emacs & org mode for scholars questions

emacs & org mode for scholars questions

[Erik Hetzner]

Hi all,

I am going to be giving a talk on how Emacs can help support scholars,
especially those who are using plain text and doing reproducible
research, at “Emacsconf 2015” in San Francisco this Saturday (the
29th).

I have done some work on managing references using Emacs & pandoc, but
what I’d like to focus on in this talk is why Emacs is a great tool
for scholarly writers (both scientists and humanists) and what Emacs
developers should be concentrating on to make it an even better tool
for the scholarly community.

I’m wondering if you any of you might have any suggestions about what
you would like to see Emacs do better to support the scholarly writing
community.

Thanks for any help you can provide!

best, Erik Hetzner
--
Sent from my free software system <http://fsf.org/>.

Re: emacs & org mode for scholars questions

[John Kitchin]

(personal bias warning;) I think org-ref+helm-bibtex is a best in class
solution to citation management for org-mode/LaTeX users. It provides
functional cite links that connect to web of science, scopus, pubmed,
and others. It provides utilities to download bibtex and org-bibtex
entries from a doi, and also to download the pdf if it knows how. It
also provides a lot of bibtex utilities to change title cases, etc... It
provides some limited support for export to other formats like html, but
that is an area that certainly could be improved, as well as support for
other formats. It would be nice to consider expanding the bibliography
database formats supported (this would also require expanding the export
code).

There is a cite element that has been developed in org-mode that may one
day supercede the link based approach that org-ref uses. Much of the
functionality of org-ref could be retained when that happens.

What would make it even better? Integrated smart search, e.g. find other
documents that cite a reference, find similar documents/references based
on what you have written.

Most important maybe: figure out how to merge narrative text in version
control! I don't want to write a sentence per line just to use the
default merge with git. I really want a word-based track-change like
diff, and merge.

Erik Hetzner writes:

> Hi all,
>
> I am going to be giving a talk on how Emacs can help support scholars,
> especially those who are using plain text and doing reproducible
> research, at “Emacsconf 2015” in San Francisco this Saturday (the
> 29th).
>
> I have done some work on managing references using Emacs & pandoc, but
> what I’d like to focus on in this talk is why Emacs is a great tool
> for scholarly writers (both scientists and humanists) and what Emacs
> developers should be concentrating on to make it an even better tool
> for the scholarly community.
>
> I’m wondering if you any of you might have any suggestions about what
> you would like to see Emacs do better to support the scholarly writing
> community.
>
> Thanks for any help you can provide!
>
> best, Erik Hetzner

--
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: emacs & org mode for scholars questions

[Matt Price]

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Don't have much bandwidth where i am on vacation, but for humanists a more
robust and reproducible export to odt and html is org's main weakness, I
think. Zotxt is great but takes a bit if setting up, and of course zotero
refa are less portable than bibtex libraries. Moving to org-ref probably
makes sense but lack of built-in odt support makes that a bit intimidating,
esp for a zotero user whose bibtex setup is a little inflexible.

I hope you post your slides!

M

On Tue, Aug 25, 2015, 09:52 John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> (personal bias warning;) I think org-ref+helm-bibtex is a best in class
> solution to citation management for org-mode/LaTeX users. It provides
> functional cite links that connect to web of science, scopus, pubmed,
> and others. It provides utilities to download bibtex and org-bibtex
> entries from a doi, and also to download the pdf if it knows how. It
> also provides a lot of bibtex utilities to change title cases, etc... It
> provides some limited support for export to other formats like html, but
> that is an area that certainly could be improved, as well as support for
> other formats. It would be nice to consider expanding the bibliography
> database formats supported (this would also require expanding the export
> code).
>
> There is a cite element that has been developed in org-mode that may one
> day supercede the link based approach that org-ref uses. Much of the
> functionality of org-ref could be retained when that happens.
>
> What would make it even better? Integrated smart search, e.g. find other
> documents that cite a reference, find similar documents/references based
> on what you have written.
>
> Most important maybe: figure out how to merge narrative text in version
> control! I don't want to write a sentence per line just to use the
> default merge with git. I really want a word-based track-change like
> diff, and merge.
>
> Erik Hetzner writes:
>
> > Hi all,
> >
> > I am going to be giving a talk on how Emacs can help support scholars,
> > especially those who are using plain text and doing reproducible
> > research, at “Emacsconf 2015” in San Francisco this Saturday (the
> > 29th).
> >
> > I have done some work on managing references using Emacs & pandoc, but
> > what I’d like to focus on in this talk is why Emacs is a great tool
> > for scholarly writers (both scientists and humanists) and what Emacs
> > developers should be concentrating on to make it an even better tool
> > for the scholarly community.
> >
> > I’m wondering if you any of you might have any suggestions about what
> > you would like to see Emacs do better to support the scholarly writing
> > community.
> >
> > Thanks for any help you can provide!
> >
> > best, Erik Hetzner
>
> --
> 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: emacs & org mode for scholars questions

[Eric S Fraga]

On Tuesday, 25 Aug 2015 at 09:51, John Kitchin wrote:

[...]

