Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
On Oct 28, 2009, at 12:19 PM, Eric Schulte wrote: Thomas S. Dye t...@tsdye.com writes: [...] Eric, I think Torsten has a clearer idea than I do about what kinds of programming structures might be appropriate here, but your suggestion looks to me like an elegant replacement for the file based technique I'm using to pass information into 'begin_src latex' blocks now. Expanding the noweb syntax in the way you propose looks extremely useful. I think it introduces an exciting range of possibilities into the workflow I'm developing with org-babel. So, yes, your proposal sounds appropriate to me. Tom This has now been implemented. To try it out grab the most recent version of Org-mode. Changes include - the ability to insert the *results* of source-code blocks through the use of noweb references in which the source-name is followed by ()s, and - the addition of the org-babel-latex.el file which should make it easier to add latex to the languages known to org-babel To try this out please run org-babel-tangle on the attached org-mode file. noweb-eval.org which should result in the attached .tex file somewhere.tex Let me know if I should make any changes to this new setup. Thanks for the ideas. -- Eric Eric, Yes, the expanded noweb syntax works here as advertised. Wonderful. I look forward to making use of it and will take you up on your offer to make changes as new possibilities make themselves known. All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Thomas S. Dye t...@tsdye.com writes: On Oct 27, 2009, at 12:55 PM, Eric Schulte wrote: Although I still don't fully understand the need to embed latex *inside* of source-code blocks, perhaps the attached org-babel-latex.el file [1] will represent a simpler solution for embedding the results of source-code blocks in latex source-code blocks. It makes use of the :var org-babel header argument as shown in the attached example file [2]. To reproduce first load org-babel-latex.el and then evaluate the latex block (note the results are already in the file from my test evaluation). Hope this helps -- Eric Footnotes: [1] org-babel-latex.el [2] latex.org Thanks for this, Eric. It looks neat. I was happy with all the little .tex files, but agree with Torsten that this path is potentially cleaner. Please let me know if you do find this useful or have any suggestions. If it proves useful I will add it to the org-mode repository. In response to the implicit question in your comment, perhaps there isn't a need to embed LaTeX inside source blocks and the uses to which I put them could be accomplished in org-mode without them. My programming skills are pretty crude and I'm aware that I'm a long way from understanding org-mode and its vast potential. With that caveat, here is my $0.02. I'm also very far from taking full advantage of Org-mode export First, practical reasons: 1) I'm comfortable writing LaTeX and am particular about the results; it is hard for me to map the inverse transformation through the org- mode LaTeX exporter to express in org the particular LaTeX result I'm after. 2) Someone on the list (Carsten?) mentioned a couple of days ago that it wasn't reasonable to expect the org LaTeX exporter to capture the full complexity of LaTeX (I'm paraphrasing, but I think that was the gist); I ran up against an example of this (or so I think) when trying to configure export to beamer code, where beamer's use of columns tripped me up. I fully understand your point. I guess that given my personal paucity of latex knowledge and abilities the same need has never occurred to me. In my case the Org-mode exported generally knows more about latex than I do. Second, conceptual reasons: 1) I consider writing LaTeX to be programming (here I mean no disrespect to real programmers) and appreciate being able to do literate LaTeX programming; the LaTeX source blocks let me write my beamer presentation a slide or two at a time, just as I want them, along with an adjacent source block for my print document, just as i want it, that covers the same conceptual space, while I use the surrounding org entries to document why I am doing things a particular way, etc. I see, you are using the org-mode file a level above the direct export. Maybe another option here would be to tag headlines based on which export target they are included within, and then base your exports on the headline tags (using #+EXPORT_INCLUDE_TAGS:), although I agree this also seems like an appropriate place to use the tangle functionality. 