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in
      > the
      > >>> >> LaTeX headers).
      > >>> >>
      > >>> >>   Titus
      > >>> >>
      > >>> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
      > >>> >> > Hi John
      > >>> >> >
      > >>> >> > a bit off topic, but do you also write your academic CV in
      > orgmode or
      > >>> >> > lateX? in anycase would you mind sharing your org/latex CV
      > template?
      > >>> it
      > >>> >> > would be helpful as a starting point for me if thats possible.
      > >>> >> >
      > >>> >> > kind regards and thanks so much in advance
      > >>> >> >
      > >>> >> > Z
      > >>> >> >
      > >>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <
      > >>> jkitchin@andrew.cmu.edu>
      > >>> >> > wrote:
      > >>> >> >
      > >>> >> >> sweet! I did not know you could do that! I will be refactoring
      > >>> org-ref
      > >>> >> >> soon to do that instead of redefining the commands!
      > >>> >> >>
      > >>> >> >> John
      > >>> >> >>
      > >>> >> >> -----------------------------------
      > >>> >> >> Professor John Kitchin
      > >>> >> >> Doherty Hall A207F
      > >>> >> >> Department of Chemical Engineering
      > >>> >> >> Carnegie Mellon University
      > >>> >> >> Pittsburgh, PA 15213
      > >>> >> >> 412-268-7803
      > >>> >> >> @johnkitchin
      > >>> >> >> http://kitchingroup.cheme.cmu.edu
      > >>> >> >>
      > >>> >> >>
      > >>> >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
      > >>> >> >> malsburg@posteo.de> wrote:
      > >>> >> >>
      > >>> >> >>>
      > >>> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
      > >>> >> >>> > Hi again Titus
      > >>> >> >>> >
      > >>> >> >>> > 2 quick questions that arose from using helm-bitex today
      > >>> extensively:
      > >>> >> >>> >
      > >>> >> >>> > how does one exclude in the search items? for example i want
      > to
      > >>> >> search
      > >>> >> >>> for
      > >>> >> >>> > xebar without keyword "progress" (I want to exclude in
      > progress
      > >>> >> articles
      > >>> >> >>> > not published yet)
      > >>> >> >>> >
      > >>> >> >>> > is it possible to define default enter command in helm-bibtex
      > ?
      > >>> >> >>>
      > >>> >> >>> Yes.  Helm uses the first action as the default action.  To
      > move an
      > >>> >> >>> action to the top of the list you can use the following code:
      > >>> >> >>>
      > >>> >> >>>   (helm-delete-action-from-source "Insert BibTeX key"
      > >>> >> helm-source-bibtex)
      > >>> >> >>>   (helm-add-action-to-source "Insert BibTeX key"
      > >>> >> 'helm-bibtex-insert-key
      > >>> >> >>> helm-source-bibtex 0)
      > >>> >> >>>
      > >>> >> >>> The second argument in the second line is the function that
      > >>> executes
      > >>> >> the
      > >>> >> >>> action.  Here is a list of all actions and their functions:
      > >>> >> >>>
      > >>> >> >>>   Open PDF file (if present): helm-bibtex-open-pdf
      > >>> >> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
      > >>> >> >>>   Insert citation: helm-bibtex-insert-citation
      > >>> >> >>>   Insert reference: helm-bibtex-insert-reference
      > >>> >> >>>   Insert BibTeX key: helm-bibtex-insert-key
      > >>> >> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
      > >>> >> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
      > >>> >> >>>   Edit notes: helm-bibtex-edit-notes
      > >>> >> >>>   Show entry: helm-bibtex-show-entry
      > >>> >> >>>
      > >>> >> >>> Best,
      > >>> >> >>>
      > >>> >> >>>   Titus
      > >>> >> >>>
      > >>> >> >>> >
      > >>> >> >>> > best
      > >>> >> >>> >
      > >>> >> >>> > Z
      > >>> >> >>> >
      > >>> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
      > >>> >> >>> malsburg@posteo.de>
      > >>> >> >>> > wrote:
      > >>> >> >>> >
      > >>> >> >>> >>
      > >>> >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
      > >>> >> >>> >> > Hi Titus and thx so much for the answers!
      > >>> >> >>> >> >
      > >>> >> >>> >> > i will in the future use the github page to make requests.
      > >>> >> >>> >> >
      > >>> >> >>> >> > "The number of matches will be displayed in the mode line.
      > "
      > >>> >> >>> >> >
      > >>> >> >>> >> > i see that now thx! :) the problem was(is) that its colored
      > >>> black
      > >>> >> on
      > >>> >> >>> my
      > >>> >> >>> >> > black modline BG which makes it invisible ;-) i assume
      > thats
      > >>> an
      > >>> >> helm
      > >>> >> >>> >> config
      > >>> >> >>> >> > i need to change
      > >>> >> >>> >> >
      > >>> >> >>> >> >
      > >>> >> >>> >> > "If you don’t want to type these search expressions, you
      > could
      > >>> >> >>> create a
      > >>> >> >>> >> > command that invokes helm-bibtex with a default search
      > >>> expression
      > >>> >> and
      > >>> >> >>> >> that
      > >>> >> >>> >> > command could be bound to a keyboard shortcut."
      > >>> >> >>> >> >
      > >>> >> >>> >> > that would be prefect for me and a solution to my issue.
      > >>> would you
      > >>> >> >>> mind
      > >>> >> >>> >> > giving an example of such a code chunk. unfortunately i
      > dont
      > >>> know
      > >>> >> >>> elisp
      > >>> >> >>> >> though
      > >>> >> >>> >> > as john recommended i will do my best this summer when the
      > >>> >> semester
      > >>> >> >>> ends
      > >>> >> >>> >> to
      > >>> >> >>> >> > try and pick it up :)
      > >>> >> >>> >>
      > >>> >> >>> >> Sure, here you go:
      > >>> >> >>> >>
      > >>> >> >>> >> #+BEGIN_SRC elisp
      > >>> >> >>> >> ;; Define helm-search with predefined search expression:
      > >>> >> >>> >> (defun helm-bibtex-my-publications ()
      > >>> >> >>> >>   "Search BibTeX entries authored by Xebar Saram."
      > >>> >> >>> >>   (interactive)
      > >>> >> >>> >>   (helm :sources '(helm-source-bibtex)
      > >>> >> >>> >>         :full-frame t
      > >>> >> >>> >>         :input "xebar saram"
      > >>> >> >>> >>         :candidate-number-limit 500))
      > >>> >> >>> >>
      > >>> >> >>> >> ;; Bind this search function to Ctrl-x p:
      > >>> >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
      > >>> >> >>> >> #+END_SRC
      > >>> >> >>> >>
      > >>> >> >>> >> > i will definitely use your tag system as you recommended,
      > >>> sounds
      > >>> >> >>> perfect
      > >>> >> >>> >> > for me
      > >>> >> >>> >>
      > >>> >> >>> >> The tag system also comes in handy when generating
      > publication
      > >>> lists
      > >>> >> >>> for
      > >>> >> >>> >> CVs and web pages because BibTeX does not distinguish between
      > >>> >> >>> conference
      > >>> >> >>> >> papers, posters, and talks.  If you have tags for that, it’s
      > >>> >> relatively
      > >>> >> >>> >> easy to create separate sections for these types of
      > publications
      > >>> >> using
      > >>> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
      > >>> >> >>> >>
      > >>> >> >>> >> > thanks again for your kind help and the amazing app ;-)
      > >>> >> >>> >>
      > >>> >> >>> >> You are welcome.
      > >>> >> >>> >>
      > >>> >> >>> >>   Titus