> What would make it even better? Integrated smart search, e.g. find other
> documents that cite a reference, find similar documents/references based
> on what you have written.

Remembrance agent [1] does this automatically to some degree ...

cheers,
eric

Footnotes: 
[1]  http://xenia.media.mit.edu/~rhodes/Papers/remembrance.html

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.1-176-g45abec

Re: emacs & org mode for scholars questions

[John Kitchin]

That looks very cool. Do you use it?

Eric S Fraga writes:

> On Tuesday, 25 Aug 2015 at 09:51, John Kitchin wrote:
>
> [...]
>
>> What would make it even better? Integrated smart search, e.g. find other
>> documents that cite a reference, find similar documents/references based
>> on what you have written.
>
> Remembrance agent [1] does this automatically to some degree ...
>
> cheers,
> eric
>
> Footnotes:
> [1]  http://xenia.media.mit.edu/~rhodes/Papers/remembrance.html

--
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: emacs & org mode for scholars questions

[Eric S Fraga]

On Tuesday, 25 Aug 2015 at 16:18, John Kitchin wrote:
> That looks very cool. Do you use it?

yes but only when I have a large enough monitor, e.g. on my 24" portrait
monitor I use for writing.

it can be useful every now and again, especially as I have both org
documents and emails trawled for keywords.  The email aspect is not as
good as it could be due to people including all previous emails in
replies so there is a lot of duplication.  I tend to start the agent
when I start writing a paper or a grant proposal and then forget about
it until I need to find something.  I then look at what remem is
suggesting just in case.

Other than screen space, it doesn't get in the way.

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.1-176-g45abec

Re: emacs & org mode for scholars questions

[John Kitchin]

Interesting. I could see some interesting extensions to it. I use
button-lock to alert me to interesting (to me) text in my buffers a lot,
which is a little less intrusive. For example, any names in my
org-contacts are highlighted in a light pink background with a context
tool tip and made clickable to access functions like open the contact,
email the contact, etc... This is done with a large regexp pattern
through font-lock, but it would be interesting do that with some kind of
asynchronously run function that doesn't get in my way. I have not used
functions in font lock yet, but I think it can be done.

When you say trawled, is this with some indexing tool, or something you
wrote?




Eric S Fraga writes:

> On Tuesday, 25 Aug 2015 at 16:18, John Kitchin wrote:
>> That looks very cool. Do you use it?
>
> yes but only when I have a large enough monitor, e.g. on my 24" portrait
> monitor I use for writing.
>
> it can be useful every now and again, especially as I have both org
> documents and emails trawled for keywords.  The email aspect is not as
> good as it could be due to people including all previous emails in
> replies so there is a lot of duplication.  I tend to start the agent
> when I start writing a paper or a grant proposal and then forget about
> it until I need to find something.  I then look at what remem is
> suggesting just in case.
>
> Other than screen space, it doesn't get in the way.

--
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: emacs & org mode for scholars questions

[Eric S Fraga]

On Wednesday, 26 Aug 2015 at 06:39, John Kitchin wrote:
> Interesting. I could see some interesting extensions to it. I use
> button-lock to alert me to interesting (to me) text in my buffers a lot,
> which is a little less intrusive. For example, any names in my

Interesting!  Indeed it would be interesting to tie these two concepts
together, sort of an automatic hyper-text facility with multiple
out-going links...

> When you say trawled, is this with some indexing tool, or something you
> wrote?

The remembrance-agent package in Debian includes the tools for trawling
through text files and creating the databases (ra-index) the emacs tool
requires (using ra-retrieve).

I run the index operation using crontab weekly.  Weekly is sufficient
for my needs as the content is not that dynamic and it is the old
content that I need help remembering ;-)

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.1-176-g45abec

Re: emacs & org mode for scholars questions

[John Kitchin]

Eric S Fraga writes:

> On Wednesday, 26 Aug 2015 at 06:39, John Kitchin wrote:
>> Interesting. I could see some interesting extensions to it. I use
>> button-lock to alert me to interesting (to me) text in my buffers a lot,
>> which is a little less intrusive. For example, any names in my
>
> Interesting!  Indeed it would be interesting to tie these two concepts
> together, sort of an automatic hyper-text facility with multiple
> out-going links...