2) I think this workflow, with an org-mode meta-document that encapsulates the print document and presentation materials, along with the SQL, R, and Python code used to create the datasets and analyze them, takes org-babel a step closer to realizing its potential as a tool for reproducible research. Here, I am thinking of an org document that captures the ways in which a piece of research is one logical path among many possibilities, implemented and expressed in one particular way (or two, if you want to distinguish print from presentation) among many possibilities. The LaTeX source blocks in org-babel give me an easy and natural way to accomplish these things. In the short time I've used them, they've yielded results that impress me. I'm confident they hold much more potential than I've been able to tap. I didn't mean to imply that because I didn't understand the need for direct inclusion of latex code there *wasn't* a need for direct inclusion of latex code :) Thanks for the explanation. It is a real pleasure leveraging your good work. It is a pleasure to be able to participate in such a nice open-source community. -- Eric Tom ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Dear thread participants, please note that we were breaking the rule of prepending the subject line with the string [babel]! One question inline below. Eric Schulte schulte.e...@gmail.com writes: Thomas S. Dye t...@tsdye.com writes: On Oct 27, 2009, at 12:55 PM, Eric Schulte wrote: Although I still don't fully understand the need to embed latex *inside* of source-code blocks, perhaps the attached org-babel-latex.el file [1] will represent a simpler solution for embedding the results of source-code blocks in latex source-code blocks. It makes use of the :var org-babel header argument as shown in the attached example file [2]. To reproduce first load org-babel-latex.el and then evaluate the latex block (note the results are already in the file from my test evaluation). Hope this helps -- Eric Footnotes: [1] org-babel-latex.el [2] latex.org Thanks for this, Eric. It looks neat. I was happy with all the little .tex files, but agree with Torsten that this path is potentially cleaner. Please let me know if you do find this useful or have any suggestions. If it proves useful I will add it to the org-mode repository. Am I right in thinking that one issue remaining in this thread is that we currently have no means of tangling the output of org-babel-latex? Thus the 'begin_src latex' blocks that we can tangle have unevaluated variables, and the resulting 'begin_latex' blocks have evaluated variables but can't be tangled? (We could extend tangling to cover such blocks, or perhaps preferably use ':results code' to generate 'begin_src latex' blocks?) Dan In response to the implicit question in your comment, perhaps there isn't a need to embed LaTeX inside source blocks and the uses to which I put them could be accomplished in org-mode without them. My programming skills are pretty crude and I'm aware that I'm a long way from understanding org-mode and its vast potential. With that caveat, here is my $0.02. I'm also very far from taking full advantage of Org-mode export First, practical reasons: 1) I'm comfortable writing LaTeX and am particular about the results; it is hard for me to map the inverse transformation through the org- mode LaTeX exporter to express in org the particular LaTeX result I'm after. 2) Someone on the list (Carsten?) mentioned a couple of days ago that it wasn't reasonable to expect the org LaTeX exporter to capture the full complexity of LaTeX (I'm paraphrasing, but I think that was the gist); I ran up against an example of this (or so I think) when trying to configure export to beamer code, where beamer's use of columns tripped me up. I fully understand your point. I guess that given my personal paucity of latex knowledge and abilities the same need has never occurred to me. In my case the Org-mode exported generally knows more about latex than I do. Second, conceptual reasons: 1) I consider writing LaTeX to be programming (here I mean no disrespect to real programmers) and appreciate being able to do literate LaTeX programming; the LaTeX source blocks let me write my beamer presentation a slide or two at a time, just as I want them, along with an adjacent source block for my print document, just as i want it, that covers the same conceptual space, while I use the surrounding org entries to document why I am doing things a particular way, etc. I see, you are using the org-mode file a level above the direct export. Maybe another option here would be to tag headlines based on which export target they are included within, and then base your exports on the headline tags (using #+EXPORT_INCLUDE_TAGS:), although I agree this also seems like an appropriate place to use the tangle functionality. 