      > >>> >> >>> >>
      > >>> >> >>> >> >
      > >>> >> >>> >> > best
      > >>> >> >>> >> >
      > >>> >> >>> >> > Z
      > >>> >> >>> >> >
      > >>> >> >>> >> >
      > >>> >> >>> >> >
      > >>> >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
      > >>> >> >>> >> malsburg@posteo.de
      > >>> >> >>> >> >> wrote:
      > >>> >> >>> >> >
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
      > >>> >> >>> >> >> > Hi Titus
      > >>> >> >>> >> >> >
      > >>> >> >>> >> >> > I have been exploring helm-bibtex a bit today and have
      > some
      > >>> >> >>> questions.
      > >>> >> >>> >> >> btw
      > >>> >> >>> >> >> > is this the preferred way to make requests/ask questions
      > >>> or is
      > >>> >> >>> >> >> > github preferred?
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> Helm-bibtex is not part of org (although it tries to work
      > >>> well
      > >>> >> with
      > >>> >> >>> >> >> org).  So I’m not sure whether this list is the best place
      > >>> for
      > >>> >> >>> >> >> discussing it.  For now the issue tracker on Github might
      > be
      > >>> a
      > >>> >> >>> better
      > >>> >> >>> >> >> option:
      > >>> >> >>> >> >>
      > >>> >> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> > in any case i was wondering a few things:
      > >>> >> >>> >> >> >
      > >>> >> >>> >> >> > 1. is it possible to have custom sorting? i want all
      > views
      > >>> to
      > >>> >> >>> sort by
      > >>> >> >>> >> >> > Author, year, month
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> I prefer to see the entries in the (inverse) order in
      > which
      > >>> they
      > >>> >> >>> appear
      > >>> >> >>> >> >> in the BibTeX file.  This way, recent additions show up at
      > >>> the
      > >>> >> >>> >> >> top.  However, I agree that sorting would be useful (see
      > >>> issues
      > >>> >> #5
      > >>> >> >>> and
      > >>> >> >>> >> >> #21); it just doesn’t have high priority for me.  Pull
      > >>> requests
      > >>> >> >>> welcome.
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> > 2. i would really like a way to have stored smart groups
      > >>> (like
      > >>> >> the
      > >>> >> >>> >> jabref
      > >>> >> >>> >> >> > dynamic groups if your aware of that). that is for
      > example
      > >>> >> create
      > >>> >> >>> a
      > >>> >> >>> >> group
      > >>> >> >>> >> >> > that auto selects all publications i have (by my
      > first/last
      > >>> >> name)
      > >>> >> >>> and
      > >>> >> >>> >> >> shows
      > >>> >> >>> >> >> > the count (in numbers) of these publications.
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> I’m not familiar with smart groups but it seems that all
      > >>> >> >>> helm-bibtex is
      > >>> >> >>> >> >> doing is giving you very flexible smart groups defined by
      > >>> your
      > >>> >> >>> search
      > >>> >> >>> >> >> expressions.  For example, if you want a list of your
      > >>> >> publications,
      > >>> >> >>> you
      > >>> >> >>> >> >> can simple enter your name.  And if you want a list of
      > your
      > >>> >> >>> articles,
      > >>> >> >>> >> >> you can enter your name + “article”.  If you want all your
      > >>> >> articles
      > >>> >> >>> from
      > >>> >> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The
      > >>> number
      > >>> >> of
      > >>> >> >>> >> >> matches will be displayed in the mode line.  If you don’t
      > >>> want to
      > >>> >> >>> type
      > >>> >> >>> >> >> these search expressions, you could create a command that
      > >>> invokes
      > >>> >> >>> >> >> helm-bibtex with a default search expression and that
      > command
      > >>> >> could
      > >>> >> >>> be
      > >>> >> >>> >> >> bound to a keyboard shortcut.
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> > Another example is a group to keep track of all the
      > papers
      > >>> im
      > >>> >> >>> working
      > >>> >> >>> >> on
      > >>> >> >>> >> >> or
      > >>> >> >>> >> >> > invloved with by matching keyword author and prep/*other
      > >>> key
      > >>> >> word
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for
      > >>> keywords
      > >>> >> >>> >> >> describing the content of the paper (as usual) and “tags”
      > for
      > >>> >> meta
      > >>> >> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
      > >>> >> “poster”,
      > >>> >> >>> >> >> “talk”, … So if I want a list of all articles in
      > progress, I
      > >>> >> search
      > >>> >> >>> for
      > >>> >> >>> >> >> “own manuscript”.  Since the tags field is non-standard,
      > it
      > >>> has
      > >>> >> to
      > >>> >> >>> be
      > >>> >> >>> >> >> added to `helm-bibtex-additional-search-fields`.
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> Another solution would be to use the pubstate field and to
      > >>> search
      > >>> >> >>> for
      > >>> >> >>> >> >> your name and “forthcoming” (add pubstate to
      > >>> >> >>> >> >> helm-bibtex-additional-search-fields for this to work).
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> > 3.is it possible to ass an option to auto generate a
      > >>> bibkey
      > >>> >> for a
      > >>> >> >>> >> >> selected
      > >>> >> >>> >> >> > citation based on user criteria such as
      > >>> >> author(date)short-title?
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> Maintaining the content of the BibTeX file not really in
      > the
      > >>> >> scope
      > >>> >> >>> of
      > >>> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
      > >>> >> Perhaps
      > >>> >> >>> >> >> org-ref or ebib can help here?  Once you have a function
      > that
      > >>> >> >>> generates
      > >>> >> >>> >> >> a new key and inserts it in the BibTeX file, you can
      > easily
      > >>> add
      > >>> >> it
      > >>> >> >>> to
      > >>> >> >>> >> >> the list of actions in helm-bibtex.
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> Hope that helps.
      > >>> >> >>> >> >>
      > >>> >> >>> >> >>   Titus
      > >>> >> >>> >> >>
      > >>> >> >>> >> >> > thx so much in advance, you and john have given me
      > >>> confidence
      > >>> >> to
      > >>> >> >>> >> finally
      > >>> >> >>> >> >> > dive into the whole latex/bibteX world
      > >>> >> >>> >> >> >
      > >>> >> >>> >> >> > best
      > >>> >> >>> >> >> >
      > >>> >> >>> >> >> > Z
      > >>> >> >>> >> >>
      > >>> >> >>> >> >>
      > >>> >> >>> >>
      > >>> >> >>> >>
      > >>> >> >>>
      > >>> >> >>>
      > >>> >> >>
      > >>> >>
      > >>> >>
      > >>>
      > >>> --
      > >>> Professor John Kitchin
      > >>> Doherty Hall A207F
      > >>> Department of Chemical Engineering
      > >>> Carnegie Mellon University
      > >>> Pittsburgh, PA 15213
      > >>> 412-268-7803
      > >>> @johnkitchin
      > >>> http://kitchingroup.cheme.cmu.edu
      > >>>
      > >>
      > >>
      >
      > --
      > Professor John Kitchin
      > Doherty Hall A207F
      > Department of Chemical Engineering
      > Carnegie Mellon University
      > Pittsburgh, PA 15213
      > 412-268-7803
      > @johnkitchin
      > http://kitchingroup.cheme.cmu.edu
      >
      