That is exactly what my code does, sometimes even with context-specific
links, e.g. if a contact has a URL property, you get an open url
action.

>
>> When you say trawled, is this with some indexing tool, or something you
>> wrote?
>
> The remembrance-agent package in Debian includes the tools for trawling
> through text files and creating the databases (ra-index) the emacs tool
> requires (using ra-retrieve).

I see. one day I will think about doing something like this with the
swish-e index (or recoll, etc...) work I did this past summer. Document
similarity has been on my mind, beyond just keywords (which I am not
good at using consistently) for a few applications. Mostly similar
bibtex entries I already have, similar entries in an RSS feed, etc...

>
> I run the index operation using crontab weekly.  Weekly is sufficient
> for my needs as the content is not that dynamic and it is the old
> content that I need help remembering ;-)

Agreed!

--
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: emacs & org mode for scholars questions

[Suvayu Ali]

Hi John,

On Tue, Aug 25, 2015 at 09:51:53AM -0400, John Kitchin wrote:
> 
> Most important maybe: figure out how to merge narrative text in version
> control! I don't want to write a sentence per line just to use the
> default merge with git. I really want a word-based track-change like
> diff, and merge.

Ages ago there was a GSoC project, Org merge driver, for use with git.
I don't recall what was the last status.  Okay, found some info:

http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/

Would be good to somehow revive this.  I guess it's not an easy problem.
If I remember correctly, there was no prior discussion on the list what
should be the merge strategy.  It happened as the project progressed.  I
think this is one of those projects where a clear path/plan how to
proceed before writing any code would be very beneficial.

Maybe someone can propose a plan?

Cheers,

-- 
Suvayu

Open source is the future. It sets us free.

Re: emacs & org mode for scholars questions

[John Kitchin]

Suvayu Ali writes:

> Hi John,
>
> On Tue, Aug 25, 2015 at 09:51:53AM -0400, John Kitchin wrote:
>>
>> Most important maybe: figure out how to merge narrative text in version
>> control! I don't want to write a sentence per line just to use the
>> default merge with git. I really want a word-based track-change like
>> diff, and merge.
>
> Ages ago there was a GSoC project, Org merge driver, for use with git.
> I don't recall what was the last status.  Okay, found some info:
>
> http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/
>
> Would be good to somehow revive this.  I guess it's not an easy problem.
> If I remember correctly, there was no prior discussion on the list what
> should be the merge strategy.  It happened as the project progressed.  I
> think this is one of those projects where a clear path/plan how to
> proceed before writing any code would be very beneficial.
>
> Maybe someone can propose a plan?
It sounds like a great addition, and (unfortunately) a summer project ;)

>
> Cheers,

--
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: emacs & org mode for scholars questions

[Marcin Borkowski]

On 2015-08-25, at 15:51, John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> What would make it even better?

Not imposing Helm on the user?

(I know nothing about Helm, but I use Icicles.)

Best,

-- 
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
Faculty of Mathematics and Computer Science
Adam Mickiewicz University

Re: emacs & org mode for scholars questions

[John Kitchin]

this is a customizable option in org-ref. Helm is not required. You can
also use the reftex mechanism for inserting references, or define your
own method using icicles.

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L131

Marcin Borkowski writes:

> On 2015-08-25, at 15:51, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>
>> What would make it even better?
>
> Not imposing Helm on the user?
>
> (I know nothing about Helm, but I use Icicles.)
>
> Best,

--
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: emacs & org mode for scholars questions

[Thomas S. Dye]

Aloha Erik,

Erik Hetzner <egh@e6h.org> writes:

> Hi all,
>
> I am going to be giving a talk on how Emacs can help support scholars,
> especially those who are using plain text and doing reproducible
> research, at “Emacsconf 2015” in San Francisco this Saturday (the
> 29th).
>
> I have done some work on managing references using Emacs & pandoc, but
> what I’d like to focus on in this talk is why Emacs is a great tool
> for scholarly writers (both scientists and humanists) and what Emacs
> developers should be concentrating on to make it an even better tool
> for the scholarly community.
>
> I’m wondering if you any of you might have any suggestions about what
> you would like to see Emacs do better to support the scholarly writing
> community.

If you'll be talking to Emacs developers, then my advice would be to
thank them for their good work.  The stable platform they've developed
supports the most congenial scholarly writing environment I can
imagine.