2) I think this workflow, with an org-mode meta-document that encapsulates the print document and presentation materials, along with the SQL, R, and Python code used to create the datasets and analyze them, takes org-babel a step closer to realizing its potential as a tool for reproducible research. Here, I am thinking of an org document that captures the ways in which a piece of research is one logical path among many possibilities, implemented and expressed in one particular way (or two, if you want to distinguish print from presentation) among many possibilities. The LaTeX source blocks in org-babel give me an easy and natural way to accomplish these things. In the short time I've used them, they've yielded results that impress me. I'm confident they hold much more potential than I've been able to tap. I didn't mean to imply that because I didn't understand the need for direct inclusion of latex code there *wasn't* a need for direct inclusion of latex code :) Thanks for the explanation. It is a real pleasure leveraging your good work. It is a pleasure to be able to participate in such a nice open-source community. -- Eric Tom
Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
On Oct 28, 2009, at 5:19 AM, Eric Schulte wrote: I see, you are using the org-mode file a level above the direct export. Maybe another option here would be to tag headlines based on which export target they are included within, and then base your exports on the headline tags (using #+EXPORT_INCLUDE_TAGS:), although I agree this also seems like an appropriate place to use the tangle functionality. Eric, Thanks for pointing this out. I'll look into this option. All the best, Tom ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Dan Davison davi...@stats.ox.ac.uk writes: Am I right in thinking that one issue remaining in this thread is that we currently have no means of tangling the output of org-babel-latex? Thus the 'begin_src latex' blocks that we can tangle have unevaluated variables, and the resulting 'begin_latex' blocks have evaluated variables but can't be tangled? (We could extend tangling to cover such blocks, or perhaps preferably use ':results code' to generate 'begin_src latex' blocks?) Sorry, I see. 'begin_latex' is inserted directly into latex export and omitted from other export targets. Still, it might sometimes be useful to use the tangling machinery in which case ':results code' is what is needed. Dan Dan In response to the implicit question in your comment, perhaps there isn't a need to embed LaTeX inside source blocks and the uses to which I put them could be accomplished in org-mode without them. My programming skills are pretty crude and I'm aware that I'm a long way from understanding org-mode and its vast potential. With that caveat, here is my $0.02. I'm also very far from taking full advantage of Org-mode export First, practical reasons: 1) I'm comfortable writing LaTeX and am particular about the results; it is hard for me to map the inverse transformation through the org- mode LaTeX exporter to express in org the particular LaTeX result I'm after. 2) Someone on the list (Carsten?) mentioned a couple of days ago that it wasn't reasonable to expect the org LaTeX exporter to capture the full complexity of LaTeX (I'm paraphrasing, but I think that was the gist); I ran up against an example of this (or so I think) when trying to configure export to beamer code, where beamer's use of columns tripped me up. I fully understand your point. I guess that given my personal paucity of latex knowledge and abilities the same need has never occurred to me. In my case the Org-mode exported generally knows more about latex than I do. Second, conceptual reasons: 1) I consider writing LaTeX to be programming (here I mean no disrespect to real programmers) and appreciate being able to do literate LaTeX programming; the LaTeX source blocks let me write my beamer presentation a slide or two at a time, just as I want them, along with an adjacent source block for my print document, just as i want it, that covers the same conceptual space, while I use the surrounding org entries to document why I am doing things a particular way, etc. I see, you are using the org-mode file a level above the direct export. Maybe another option here would be to tag headlines based on which export target they are included within, and then base your exports on the headline tags (using #+EXPORT_INCLUDE_TAGS:), although I agree this also seems like an appropriate place to use the tangle functionality. 2) I think this workflow, with an org-mode meta-document that encapsulates the print document and presentation materials, along with the SQL, R, and Python code used to create the datasets and analyze them, takes org-babel a step closer to realizing its potential as a tool for reproducible research. Here, I am thinking of an org document that captures the ways in which a piece of research is one logical path among many possibilities, implemented and expressed in one particular way (or two, if you want to distinguish print from presentation) among many possibilities. The LaTeX source blocks in org-babel give me an easy and natural way to accomplish these things. In the short time I've used them, they've yielded results that impress me. I'm confident they hold much more potential than I've been able to tap. I didn't mean to imply that because I didn't understand the need for direct inclusion of latex code there *wasn't* a need for direct inclusion of latex code :) Thanks for the explanation. It is a real pleasure leveraging your good work. It is a pleasure to be able to participate in such a nice open-source community. -- Eric Tom ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