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      ^ permalink raw reply	[flat|nested] 26+ messages in thread

    • • * Re: helm-bibtex questions
          2015-06-27  6:11     ` Xebar Saram
        @ 2015-06-27 11:44       ` John Kitchin
          2015-06-30  9:15       ` Eric S Fraga
          1 sibling, 0 replies; 26+ messages in thread
        From: John Kitchin @ 2015-06-27 11:44 UTC (permalink / raw)
          To: Xebar Saram; +Cc: org mode
        
        You need:
        
        % -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
        
        You probably have to close and reopen the file, and you will probably be
        prompted for running local variables (or use C-x C-e after the command
        above it
        
        With this, it works fine for me.
        
        
        This isn't really an org-ref problem,  it is happening in
        bibtex-clean-entry. it might be better to move it to github. I just
        noticed a similar issue already there:
        https://github.com/jkitchin/org-ref/issues/40
        
        ;)
        
        Xebar Saram writes:
        
        > hmm strange still dosent work for me. here is the top section of my bib file
        >
        > -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
        >
        > @article{ackerman-1998-discr-clear,
        >   author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
        >                   {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
        >                   Gumley, {L.E.}},
        >   title = {Discriminating Clear Sky From Clouds With Modis},
        >   journal = {Journal of Geophysical Research},
        >   volume = 103,
        >   number = {D24},
        >   pages = {32,141--32,157},
        >   year = 1998,
        >   shorttitle = {Discriminating clear sky from clouds with {MODIS}},
        > }
        >
        >
        > when i use the org ref clean i still get
        >
        > bibtex-format-entry: Mandatory field `journal' is missing
        >
        >
        > also in the emacs menu the entry type is still bibtex. i tried restarting
        > emacs and still no go.
        >
        > any clue? also do you prefer I continue this discussion on the github
        > org-ref site?
        >
        > best!
        >
        > Z
        >
        >
        > On Fri, Jun 26, 2015 at 5:28 PM, John Kitchin <jkitchin@andrew.cmu.edu>
        > wrote:
        >
        >>
        >> http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bibliography-files-for-biblatex
        >>
        >> I think you need this in your bibtex file:
        >>
        >> -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
        >>
        >>
        >> Xebar Saram writes:
        >>
        >> > thanks so much again John
        >> >
        >> > i did add this line
        >> > (bibtex-set-dialect 'biblatex)
        >> > in my init but that dosent seem to do much as i still get the "journal
        >> > mandatory field missing" error. anything else i can try?
        >> >
        >> > best
        >> >
        >> > Z
        >> >
        >> >
        >> > On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin <johnrkitchin@gmail.com>
        >> > wrote:
        >> >
        >> >> I believe that is an emacs bibtex issue. You need some kind of line in
        >> >> your bibtex file to specify it is the biblatex dialect.
        >> >>
        >> >>
        >> >> On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> wrote:
        >> >>
        >> >>
        >> >> Great, works well. one question though (and this may very well be due to
        >> >> my inexperience). the jabref export i had used 'journaltitle' instead of
        >> >> journal to be (to my understanding) compatible with the newer .bib files
        >> >> used by biblatex (and biber). when i ran org-ref clean it gave an error
        >> on"
        >> >> journal mandatory field missing". i had to replace all 'journaltitle'
        >> to
        >> >> 'journal' to get it to work.
        >> >> is this by design? does org-ref not support the new biblatex/biber .bib
        >> >> file format?
        >> >>
        >> >> kind regards
        >> >>
        >> >> Itai
        >> >>
        >> >> On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin <jkitchin@andrew.cmu.edu
        >> >
        >> >> wrote:
        >> >>
        >> >>> yes, there is a way ;)
        >> >>>
        >> >>> First. Make sure you have a backup of the references. I like to keep
        >> >>> mine in a local git repo so you can undo any mistakes that get made.
        >> >>>
        >> >>> I suggest you run these first:
        >> >>> %% (bibtex-validate-globally)   ; checks for duplicate keys
        >> >>> %% (bibtex-validate)
        >> >>>
        >> >>> I also recommend you run bibtex-sort (it is easier to spot duplicates
        >> in
        >> >>> a sorted list).
        >> >>>
        >> >>> and (org-ref-build-full-bibliography) <- makes a pdf of all references.
        >> >>>
        >> >>> to make sure everything is compliant and functional.
        >> >>>
        >> >>> Then, put this next line at the top of your bibtex file. The t
        >> argument to
        >> >>> org-ref-clean-bibtex-entry will preserve your existing keys.
        >> >>>
        >> >>> % (bibtex-map-entries (lambda (key start end)
        >> (org-ref-clean-bibtex-entry
        >> >>> t)))
        >> >>>
        >> >>> Put your cursor at the end of that line, and type C-x C-e to run the
        >> >>> function, and
        >> >>> wait patiently. It took a few minutes on my 1300 entries, and I had to
        >> >>> restart it once on some entry.
        >> >>>
        >> >>> when it is done, run (org-ref-build-full-bibliography) again to make
        >> >>> sure it works and review the ~200 page pdf ;). fix errors and repeat
