helm-bibtex questions

helm-bibtex questions

[Xebar Saram]

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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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Re: helm-bibtex questions

[Titus von der Malsburg]

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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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Re: helm-bibtex questions

[Xebar Saram]

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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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Re: helm-bibtex questions

[Titus von der Malsburg]

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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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Re: helm-bibtex questions

[Xebar Saram]

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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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Re: helm-bibtex questions

[John Kitchin]

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

Re: helm-bibtex questions

[John Kitchin]

>
>> 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

Re: helm-bibtex questions

[Titus von der Malsburg]

[-- 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
>> >>
>> >>
>>
>>


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Re: helm-bibtex questions

[John Kitchin]

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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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Re: helm-bibtex questions

[Xebar Saram]

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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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Re: helm-bibtex questions

[Titus von der Malsburg]

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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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Re: helm-bibtex questions

[Xebar Saram]

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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
> >>> >> >>
> >>> >> >>
> >>> >>
> >>> >>
> >>>
> >>>
> >>
>
>

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Re: helm-bibtex questions

[John Kitchin]

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

Re: helm-bibtex questions

[Xebar Saram]

[-- 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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Re: helm-bibtex questions

[Xebar Saram]

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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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Re: helm-bibtex questions

[John Kitchin]

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

Re: helm-bibtex questions

[Titus von der Malsburg]

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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
>> >>> >> >>
>> >>> >> >>
>> >>> >>
>> >>> >>
>> >>>
>> >>>
>> >>
>>
>>


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Re: helm-bibtex questions

[Titus von der Malsburg]

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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
>>> >>> >> >>
>>> >>> >> >>
>>> >>> >>
>>> >>> >>
>>> >>>
>>> >>>
>>> >>
>>>
>>>


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Re: helm-bibtex questions

[John Kitchin]

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

Re: helm-bibtex questions

[Xebar Saram]

[-- 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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Re: helm-bibtex questions

[John Kitchin]

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

Re: helm-bibtex questions

[Eric S Fraga]

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

Re: helm-bibtex questions

[John Kitchin]

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

Re: helm-bibtex questions

[Xebar Saram]

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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
>

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Re: helm-bibtex questions

[Eric S Fraga]

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

Re: helm-bibtex questions

[Xebar Saram]

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:)

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
>

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