On Oct 28, 2009, at 6:10 AM, Dan Davison wrote: Dear thread participants, please note that we were breaking the rule of prepending the subject line with the string [babel]! One question inline below. Eric Schulte schulte.e...@gmail.com writes: Thomas S. Dye t...@tsdye.com writes: On Oct 27, 2009, at 12:55 PM, Eric Schulte wrote: Although I still don't fully understand the need to embed latex *inside* of source-code blocks, perhaps the attached org-babel-latex.el file [1] will represent a simpler solution for embedding the results of source-code blocks in latex source-code blocks. It makes use of the :var org-babel header argument as shown in the attached example file [2]. To reproduce first load org-babel-latex.el and then evaluate the latex block (note the results are already in the file from my test evaluation). Hope this helps -- Eric Footnotes: [1] org-babel-latex.el [2] latex.org Thanks for this, Eric. It looks neat. I was happy with all the little .tex files, but agree with Torsten that this path is potentially cleaner. Please let me know if you do find this useful or have any suggestions. If it proves useful I will add it to the org-mode repository. Am I right in thinking that one issue remaining in this thread is that we currently have no means of tangling the output of org-babel-latex? Thus the 'begin_src latex' blocks that we can tangle have unevaluated variables, and the resulting 'begin_latex' blocks have evaluated variables but can't be tangled? (We could extend tangling to cover such blocks, or perhaps preferably use ':results code' to generate 'begin_src latex' blocks?) Dan Hi Dan, I haven't found time to evaluate org-babel-latex, but, yes, the example provided with the code raised a concern that the 'begin_latex' blocks are divorced from the literate programming structure built up by the named 'begin_src latex' blocks. Ideally, I think, the 'begin_latex' blocks would replace noweb references to their source 'begin_src latex' blocks, or would employ some other mechanism that doesn't break the literate programming structure I create. Tom ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
[cc'ing list who were accidentally omitted]
Torsten Wagner torsten.wag...@gmail.com writes:
Hi Dan,
1. Hiding of the source code blocks for export
I like to export the results of the source code block to LaTeX only.
However,
Using ':exports results' specifies that only the results should appear
in the exported document. This
#+begin_src python :exports results
6 + 6
#+end_src
Hi Torsten
I tried this but the result is first the source code block followed by the
result:
If it's not working, could you provide the exact example and tell us
your operating system, git version etc?
Furthermore, I tried to create some LaTeX code as result of the code block
You need to use the ':results latex' header if you want the result to be
output as latex.
...
In general I could try to use org-mode as much as possible. However, in that
special case I like to merge three (or more) documents together.
1. The source code (e.g. python)
2. A laboratory journal (this would use org-mode magic)
3. An official report e.g. a manuscript to be submitted to a journal (this
would be a LaTeX file)
The idea is to be able to merge all this together to make sure data
manipulation and calculus (source code) are as close as possible to the
specific journal entry, which may supply additional important information and
the final manuscript snippets which presents officially the particular result.
A short example would be (without real headers)
--8--8---
* 23.10.09
Measurement this morning was performed as usual but this time without warm up
of device foo.
Measurement file is saved under _link_.
TODO: Don't forget to prepare for meeting tomorrow
Python
for foo import *
a = load(data.csv)
b = apply_filter(a,lp)
plot(b)
saveplot(bar.pdf)
Python
OK, currently, the way to do that is something like
#+srcname: pyplot(file=bar.pdf)
#+begin_src python :results file
plot(outfile=file)
file
#+end_src
#+resname: pyplot
[[file:bar.pdf]]
Note that for a generalist language like python (which does not always
create output to file) you currently need to
1. specify that it outputs a file with ':results file'
2. explicitly send output to the file in your python code
3. explicitly return the filepath as a string at the end of the
block. it will get inserted as a link.