        >> >>> until it builds ;)
        >> >>>
        >> >>> Note if you want to change title cases in all entries you can use
        >> >>>
        >> >>> % (bibtex-map-entries 'jmax-title-case-article)
        >> >>> % (bibtex-map-entries 'jmax-sentence-case-article)
        >> >>>
        >> >>> I hope that helps!
        >> >>>
        >> >>> Xebar Saram writes:
        >> >>>
        >> >>> > John
        >> >>> >
        >> >>> > First of all thanks so much for the excellent
        >> org-ref-clean-bibtex-entry
        >> >>> > function i love it!
        >> >>> > also your blog post on cleaning the bib file is a life saver
        >> >>> >
        >> >>> > i have 800 references, is there a way to auto
        >> >>> > make org-ref-clean-bibtex-entry go thorough my whole bib file instead
        >> >>> of me
        >> >>> > going and cleaning it 1 by 1?
        >> >>> >
        >> >>> > kind regards
        >> >>> >
        >> >>> > Z.
        >> >>> >
        >> >>> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <
        >> >>> malsburg@posteo.de>
        >> >>> > wrote:
        >> >>> >
        >> >>> >>
        >> >>> >>
        >> >>> >> Here is my CV in org-mode:
        >> >>> >>
        >> >>> >>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
        >> >>> >>
        >> >>> >> It’s a pretty straightforward org document except for one thing: the
        >> >>> key
        >> >>> >> to making this work was biblatex which can be used to create several
        >> >>> >> lists of references filtered according to keywords, author, etc.
        >> This
        >> >>> >> allowed me to have separate sections for journal articles,
        >> conference
        >> >>> >> presentations, etc.  I store the relevant keywords in the tags
        >> field of
        >> >>> >> the BibTeX entries and since biblatex doesn’t know this field, I
        >> copy
        >> >>> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in
        >> the
        >> >>> >> LaTeX headers).
        >> >>> >>
        >> >>> >>   Titus
        >> >>> >>
        >> >>> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
        >> >>> >> > Hi John
        >> >>> >> >
        >> >>> >> > a bit off topic, but do you also write your academic CV in
        >> orgmode or
        >> >>> >> > lateX? in anycase would you mind sharing your org/latex CV
        >> template?
        >> >>> it
        >> >>> >> > would be helpful as a starting point for me if thats possible.
        >> >>> >> >
        >> >>> >> > kind regards and thanks so much in advance
        >> >>> >> >
        >> >>> >> > Z
        >> >>> >> >
        >> >>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <
        >> >>> jkitchin@andrew.cmu.edu>
        >> >>> >> > wrote:
        >> >>> >> >
        >> >>> >> >> sweet! I did not know you could do that! I will be refactoring
        >> >>> org-ref
        >> >>> >> >> soon to do that instead of redefining the commands!
        >> >>> >> >>
        >> >>> >> >> John
        >> >>> >> >>
        >> >>> >> >> -----------------------------------
        >> >>> >> >> Professor John Kitchin
        >> >>> >> >> Doherty Hall A207F
        >> >>> >> >> Department of Chemical Engineering
        >> >>> >> >> Carnegie Mellon University
        >> >>> >> >> Pittsburgh, PA 15213
        >> >>> >> >> 412-268-7803
        >> >>> >> >> @johnkitchin
        >> >>> >> >> http://kitchingroup.cheme.cmu.edu
        >> >>> >> >>
        >> >>> >> >>
        >> >>> >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
        >> >>> >> >> malsburg@posteo.de> wrote:
        >> >>> >> >>
        >> >>> >> >>>
        >> >>> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
        >> >>> >> >>> > Hi again Titus
        >> >>> >> >>> >
        >> >>> >> >>> > 2 quick questions that arose from using helm-bitex today
        >> >>> extensively:
        >> >>> >> >>> >
        >> >>> >> >>> > how does one exclude in the search items? for example i want
        >> to
        >> >>> >> search
        >> >>> >> >>> for
        >> >>> >> >>> > xebar without keyword "progress" (I want to exclude in
        >> progress
        >> >>> >> articles
        >> >>> >> >>> > not published yet)
        >> >>> >> >>> >
        >> >>> >> >>> > is it possible to define default enter command in helm-bibtex
        >> ?
        >> >>> >> >>>
        >> >>> >> >>> Yes.  Helm uses the first action as the default action.  To
        >> move an
        >> >>> >> >>> action to the top of the list you can use the following code:
        >> >>> >> >>>
        >> >>> >> >>>   (helm-delete-action-from-source "Insert BibTeX key"
        >> >>> >> helm-source-bibtex)
        >> >>> >> >>>   (helm-add-action-to-source "Insert BibTeX key"
        >> >>> >> 'helm-bibtex-insert-key
        >> >>> >> >>> helm-source-bibtex 0)
        >> >>> >> >>>
        >> >>> >> >>> The second argument in the second line is the function that
        >> >>> executes
        >> >>> >> the
        >> >>> >> >>> action.  Here is a list of all actions and their functions:
        >> >>> >> >>>
        >> >>> >> >>>   Open PDF file (if present): helm-bibtex-open-pdf
        >> >>> >> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
        >> >>> >> >>>   Insert citation: helm-bibtex-insert-citation
        >> >>> >> >>>   Insert reference: helm-bibtex-insert-reference
        >> >>> >> >>>   Insert BibTeX key: helm-bibtex-insert-key
        >> >>> >> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
        >> >>> >> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
        >> >>> >> >>>   Edit notes: helm-bibtex-edit-notes
        >> >>> >> >>>   Show entry: helm-bibtex-show-entry
        >> >>> >> >>>
        >> >>> >> >>> Best,
        >> >>> >> >>>
        >> >>> >> >>>   Titus
        >> >>> >> >>>