From my point of view, most of the development action that directly
affects scholarly writers takes place outside of Emacs proper in the
various modes and packages that run on top of it, especially Org mode.
The shifting community of volunteers that regularly congregates around
Org mode development is open to and interested in the needs of the
scholarly writing community.  This is one of the lasting legacies
established by Org mode's creator, Carsten Dominik, a scholar and writer
himself. Early on, he recognized the potential of Babel and the support
and guidance he offered Eric Shulte and Dan Davison were integral to the
success of that audacious project.  When Nicolas Goaziou rebuilt the
export framework a few years ago, the last piece of the puzzle was in
place.  Now, a single plain text computer file on my computer regularly
contains reading notes, a laboratory notebook, work schedules, data
sets, computer code designed to analyze the data, and one or more
scholarly papers ready to be exported to publishers' specs.  How
incredible is that!

From the end-user's perspective, the Achilles' heel is the staggering
complexity right at the surface.  Of course, this is part of what makes
Emacs a great development platform.  But for the scholarly writer the
complexity can be daunting, and it is here that I think Emacs
development might give more help to mode and package developers.  The
customization facilities of Emacs are fine if you're willing to spend
time trying to grasp the fine-grained structure of the Emacs
environment, and want your customization to apply globally, but in my
experience this is a consistent source of frustration.  When I set a
variable I'm reasonably confident that my setting will solve a
particular issue I'm having, but I lack the ability to understand what
other effects it might have when I'm working later on another task with
other issues.  Over the years I've come to set most variables locally,
either individually and directly or indirectly in batches by executing
code I keep in the library of Babel.  It would be great to have a
customization tool whose effects are buffer local, sensitive to the
task at hand, and easily accessed by the user. 

But, really, I can't imagine doing my scholarly writing outside of
Emacs.

All the best,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: emacs & org mode for scholars questions

[Eric S Fraga]

On Tuesday, 25 Aug 2015 at 06:48, Thomas S.Dye wrote:

[...]

> If you'll be talking to Emacs developers, then my advice would be to
> thank them for their good work.  The stable platform they've developed
> supports the most congenial scholarly writing environment I can
> imagine.

[...]

> established by Org mode's creator, Carsten Dominik, a scholar and writer
> himself. Early on, he recognized the potential of Babel and the support
> and guidance he offered Eric Shulte and Dan Davison were integral to the

+1 to all of the above.  We don't say this often enough probably: many
thanks are owed to all of the above people including the very many emacs
developers as you say.  I am reminded of this every time I have to use
something like MS Office tools or Libreoffice for some task...

> It would be great to have a customization tool whose effects are
> buffer local, sensitive to the task at hand, and easily accessed by
> the user.

I increasingly have

,----
| # Local Variables:
| # eval: (esf/execute-startup-block)
| # End:
`----

at the bottom of my org files to do just that, putting document specific
settings in an (Emacs lisp) org babel src block named "startup" which is
invoked by this code:

#+begin_src emacs-lisp
  (defun esf/execute-startup-block ()
    (interactive)
    (org-babel-goto-named-src-block "startup")
    (org-babel-execute-src-block))
#+end_src

The only problem is that many of the variables I would like to customise
are global to the emacs instance and so cause problems if I am editing
more than one document which may have different requirements.  A greater
move towards buffer local variables would be of great benefit.

Or, knowing Emacs's capabilities, it is probably already possible to do
this and I just don't know how to do it... ;-)

> But, really, I can't imagine doing my scholarly writing outside of
> Emacs.

+∞

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.1-176-g45abec

Re: emacs & org mode for scholars questions

[Erik Hetzner]

Hi all,

Thanks for all your responses! They were a great help when putting
together my talk. I’ve posted my slides from EmacsConf 2015 here:

  http://www.e6h.org/talks/emacsconf-2015/index.html

I think the planners are planning to post videos as soon as they can
get them edited to

  http://emacsconf2015.org/

EmacsConf 2015 was a lot of fun. Almost everyone there was an Org mode
user, which was no great surprise.