You have the option of not hard-wiring the filepath in the python code
by using a variable as I did there.
[We may want to change this so that (3) happens automatically when
':file filepath' or ':results file' is provided]
First low pass filter was applied then a plot is generated
This plot will be used in publication for journal foo
DEADLINE: 2009-12-14 Mo
LaTeX
\begin{figure}
\includegraphics{bar.pdf}
\end{figure}
LaTeX
To avoid hard-wiring the filename into the latex block you could use the
org-babel-latex.el that Eric has posted.
--8--8---
Text outside should be org-mode text.
Now I like to export with three scenarios
1. Only the LaTeX part (e.g. by using tangle) resulting in a pure native
LaTeX-file ready for submission
See emails in the concurrent main thread on this topic.
Above example will result in
\begin{figure}
\includegraphics{bar.pdf}
\end{figure}
2. The LaTeX part and the org-mode parts whereas the LaTeX blocks should be
somehow verbatim
or in a some way marked inline. Above example should result in a LaTeX export
like
'begin_src latex' blocks are exported as code blocks with appropriate
fontification under org-mode.
I hope this is getting clearer now :)
Dan
\section{23.10.09}
Measurement this morning was performed as usual but this time without warm up
time.
Measurement file is saved under \footnote[/home/foo/data.csv]{link}.
First low pass filter was applied then a plot is generated
This plot will be used in publication for journal foo
\begin{minipage}
\begin{figure}
\includegraphics{bar.pdf}
\end{figure}
\end{minipage}
3. Export of all which will include the python blocks in a inline form as
well.
First of all I would be happy if I could avoid to have the source code blocks
in the export file.
I simply like to generate LaTeX-snipplets in python and export a LaTeX file
finally.
Thus,
#+srcname: LaTeX
#+begin_src python :session :exports results
plot([1,2,3,4,5],[2,4,6,8,10])
savefig(file,f-acecolor='w', edgecolor='w',format=None)
param1 = 19.7
perf = 77
#+end_src
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Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Thomas S. Dye t...@tsdye.com writes:
On Oct 28, 2009, at 6:10 AM, Dan Davison wrote:
Am I right in thinking that one issue remaining in this thread is that
we currently have no means of tangling the output of org-babel-latex?
Thus the 'begin_src latex' blocks that we can tangle have unevaluated
variables, and the resulting 'begin_latex' blocks have evaluated
variables but can't be tangled? (We could extend tangling to cover
such
blocks, or perhaps preferably use ':results code' to generate
begin_src
latex' blocks?)
Dan
Hi Dan,
I haven't found time to evaluate org-babel-latex, but, yes, the
example provided with the code raised a concern that the 'begin_latex'
blocks are divorced from the literate programming structure built up
by the named 'begin_src latex' blocks. Ideally, I think, the
begin_latex' blocks would replace noweb references to their
source 'begin_src latex' blocks, or would employ some other mechanism
that doesn't break the literate programming structure I create.
I just started a new branch [1] in the org-mode/babel [2] repository
where we should be able to implement a solution without too much
trouble. If we expand the noweb syntax such that if a source-code block
name has parenthesis () appended to the end of it's name, then the
block will be evaluated during noweb reference expansion and it's
results will be placed in the source-code block. That structure should
even allow simple literal arguments to be passed to the referenced
block.