        >> >>> >> >>> >
        >> >>> >> >>> > best
        >> >>> >> >>> >
        >> >>> >> >>> > Z
        >> >>> >> >>> >
        >> >>> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
        >> >>> >> >>> malsburg@posteo.de>
        >> >>> >> >>> > wrote:
        >> >>> >> >>> >
        >> >>> >> >>> >>
        >> >>> >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
        >> >>> >> >>> >> > Hi Titus and thx so much for the answers!
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > i will in the future use the github page to make requests.
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > "The number of matches will be displayed in the mode line.
        >> "
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > i see that now thx! :) the problem was(is) that its colored
        >> >>> black
        >> >>> >> on
        >> >>> >> >>> my
        >> >>> >> >>> >> > black modline BG which makes it invisible ;-) i assume
        >> thats
        >> >>> an
        >> >>> >> helm
        >> >>> >> >>> >> config
        >> >>> >> >>> >> > i need to change
        >> >>> >> >>> >> >
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > "If you don’t want to type these search expressions, you
        >> could
        >> >>> >> >>> create a
        >> >>> >> >>> >> > command that invokes helm-bibtex with a default search
        >> >>> expression
        >> >>> >> and
        >> >>> >> >>> >> that
        >> >>> >> >>> >> > command could be bound to a keyboard shortcut."
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > that would be prefect for me and a solution to my issue.
        >> >>> would you
        >> >>> >> >>> mind
        >> >>> >> >>> >> > giving an example of such a code chunk. unfortunately i
        >> dont
        >> >>> know
        >> >>> >> >>> elisp
        >> >>> >> >>> >> though
        >> >>> >> >>> >> > as john recommended i will do my best this summer when the
        >> >>> >> semester
        >> >>> >> >>> ends
        >> >>> >> >>> >> to
        >> >>> >> >>> >> > try and pick it up :)
        >> >>> >> >>> >>
        >> >>> >> >>> >> Sure, here you go:
        >> >>> >> >>> >>
        >> >>> >> >>> >> #+BEGIN_SRC elisp
        >> >>> >> >>> >> ;; Define helm-search with predefined search expression:
        >> >>> >> >>> >> (defun helm-bibtex-my-publications ()
        >> >>> >> >>> >>   "Search BibTeX entries authored by Xebar Saram."
        >> >>> >> >>> >>   (interactive)
        >> >>> >> >>> >>   (helm :sources '(helm-source-bibtex)
        >> >>> >> >>> >>         :full-frame t
        >> >>> >> >>> >>         :input "xebar saram"
        >> >>> >> >>> >>         :candidate-number-limit 500))
        >> >>> >> >>> >>
        >> >>> >> >>> >> ;; Bind this search function to Ctrl-x p:
        >> >>> >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
        >> >>> >> >>> >> #+END_SRC
        >> >>> >> >>> >>
        >> >>> >> >>> >> > i will definitely use your tag system as you recommended,
        >> >>> sounds
        >> >>> >> >>> perfect
        >> >>> >> >>> >> > for me
        >> >>> >> >>> >>
        >> >>> >> >>> >> The tag system also comes in handy when generating
        >> publication
        >> >>> lists
        >> >>> >> >>> for
        >> >>> >> >>> >> CVs and web pages because BibTeX does not distinguish between
        >> >>> >> >>> conference
        >> >>> >> >>> >> papers, posters, and talks.  If you have tags for that, it’s
        >> >>> >> relatively
        >> >>> >> >>> >> easy to create separate sections for these types of
        >> publications
        >> >>> >> using
        >> >>> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
        >> >>> >> >>> >>
        >> >>> >> >>> >> > thanks again for your kind help and the amazing app ;-)
        >> >>> >> >>> >>
        >> >>> >> >>> >> You are welcome.
        >> >>> >> >>> >>
        >> >>> >> >>> >>   Titus
        >> >>> >> >>> >>
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > best
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > Z
        >> >>> >> >>> >> >
        >> >>> >> >>> >> >
        >> >>> >> >>> >> >
        >> >>> >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
        >> >>> >> >>> >> malsburg@posteo.de
        >> >>> >> >>> >> >> wrote:
        >> >>> >> >>> >> >
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
        >> >>> >> >>> >> >> > Hi Titus
        >> >>> >> >>> >> >> >
        >> >>> >> >>> >> >> > I have been exploring helm-bibtex a bit today and have
        >> some
        >> >>> >> >>> questions.
        >> >>> >> >>> >> >> btw
        >> >>> >> >>> >> >> > is this the preferred way to make requests/ask questions
        >> >>> or is
        >> >>> >> >>> >> >> > github preferred?
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> Helm-bibtex is not part of org (although it tries to work
        >> >>> well
        >> >>> >> with
        >> >>> >> >>> >> >> org).  So I’m not sure whether this list is the best place
        >> >>> for
        >> >>> >> >>> >> >> discussing it.  For now the issue tracker on Github might
        >> be
        >> >>> a
        >> >>> >> >>> better
        >> >>> >> >>> >> >> option:
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> > in any case i was wondering a few things:
        >> >>> >> >>> >> >> >
        >> >>> >> >>> >> >> > 1. is it possible to have custom sorting? i want all
        >> views
        >> >>> to
        >> >>> >> >>> sort by
        >> >>> >> >>> >> >> > Author, year, month
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> I prefer to see the entries in the (inverse) order in
        >> which
        >> >>> they
        >> >>> >> >>> appear
        >> >>> >> >>> >> >> in the BibTeX file.  This way, recent additions show up at
        >> >>> the
        >> >>> >> >>> >> >> top.  However, I agree that sorting would be useful (see