One thing that I came out of the conference thinking was that a
curated meta-package for Emacs (like elpy) that brought together tools
for scholarly writers (in LaTeX and markdown and org-mode) might be a
great help for Emacs beginners.

best, Erik

On Mon, 24 Aug 2015 22:38:30 -0700,
Erik Hetzner <egh@e6h.org> wrote:
> 
> Hi all,
> 
> I am going to be giving a talk on how Emacs can help support scholars,
> especially those who are using plain text and doing reproducible
> research, at “Emacsconf 2015” in San Francisco this Saturday (the
> 29th).
> 
> I have done some work on managing references using Emacs & pandoc, but
> what I’d like to focus on in this talk is why Emacs is a great tool
> for scholarly writers (both scientists and humanists) and what Emacs
> developers should be concentrating on to make it an even better tool
> for the scholarly community.
> 
> I’m wondering if you any of you might have any suggestions about what
> you would like to see Emacs do better to support the scholarly writing
> community.
> 
> Thanks for any help you can provide!
> 
> best, Erik Hetzner
> --
> Sent from my free software system <http://fsf.org/>.
> 
> 

Re: emacs & org mode for scholars questions

[John Kitchin]

Cool! Thanks for the shout out to org-ref!

my jmax starter package (http://github.com/jkitchin/jmax) is basically
designed for the last point you described. I use it with students (41
this semester!) as a standalone "package". It isn't as polished as
prelude or others, but it allows them to do things like I do out of the
box.

The conference sounds like it was fun! Best wishes,

Erik Hetzner writes:

> Hi all,
>
> Thanks for all your responses! They were a great help when putting
> together my talk. I’ve posted my slides from EmacsConf 2015 here:
>
>   http://www.e6h.org/talks/emacsconf-2015/index.html
>
> I think the planners are planning to post videos as soon as they can
> get them edited to
>
>   http://emacsconf2015.org/
>
> EmacsConf 2015 was a lot of fun. Almost everyone there was an Org mode
> user, which was no great surprise.
>
> One thing that I came out of the conference thinking was that a
> curated meta-package for Emacs (like elpy) that brought together tools
> for scholarly writers (in LaTeX and markdown and org-mode) might be a
> great help for Emacs beginners.
>
> best, Erik
>
> On Mon, 24 Aug 2015 22:38:30 -0700,
> Erik Hetzner <egh@e6h.org> wrote:
>>
>> Hi all,
>>
>> I am going to be giving a talk on how Emacs can help support scholars,
>> especially those who are using plain text and doing reproducible
>> research, at “Emacsconf 2015” in San Francisco this Saturday (the
>> 29th).
>>
>> I have done some work on managing references using Emacs & pandoc, but
>> what I’d like to focus on in this talk is why Emacs is a great tool
>> for scholarly writers (both scientists and humanists) and what Emacs
>> developers should be concentrating on to make it an even better tool
>> for the scholarly community.
>>
>> I’m wondering if you any of you might have any suggestions about what
>> you would like to see Emacs do better to support the scholarly writing
>> community.
>>
>> Thanks for any help you can provide!
>>
>> best, Erik Hetzner
>> --
>> Sent from my free software system <http://fsf.org/>.
>>
>>

--
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: emacs & org mode for scholars questions

[Erik Hetzner]

Thanks, John.

I was really blown away by org-ref. It’s a great package. I love, for
instance, the citation displayed in the minibuffer when the cursor is
on a cite. If you need help with the MELPA packaging process, let me
know.

best, Erik

On Wed, 02 Sep 2015 03:40:42-0700,
John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> 
> Cool! Thanks for the shout out to org-ref!
> 
> my jmax starter package (http://github.com/jkitchin/jmax) is basically
> designed for the last point you described. I use it with students (41
> this semester!) as a standalone "package". It isn't as polished as
> prelude or others, but it allows them to do things like I do out of the
> box.
> 
> The conference sounds like it was fun! Best wishes,
> 
> Erik Hetzner writes:
> 
> > Hi all,
> >
> > Thanks for all your responses! They were a great help when putting
> > together my talk. I’ve posted my slides from EmacsConf 2015 here:
> >
> >   http://www.e6h.org/talks/emacsconf-2015/index.html
> >
> > I think the planners are planning to post videos as soon as they can
> > get them edited to
> >
> >   http://emacsconf2015.org/
> >
> > EmacsConf 2015 was a lot of fun. Almost everyone there was an Org mode
> > user, which was no great surprise.
> >
> > One thing that I came out of the conference thinking was that a
> > curated meta-package for Emacs (like elpy) that brought together tools
> > for scholarly writers (in LaTeX and markdown and org-mode) might be a
> > great help for Emacs beginners.
> >
> > best, Erik
> >
> > On Mon, 24 Aug 2015 22:38:30 -0700,
> > Erik Hetzner <egh@e6h.org> wrote:
> >>
> >> Hi all,
> >>
> >> I am going to be giving a talk on how Emacs can help support scholars,
> >> especially those who are using plain text and doing reproducible
> >> research, at “Emacsconf 2015” in San Francisco this Saturday (the
> >> 29th).
> >>
> >> I have done some work on managing references using Emacs & pandoc, but
> >> what I’d like to focus on in this talk is why Emacs is a great tool
> >> for scholarly writers (both scientists and humanists) and what Emacs
> >> developers should be concentrating on to make it an even better tool
> >> for the scholarly community.
> >>
> >> I’m wondering if you any of you might have any suggestions about what
> >> you would like to see Emacs do better to support the scholarly writing
> >> community.
> >>
> >> Thanks for any help you can provide!
> >>
> >> best, Erik Hetzner
> >> --
> >> Sent from my free software system <http://fsf.org/>.
> >>
> >>
> 
> --
> 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: emacs & org mode for scholars questions