So for example what I'm proposing is that in the following case this
--8---cut here---start-8---
#+srcname: noweb-example
#+begin_src python :var a=0
a+10
#+end_src
#+begin_src latex :tangle somewhere
\begin{itemize}
\item noweb-example
\item noweb-example()
\item noweb-example(a=8)
\end{itemize}
#+end_src
--8---cut here---end---8---
would tangle to somewhere.tex as
--8---cut here---start-8---
\begin{itemize}
\item a+10
\item 10
\item 18
\end{itemize}
--8---cut here---end---8---
Does that sound appropriate? -- Eric
Footnotes:
[1]
http://repo.or.cz/w/org-mode/babel.git?a=shortlog;h=refs/heads/noweb-evaluate
[2] http://repo.or.cz/w/org-mode/babel.git
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Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
On Oct 28, 2009, at 7:15 AM, Eric Schulte wrote:
Thomas S. Dye t...@tsdye.com writes:
On Oct 28, 2009, at 6:10 AM, Dan Davison wrote:
Am I right in thinking that one issue remaining in this thread is
that
we currently have no means of tangling the output of org-babel-
latex?
Thus the 'begin_src latex' blocks that we can tangle have
unevaluated
variables, and the resulting 'begin_latex' blocks have evaluated
variables but can't be tangled? (We could extend tangling to cover
such
blocks, or perhaps preferably use ':results code' to generate
begin_src
latex' blocks?)
Dan
Hi Dan,
I haven't found time to evaluate org-babel-latex, but, yes, the
example provided with the code raised a concern that the
'begin_latex'
blocks are divorced from the literate programming structure built up
by the named 'begin_src latex' blocks. Ideally, I think, the
begin_latex' blocks would replace noweb references to their
source 'begin_src latex' blocks, or would employ some other mechanism
that doesn't break the literate programming structure I create.
I just started a new branch [1] in the org-mode/babel [2] repository
where we should be able to implement a solution without too much
trouble. If we expand the noweb syntax such that if a source-code
block
name has parenthesis () appended to the end of it's name, then the
block will be evaluated during noweb reference expansion and it's
results will be placed in the source-code block. That structure
should
even allow simple literal arguments to be passed to the referenced
block.
So for example what I'm proposing is that in the following case this
--8---cut here---start-8---
#+srcname: noweb-example
#+begin_src python :var a=0
a+10
#+end_src
#+begin_src latex :tangle somewhere
\begin{itemize}
\item noweb-example
\item noweb-example()
\item noweb-example(a=8)
\end{itemize}
#+end_src
--8---cut here---end---8---
would tangle to somewhere.tex as
--8---cut here---start-8---
\begin{itemize}
\item a+10
\item 10
\item 18
\end{itemize}
--8---cut here---end---8---
Does that sound appropriate? -- Eric
Footnotes:
[1]
http://repo.or.cz/w/org-mode/babel.git?a=shortlog;h=refs/heads/noweb-evaluate
[2] http://repo.or.cz/w/org-mode/babel.git
Eric,
I think Torsten has a clearer idea than I do about what kinds of
programming structures might be appropriate here, but your suggestion
looks to me like an elegant replacement for the file based technique
I'm using to pass information into 'begin_src latex' blocks now.
Expanding the noweb syntax in the way you propose looks extremely
useful. I think it introduces an exciting range of possibilities into
the workflow I'm developing with org-babel. So, yes, your proposal
sounds appropriate to me.
Tom
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Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Thomas S. Dye t...@tsdye.com writes: [...] Eric, I think Torsten has a clearer idea than I do about what kinds of programming structures might be appropriate here, but your suggestion looks to me like an elegant replacement for the file based technique I'm using to pass information into 'begin_src latex' blocks now. Expanding the noweb syntax in the way you propose looks extremely useful. I think it introduces an exciting range of possibilities into the workflow I'm developing with org-babel. So, yes, your proposal sounds appropriate to me. Tom This has now been implemented. To try it out grab the most recent version of Org-mode. Changes include - the ability to insert the *results* of source-code blocks through the use of noweb references in which the source-name is followed by ()s, and - the addition of the org-babel-latex.el file which should make it easier to add latex to the languages known to org-babel To try this out please run org-babel-tangle on the attached org-mode file. noweb-eval.org Description: Binary data which should result in the attached .tex file somewhere.tex Description: TeX document Let me know if I should make any changes to this new setup. Thanks for the ideas. -- Eric ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
On Oct 26, 2009, at 2:24 PM, Dan Davison wrote:
Torsten Wagner torsten.wag...@gmail.com writes:
...