        >> >>> issues
        >> >>> >> #5
        >> >>> >> >>> and
        >> >>> >> >>> >> >> #21); it just doesn’t have high priority for me.  Pull
        >> >>> requests
        >> >>> >> >>> welcome.
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> > 2. i would really like a way to have stored smart groups
        >> >>> (like
        >> >>> >> the
        >> >>> >> >>> >> jabref
        >> >>> >> >>> >> >> > dynamic groups if your aware of that). that is for
        >> example
        >> >>> >> create
        >> >>> >> >>> a
        >> >>> >> >>> >> group
        >> >>> >> >>> >> >> > that auto selects all publications i have (by my
        >> first/last
        >> >>> >> name)
        >> >>> >> >>> and
        >> >>> >> >>> >> >> shows
        >> >>> >> >>> >> >> > the count (in numbers) of these publications.
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> I’m not familiar with smart groups but it seems that all
        >> >>> >> >>> helm-bibtex is
        >> >>> >> >>> >> >> doing is giving you very flexible smart groups defined by
        >> >>> your
        >> >>> >> >>> search
        >> >>> >> >>> >> >> expressions.  For example, if you want a list of your
        >> >>> >> publications,
        >> >>> >> >>> you
        >> >>> >> >>> >> >> can simple enter your name.  And if you want a list of
        >> your
        >> >>> >> >>> articles,
        >> >>> >> >>> >> >> you can enter your name + “article”.  If you want all your
        >> >>> >> articles
        >> >>> >> >>> from
        >> >>> >> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The
        >> >>> number
        >> >>> >> of
        >> >>> >> >>> >> >> matches will be displayed in the mode line.  If you don’t
        >> >>> want to
        >> >>> >> >>> type
        >> >>> >> >>> >> >> these search expressions, you could create a command that
        >> >>> invokes
        >> >>> >> >>> >> >> helm-bibtex with a default search expression and that
        >> command
        >> >>> >> could
        >> >>> >> >>> be
        >> >>> >> >>> >> >> bound to a keyboard shortcut.
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> > Another example is a group to keep track of all the
        >> papers
        >> >>> im
        >> >>> >> >>> working
        >> >>> >> >>> >> on
        >> >>> >> >>> >> >> or
        >> >>> >> >>> >> >> > invloved with by matching keyword author and prep/*other
        >> >>> key
        >> >>> >> word
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for
        >> >>> keywords
        >> >>> >> >>> >> >> describing the content of the paper (as usual) and “tags”
        >> for
        >> >>> >> meta
        >> >>> >> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
        >> >>> >> “poster”,
        >> >>> >> >>> >> >> “talk”, … So if I want a list of all articles in
        >> progress, I
        >> >>> >> search
        >> >>> >> >>> for
        >> >>> >> >>> >> >> “own manuscript”.  Since the tags field is non-standard,
        >> it
        >> >>> has
        >> >>> >> to
        >> >>> >> >>> be
        >> >>> >> >>> >> >> added to `helm-bibtex-additional-search-fields`.
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> Another solution would be to use the pubstate field and to
        >> >>> search
        >> >>> >> >>> for
        >> >>> >> >>> >> >> your name and “forthcoming” (add pubstate to
        >> >>> >> >>> >> >> helm-bibtex-additional-search-fields for this to work).
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> > 3.is it possible to ass an option to auto generate a
        >> >>> bibkey
        >> >>> >> for a
        >> >>> >> >>> >> >> selected
        >> >>> >> >>> >> >> > citation based on user criteria such as
        >> >>> >> author(date)short-title?
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> Maintaining the content of the BibTeX file not really in
        >> the
        >> >>> >> scope
        >> >>> >> >>> of
        >> >>> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
        >> >>> >> Perhaps
        >> >>> >> >>> >> >> org-ref or ebib can help here?  Once you have a function
        >> that
        >> >>> >> >>> generates
        >> >>> >> >>> >> >> a new key and inserts it in the BibTeX file, you can
        >> easily
        >> >>> add
        >> >>> >> it
        >> >>> >> >>> to
        >> >>> >> >>> >> >> the list of actions in helm-bibtex.
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> Hope that helps.
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >>   Titus
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >> > thx so much in advance, you and john have given me
        >> >>> confidence
        >> >>> >> to
        >> >>> >> >>> >> finally
        >> >>> >> >>> >> >> > dive into the whole latex/bibteX world
        >> >>> >> >>> >> >> >
        >> >>> >> >>> >> >> > best
        >> >>> >> >>> >> >> >
        >> >>> >> >>> >> >> > Z
        >> >>> >> >>> >> >>
        >> >>> >> >>> >> >>
        >> >>> >> >>> >>
        >> >>> >> >>> >>
        >> >>> >> >>>
        >> >>> >> >>>
        >> >>> >> >>
        >> >>> >>
        >> >>> >>
        >> >>>
        >> >>> --
        >> >>> Professor John Kitchin
        >> >>> Doherty Hall A207F
        >> >>> Department of Chemical Engineering
        >> >>> Carnegie Mellon University
        >> >>> Pittsburgh, PA 15213
        >> >>> 412-268-7803
        >> >>> @johnkitchin
        >> >>> http://kitchingroup.cheme.cmu.edu
        >> >>>
        >> >>
        >> >>
        >>
        >> --
        >> Professor John Kitchin
        >> Doherty Hall A207F
        >> Department of Chemical Engineering
        >> Carnegie Mellon University
        >> Pittsburgh, PA 15213
        >> 412-268-7803
        >> @johnkitchin
        >> http://kitchingroup.cheme.cmu.edu
        >>
        