[John Kitchin]

Thanks. org-ref has been pretty stable lately, and given my fall
schedule it is likely to stay that way ;)

It might be ready for MELPA. I don't have a lot of experience packaging
for MELPA. Is there a set of instructions on how to do that somewhere?

Erik Hetzner writes:

> Thanks, John.
>
> I was really blown away by org-ref. It’s a great package. I love, for
> instance, the citation displayed in the minibuffer when the cursor is
> on a cite. If you need help with the MELPA packaging process, let me
> know.
>
> best, Erik
>
> On Wed, 02 Sep 2015 03:40:42-0700,
> John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>>
>> Cool! Thanks for the shout out to org-ref!
>>
>> my jmax starter package (http://github.com/jkitchin/jmax) is basically
>> designed for the last point you described. I use it with students (41
>> this semester!) as a standalone "package". It isn't as polished as
>> prelude or others, but it allows them to do things like I do out of the
>> box.
>>
>> The conference sounds like it was fun! Best wishes,
>>
>> Erik Hetzner writes:
>>
>> > Hi all,
>> >
>> > Thanks for all your responses! They were a great help when putting
>> > together my talk. I’ve posted my slides from EmacsConf 2015 here:
>> >
>> >   http://www.e6h.org/talks/emacsconf-2015/index.html
>> >
>> > I think the planners are planning to post videos as soon as they can
>> > get them edited to
>> >
>> >   http://emacsconf2015.org/
>> >
>> > EmacsConf 2015 was a lot of fun. Almost everyone there was an Org mode
>> > user, which was no great surprise.
>> >
>> > One thing that I came out of the conference thinking was that a
>> > curated meta-package for Emacs (like elpy) that brought together tools
>> > for scholarly writers (in LaTeX and markdown and org-mode) might be a
>> > great help for Emacs beginners.
>> >
>> > best, Erik
>> >
>> > On Mon, 24 Aug 2015 22:38:30 -0700,
>> > Erik Hetzner <egh@e6h.org> wrote:
>> >>
>> >> Hi all,
>> >>
>> >> I am going to be giving a talk on how Emacs can help support scholars,
>> >> especially those who are using plain text and doing reproducible
>> >> research, at “Emacsconf 2015” in San Francisco this Saturday (the
>> >> 29th).
>> >>
>> >> I have done some work on managing references using Emacs & pandoc, but
>> >> what I’d like to focus on in this talk is why Emacs is a great tool
>> >> for scholarly writers (both scientists and humanists) and what Emacs
>> >> developers should be concentrating on to make it an even better tool
>> >> for the scholarly community.
>> >>
>> >> I’m wondering if you any of you might have any suggestions about what
>> >> you would like to see Emacs do better to support the scholarly writing
>> >> community.
>> >>
>> >> Thanks for any help you can provide!
>> >>
>> >> best, Erik Hetzner
>> >> --
>> >> Sent from my free software system <http://fsf.org/>.
>> >>
>> >>
>>
>> --
>> 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: emacs & org mode for scholars questions

[Thierry Banel]

Le 05/09/2015 02:29, John Kitchin a écrit :
> Thanks. org-ref has been pretty stable lately, and given my fall
> schedule it is likely to stay that way ;)
>
> It might be ready for MELPA. I don't have a lot of experience packaging
> for MELPA. Is there a set of instructions on how to do that somewhere?
>
I wrote a step by step guide for publishing on Melpa:
http://orgmode.org/worg/org-tutorials/melpa-github.html

Thierry

Re: emacs & org mode for scholars questions

[Christian Wittern]

On 2015-09-02 19:40, John Kitchin wrote:
> Cool! Thanks for the shout out to org-ref!
>
> my jmax starter package (http://github.com/jkitchin/jmax) is basically
> designed for the last point you described. I use it with students (41
> this semester!) as a standalone "package". It isn't as polished as
> prelude or others, but it allows them to do things like I do out of the
> box.

Great slides and a great activity.  I totally agree that we need to teach
our students to use real tools they can use sustainably throughout their
career.