...
The inline code blocks will not be processed inside source blocks. I'm
not sure how to achieve what you want with the current machinery, but
have you read the recent posts by Thomas Dye describing how he uses
latex blocks with org-babel? In particular you should look at the
noweb
reference expansions. These are also documented on the Worg page. In
general of course, the more you can write in org rather than latex,
the
more functionality you'll get out of org-babel. Is it possible write
the
abstract in org and defer export to latex?
...
Hi Torsten,
Perhaps this will do what you want? When I run org-babel-tangle on
the following org file, and then LaTeX the output, the resulting pdf
file says: A bit of LATEX code, with the result: 6
* Test org
#+begin_src python
x = 6
f = open('python_results.tex', 'w')
f.write(str(x))
f.close()
#+end_src
#+resname:
: None
#+begin_src latex :tangle test_arg_passing
\documentclass{article}
\begin{document}
A bit of \LaTeX code, with the result: \input{python_results}
\end{document}
#+end_src
HTH,
Tom
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Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Ups, sorry that happens if you are working normally with emacs and compose a message in a online editor (gmail). My fingers hit some emacs shortcuts without my brain was telling them ;) ... and fired up the unfinished mail. Anyhow I hope it is somehow clear what I like to do Thus, just the greetings where missing Thanks for help and reading Torsten ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Perhaps this will do what you want? When I run org-babel-tangle on the
following org file, and then LaTeX the output, the resulting pdf file
says: A bit of LATEX code, with the result: 6
* Test org
#+begin_src python
x = 6
f = open('python_results.tex', 'w')
f.write(str(x))
f.close()
#+end_src
#+resname:
: None
#+begin_src latex :tangle test_arg_passing
\documentclass{article}
\begin{document}
A bit of \LaTeX code, with the result: \input{python_results}
\end{document}
#+end_src
HTH,
Tom
Hi Tom
Thanks for sharing this idea. Actually my first (org-babel free) attempt was
working like that. However, it becomes fast difficult and complex. On the
other hand it solves nicely the problem with the code evaluation in another
source block. I just wonder if there is a more comfortable method rather
then creating a file.
Thanks again for sharing
Torsten
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Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
On Oct 27, 2009, at 12:55 PM, Eric Schulte wrote: Torsten Wagner torsten.wag...@gmail.com writes: Perhaps this will do what you want? When I run org-babel-tangle on the following org file, and then LaTeX the output, the resulting pdf file says: A bit of LATEX code, with the result: 6 I just wonder if there is a more comfortable method rather then creating a file. Although I still don't fully understand the need to embed latex *inside* of source-code blocks, perhaps the attached org-babel-latex.el file [1] will represent a simpler solution for embedding the results of source-code blocks in latex source-code blocks. It makes use of the :var org-babel header argument as shown in the attached example file [2]. To reproduce first load org-babel-latex.el and then evaluate the latex block (note the results are already in the file from my test evaluation). Hope this helps -- Eric Footnotes: [1] org-babel-latex.el [2] latex.org Thanks for this, Eric. It looks neat. I was happy with all the little .tex files, but agree with Torsten that this path is potentially cleaner. In response to the implicit question in your comment, perhaps there isn't a need to embed LaTeX inside source blocks and the uses to which I put them could be accomplished in org-mode without them. My programming skills are pretty crude and I'm aware that I'm a long way from understanding org-mode and its vast potential. With that caveat, here is my $0.02. First, practical reasons: 1) I'm comfortable writing LaTeX and am particular about the results; it is hard for me to map the inverse transformation through the org- mode LaTeX exporter to express in org the particular LaTeX result I'm after. 