        --
        Professor John Kitchin
        Doherty Hall A207F
        Department of Chemical Engineering
        Carnegie Mellon University
        Pittsburgh, PA 15213
        412-268-7803
        @johnkitchin
        http://kitchingroup.cheme.cmu.edu
        
        ^ permalink raw reply	[flat|nested] 26+ messages in thread

      • * Re: helm-bibtex questions
          2015-06-27  6:11     ` Xebar Saram
          2015-06-27 11:44       ` John Kitchin
        @ 2015-06-30  9:15       ` Eric S Fraga
          2015-06-30 13:19         ` John Kitchin
          1 sibling, 1 reply; 26+ messages in thread
        From: Eric S Fraga @ 2015-06-30  9:15 UTC (permalink / raw)
          To: Xebar Saram; +Cc: org mode, John Kitchin
        
        On Saturday, 27 Jun 2015 at 09:11, Xebar Saram wrote:
        > hmm strange still dosent work for me. here is the top section of my bib file
        >
        > -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
        >
        > @article{ackerman-1998-discr-clear,
        >   author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
        >                   {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
        >                   Gumley, {L.E.}},
        >   title = {Discriminating Clear Sky From Clouds With Modis},
        >   journal = {Journal of Geophysical Research},
        >   volume = 103,
        >   number = {D24},
        >   pages = {32,141--32,157},
        >   year = 1998,
        >   shorttitle = {Discriminating clear sky from clouds with {MODIS}},
        > }
        
        [...]
        
        Try removing the comma in the last entry.  I've found that having this
        comma confuses bibtex and/or emacs at times...
        
        Just grasping at straws here for you :-)
        
        -- 
        : Eric S Fraga (0xFFFCF67D), Emacs 24.4.1, Org release_8.3beta-1229-ge900eb
        
        ^ permalink raw reply	[flat|nested] 26+ messages in thread

      • • * Re: helm-bibtex questions
            2015-06-30  9:15       ` Eric S Fraga
          @ 2015-06-30 13:19         ` John Kitchin
            2015-06-30 13:44           ` Xebar Saram
            0 siblings, 1 reply; 26+ messages in thread
          From: John Kitchin @ 2015-06-30 13:19 UTC (permalink / raw)
            To: Eric S Fraga; +Cc: Xebar Saram, org mode
          
          I think you are also still missing a % sign at the beginning of the -*-
          line.
          
          What if you change the dialect from the bibtex Entry-types  menu?
          
          also, what still doesn't work?
          
          Eric S Fraga writes:
          
          > On Saturday, 27 Jun 2015 at 09:11, Xebar Saram wrote:
          >> hmm strange still dosent work for me. here is the top section of my bib file
          >>
          >> -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
          >>
          >> @article{ackerman-1998-discr-clear,
          >>   author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
          >>                   {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
          >>                   Gumley, {L.E.}},
          >>   title = {Discriminating Clear Sky From Clouds With Modis},
          >>   journal = {Journal of Geophysical Research},
          >>   volume = 103,
          >>   number = {D24},
          >>   pages = {32,141--32,157},
          >>   year = 1998,
          >>   shorttitle = {Discriminating clear sky from clouds with {MODIS}},
          >> }
          >
          > [...]
          >
          > Try removing the comma in the last entry.  I've found that having this
          > comma confuses bibtex and/or emacs at times...
          >
          > Just grasping at straws here for you :-)
          
          --
          Professor John Kitchin
          Doherty Hall A207F
          Department of Chemical Engineering
          Carnegie Mellon University
          Pittsburgh, PA 15213
          412-268-7803
          @johnkitchin
          http://kitchingroup.cheme.cmu.edu
          
          ^ permalink raw reply	[flat|nested] 26+ messages in thread

        • • * Re: helm-bibtex questions
              2015-06-30 13:19         ` John Kitchin
            @ 2015-06-30 13:44           ` Xebar Saram
              2015-06-30 14:37             ` Eric S Fraga
              0 siblings, 1 reply; 26+ messages in thread
            From: Xebar Saram @ 2015-06-30 13:44 UTC (permalink / raw)
              To: John Kitchin; +Cc: org mode
            