I am developing a package and a bundle for people in Chinese Studies and
neighbouring fields.  This needs a slightly different set of packages and
settings so I don't think a one-size-fits-all approach would be productive
here, neither on the Emacs level, nor on the level of something like jmax. 
I think being able to have something like

$> pip --freeze > requirements   and
$> pip install -r <requirements

might provide both a flexible and extensible way to maintain meta packages. 
Or is there already a better way in the Emacs universe?


All the best,

Christian


-- 
Christian Wittern, Kyoto

Re: emacs & org mode for scholars questions

[Rasmus]

Christian Wittern <cwittern@gmail.com> writes:

> $> pip --freeze > requirements   and
> $> pip install -r <requirements
>
> might provide both a flexible and extensible way to maintain meta packages. 
> Or is there already a better way in the Emacs universe?

Why make it so hard?  Just use the facilities built into Emacs, namely
init.el and package.el and put something like this in your init.

    (setq package-selected-packages
          '(auctex ess
            company
            js2-mode
            magit
            nyan-mode
            pdf-tools
            paredit
            visual-regexp))

    (package-initialize)
    (when (fboundp 'package-install-selected-packages) ; Emacs-v25 
      (package-install-selected-packages))


Rasmus

-- 
Dobbelt-A

Re: emacs & org mode for scholars questions

[Rasmus]

Hi,

Erik Hetzner <egh@e6h.org> writes:

>   http://www.e6h.org/talks/emacsconf-2015/index.html

Thanks, I really enjoyed them.  One technical question.  Why do the flow
of the slides sometimes change from L→R to T→B?  It's quite confusing and
makes it hard to go back and forth between slides (IMO of course).  None
of your slides seem optional.

If find whom you choose to mention by name in the Org part particular.
E.g. add-on authors are named, the original author isn't mentioned, but
his profession is, ob is mentioned, but the main author isn't mentioned...

> Latex v. plain text
> [...]
> But the [ox] toolchains can be fragile [...]

{{citation needed}}

> One thing that I came out of the conference thinking was that a
> curated meta-package for Emacs (like elpy) that brought together tools
> for scholarly writers (in LaTeX and markdown and org-mode) might be a
> great help for Emacs beginners.

IMO, we should aim to DISTRIBUTE the needed packages *within* Emacs and
have SANE defaults.  Even with package.el, maintaining software on a
computer that you do not have full access to, can be a pain.  The value of
"batteries included" cannot be emphasized enough!  Instead of adding
another project to github, it would be better to fix it in Emacs.

EmacsW32 is great in this regard 'cause it's a just a zip, which you can
use even on constrained systems.  I still have to install AUCTEX and ESS
"manually", but at least package.el can handle compressed archives.

Thanks,
Rasmus

-- 
May contains speling mistake

Re: emacs & org mode for scholars questions

[Xebar Saram]

[-- Attachment #1: Type: text/plain, Size: 1800 bytes --]

Hi

the slides are really nice! are they done in org and beamer?

best

z

On Wed, Sep 2, 2015 at 2:00 PM, Rasmus <rasmus@gmx.us> wrote:

> Hi,
>
> Erik Hetzner <egh@e6h.org> writes:
>
> >   http://www.e6h.org/talks/emacsconf-2015/index.html
>
> Thanks, I really enjoyed them.  One technical question.  Why do the flow
> of the slides sometimes change from L→R to T→B?  It's quite confusing and
> makes it hard to go back and forth between slides (IMO of course).  None
> of your slides seem optional.
>
> If find whom you choose to mention by name in the Org part particular.
> E.g. add-on authors are named, the original author isn't mentioned, but
> his profession is, ob is mentioned, but the main author isn't mentioned...
>
> > Latex v. plain text
> > [...]
> > But the [ox] toolchains can be fragile [...]
>
> {{citation needed}}
>
> > One thing that I came out of the conference thinking was that a
> > curated meta-package for Emacs (like elpy) that brought together tools
> > for scholarly writers (in LaTeX and markdown and org-mode) might be a
> > great help for Emacs beginners.
>
> IMO, we should aim to DISTRIBUTE the needed packages *within* Emacs and
> have SANE defaults.  Even with package.el, maintaining software on a
> computer that you do not have full access to, can be a pain.  The value of
> "batteries included" cannot be emphasized enough!  Instead of adding
> another project to github, it would be better to fix it in Emacs.
>
> EmacsW32 is great in this regard 'cause it's a just a zip, which you can
> use even on constrained systems.  I still have to install AUCTEX and ESS
> "manually", but at least package.el can handle compressed archives.
>
> Thanks,
> Rasmus
>
> --
> May contains speling mistake
>
>
>

[-- Attachment #2: Type: text/html, Size: 2536 bytes --]

Re: emacs & org mode for scholars questions

[Rasmus]

Hi,

Xebar Saram <zeltakc@gmail.com> writes:

> the slides are really nice! are they done in org and beamer?

Not my slides, but: Reveal.js

        http://lab.hakim.se/reveal-js/

It's a very capable program¹ as long as you don't require too complicated
math.

There's an ox exporter, with I havne't tried:

         https://github.com/yjwen/org-reveal

Rasmus

Footnotes: 
¹   The theme used in this class is really excellent BTW:
         http://www.unomaha.edu/mahbubulmajumder/data-science/fall-2014/

-- 
When the facts change, I change my mind. What do you do, sir?

Re: emacs & org mode for scholars questions

[Marcin Borkowski]

On 2015-09-02, at 14:51, Rasmus <rasmus@gmx.us> wrote:

> Hi,
>
> Xebar Saram <zeltakc@gmail.com> writes:
>
>> the slides are really nice! are they done in org and beamer?
>
> Not my slides, but: Reveal.js
>
>         http://lab.hakim.se/reveal-js/
>
> It's a very capable program¹ as long as you don't require too complicated
> math.

Even with complicated math, it uses MathJax, which handles LaTeX math
pretty well.  (For some values of "complicated", of course.)

> There's an ox exporter, with I havne't tried:
>
>          https://github.com/yjwen/org-reveal

I have, and it's very nice.

> Rasmus
>
> Footnotes: 
> ¹   The theme used in this class is really excellent BTW:
>          http://www.unomaha.edu/mahbubulmajumder/data-science/fall-2014/

Best,

-- 
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
Faculty of Mathematics and Computer Science
Adam Mickiewicz University

Re: emacs & org mode for scholars questions

[Jorge A. Alfaro-Murillo]

Rasmus writes: 
 
> One technical question. Why do the flow of the slides sometimes 
> change from L→R to T→B? It's quite confusing and makes it hard 
> to go back and forth between slides (IMO of course). None of 
> your slides seem optional. 
 
That is reveal.js standard, left to right are "sections" and top 
to bottom are slides. It is good if one has to go back to a slide, 
you can press ESC and see the sections and search for the slide. 
To pass the slides you can use SPACE, which goes top to bottom and 
them right when there are no more slides below.

Best,
-- 
Jorge.

Re: emacs & org mode for scholars questions

[Erik Hetzner]

Hi Rasmus,

On Wed, 02 Sep 2015 04:00:50 -0700,
Rasmus <rasmus@gmx.us> wrote:
> 
> Hi,
>
> Thanks, I really enjoyed them.  One technical question.  Why do the flow
> of the slides sometimes change from L→R to T→B?  It's quite confusing and
> makes it hard to go back and forth between slides (IMO of course).  None
> of your slides seem optional.

What Jorge said. I’m not a huge fan but I didn’t bother to fix it.
Since I used org-reveal it looks easily fixed, see:

  https://github.com/yjwen/org-reveal#the-hlevel

> If find whom you choose to mention by name in the Org part particular.
> E.g. add-on authors are named, the original author isn't mentioned, but
> his profession is, ob is mentioned, but the main author isn't mentioned...

That’s a good point, thanks! I’ll update the slides to include authors
of all packages mentioned.

> > Latex v. plain text
> > [...]
> > But the [ox] toolchains can be fragile [...]
> 
> {{citation needed}}

I was thinking in particular of the org -> pandoc toolchain. I agree
that org export is pretty rock-solid.

> > One thing that I came out of the conference thinking was that a
> > curated meta-package for Emacs (like elpy) that brought together tools
> > for scholarly writers (in LaTeX and markdown and org-mode) might be a
> > great help for Emacs beginners.
> 
> IMO, we should aim to DISTRIBUTE the needed packages *within* Emacs and
> have SANE defaults.  Even with package.el, maintaining software on a
> computer that you do not have full access to, can be a pain.  The value of
> "batteries included" cannot be emphasized enough!  Instead of adding
> another project to github, it would be better to fix it in Emacs.
>
> EmacsW32 is great in this regard 'cause it's a just a zip, which you can
> use even on constrained systems.  I still have to install AUCTEX and ESS
> "manually", but at least package.el can handle compressed archives.

I think that getting a lot of packages into Emacs and changing the
defaults is a much bigger project, that I wouldn’t be able to help out
with.

best, Erik
--
Sent from my free software system <http://fsf.org/>.