            [-- Attachment #1: Type: text/plain, Size: 1467 bytes --]
            
            Thanks guys
            
            it works now !
            
            best
            
            z
            
            
            
            On Tue, Jun 30, 2015 at 4:19 PM, John Kitchin <jkitchin@andrew.cmu.edu>
            wrote:
            
            > I think you are also still missing a % sign at the beginning of the -*-
            > line.
            >
            > What if you change the dialect from the bibtex Entry-types  menu?
            >
            > also, what still doesn't work?
            >
            > Eric S Fraga writes:
            >
            > > On Saturday, 27 Jun 2015 at 09:11, Xebar Saram wrote:
            > >> hmm strange still dosent work for me. here is the top section of my bib
            > file
            > >>
            > >> -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
            > >>
            > >> @article{ackerman-1998-discr-clear,
            > >>   author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
            > >>                   {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
            > >>                   Gumley, {L.E.}},
            > >>   title = {Discriminating Clear Sky From Clouds With Modis},
            > >>   journal = {Journal of Geophysical Research},
            > >>   volume = 103,
            > >>   number = {D24},
            > >>   pages = {32,141--32,157},
            > >>   year = 1998,
            > >>   shorttitle = {Discriminating clear sky from clouds with {MODIS}},
            > >> }
            > >
            > > [...]
            > >
            > > Try removing the comma in the last entry.  I've found that having this
            > > comma confuses bibtex and/or emacs at times...
            > >
            > > Just grasping at straws here for you :-)
            >
            > --
            > Professor John Kitchin
            > Doherty Hall A207F
            > Department of Chemical Engineering
            > Carnegie Mellon University
            > Pittsburgh, PA 15213
            > 412-268-7803
            > @johnkitchin
            > http://kitchingroup.cheme.cmu.edu
            >
            
            [-- Attachment #2: Type: text/html, Size: 2398 bytes --]
            
            ^ permalink raw reply	[flat|nested] 26+ messages in thread

          • • * Re: helm-bibtex questions
                2015-06-30 13:44           ` Xebar Saram
              @ 2015-06-30 14:37             ` Eric S Fraga
                2015-07-01  4:53               ` Xebar Saram
                0 siblings, 1 reply; 26+ messages in thread
              From: Eric S Fraga @ 2015-06-30 14:37 UTC (permalink / raw)
                To: Xebar Saram; +Cc: org mode
              
              On Tuesday, 30 Jun 2015 at 16:44, Xebar Saram wrote:
              > Thanks guys
              >
              > it works now !
              
              Which fix worked?  The , or the %?  Enquiring minds wish to know...
              
              Excellent news, in any case.
              
              -- 
              : Eric S Fraga (0xFFFCF67D), Emacs 24.4.1, Org release_8.3beta-1261-g304f84
              
              ^ permalink raw reply	[flat|nested] 26+ messages in thread

            • • * Re: helm-bibtex questions
                  2015-06-30 14:37             ` Eric S Fraga
                @ 2015-07-01  4:53               ` Xebar Saram
                  0 siblings, 0 replies; 26+ messages in thread
                From: Xebar Saram @ 2015-07-01  4:53 UTC (permalink / raw)
                  To: Xebar Saram, org mode
                
                [-- Attachment #1: Type: text/plain, Size: 415 bytes --]
                
                :)
                
                it was the % at the start
                
                thx again all
                
                best
                
                Z
                
                On Tue, Jun 30, 2015 at 5:37 PM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
                
                > On Tuesday, 30 Jun 2015 at 16:44, Xebar Saram wrote:
                > > Thanks guys
                > >
                > > it works now !
                >
                > Which fix worked?  The , or the %?  Enquiring minds wish to know...
                >
                > Excellent news, in any case.
                >
                > --
                > : Eric S Fraga (0xFFFCF67D), Emacs 24.4.1, Org release_8.3beta-1261-g304f84
                >
                
                [-- Attachment #2: Type: text/html, Size: 927 bytes --]
                
                ^ permalink raw reply	[flat|nested] 26+ messages in thread

end of thread, other threads:[~2015-07-01  4:53 UTC | newest]

Thread overview: 26+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2015-06-17 18:08 helm-bibtex questions Xebar Saram
2015-06-17 20:02 ` Titus von der Malsburg
2015-06-18 11:32   ` Xebar Saram
2015-06-18 18:38     ` Titus von der Malsburg
2015-06-19 10:56       ` Xebar Saram
2015-06-19 21:02         ` John Kitchin
2015-06-21 18:29         ` Titus von der Malsburg
2015-06-21 18:40           ` John Kitchin
2015-06-22 14:28             ` Xebar Saram
2015-06-22 15:12               ` Titus von der Malsburg
2015-06-24 19:54                 ` Xebar Saram
2015-06-24 21:03                   ` John Kitchin
2015-06-26  7:21                 ` Xebar Saram
2015-06-26 17:21                   ` Titus von der Malsburg
2015-06-26 17:35                     ` Titus von der Malsburg
2015-06-26 17:54                     ` John Kitchin
2015-06-19 21:08   ` John Kitchin
     [not found] <s7xudwyj5ehe8r98klrf3034.1435230561139@email.android.com>
2015-06-26  7:14 ` Xebar Saram
2015-06-26 14:28   ` John Kitchin
2015-06-27  6:11     ` Xebar Saram
2015-06-27 11:44       ` John Kitchin
2015-06-30  9:15       ` Eric S Fraga
2015-06-30 13:19         ` John Kitchin
2015-06-30 13:44           ` Xebar Saram
2015-06-30 14:37             ` Eric S Fraga
2015-07-01  4:53               ` Xebar Saram

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