2) Someone on the list (Carsten?) mentioned a couple of days ago that it wasn't reasonable to expect the org LaTeX exporter to capture the full complexity of LaTeX (I'm paraphrasing, but I think that was the gist); I ran up against an example of this (or so I think) when trying to configure export to beamer code, where beamer's use of columns tripped me up. Second, conceptual reasons: 1) I consider writing LaTeX to be programming (here I mean no disrespect to real programmers) and appreciate being able to do literate LaTeX programming; the LaTeX source blocks let me write my beamer presentation a slide or two at a time, just as I want them, along with an adjacent source block for my print document, just as i want it, that covers the same conceptual space, while I use the surrounding org entries to document why I am doing things a particular way, etc. 2) I think this workflow, with an org-mode meta-document that encapsulates the print document and presentation materials, along with the SQL, R, and Python code used to create the datasets and analyze them, takes org-babel a step closer to realizing its potential as a tool for reproducible research. Here, I am thinking of an org document that captures the ways in which a piece of research is one logical path among many possibilities, implemented and expressed in one particular way (or two, if you want to distinguish print from presentation) among many possibilities. The LaTeX source blocks in org-babel give me an easy and natural way to accomplish these things. In the short time I've used them, they've yielded results that impress me. I'm confident they hold much more potential than I've been able to tap. It is a real pleasure leveraging your good work. Tom ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment
Torsten Wagner torsten.wag...@gmail.com writes:
...
Within a LaTeX-file (org-file) I like to use python snippets to perform
calculus
and other tasks which are otherwise extremely difficult or time consuming to
perform directly in LaTeX. E.g. on-the-fly-generation of graphs or calculus
of
statistical values (e.g., (very simple) the mean value of n numbers).
I guess org-mode together with org-babel can do most of this already. I
played
around with it and it is very nice, many thanks to the developers. However, I
found the following point which I wasn't able to figure out yet.
Hi Torsten,
1. Hiding of the source code blocks for export
I like to export the results of the source code block to LaTeX only. However,
Using ':exports results' specifies that only the results should appear
in the exported document. This
#+begin_src python :exports results
6 + 6
#+end_src
is exported to latex as this:
\begin{verbatim}
12
\end{verbatim}
Is that working for you?
I tried different options all resulting in embedding the source-code itself
inside the final LaTeX file. I guess this is more due to the org-export
function
rather then org-babel
2. Inline source code blocks
I guess this was discussed once already. Instead of a verbose source code
block a single short command to elaborate a python variable or a one line
calculus would be nice e.g., #:session_name a# to replace this command by
the results of variable a of the session session_name during the export to
LaTeX.
Yes, you can do that (and it is now doumented on worg). The syntax for
that is src_lang[optional header args]{code}
See below for examples.
I like to combine this with a little python module specialised in creating
proper LaTeX export for all kind of python data types.
E.g. tab_export([1,2,3,4,5]) could generate the string 1 2 3 4 5 \\
The idea is to use this as a form of reproducible research allowing the data
evaluation together with the textual and graphical representation.
Furthermore, I would like to use org as a publication system with meta-
description capabilities. This would allow to commentary what someone is
doing
between the lines. By this one could merge somehow the lab-book, data
analysis and the final paper into one org-file (or org-project) and keep
always
all infos and data close together
Something like (pseudo code):
/-/
12.03.2148: Scotty
I'm going to create a better warp drive system:
...
First measurements should show the better efficiency. The old set-up is moved
to
the lab downstairs the old measurement files back-up is at
First lets load the values and calculate the performance:
#+srcname: measurement
#+begin_src python
data=load(measurement.csv)
perf = calculate_performance(data.values)
#+end_src
This was the final measurement performed with the new set-up. It shows
already
the nice improvements...
Just some infos of the measurement
Measurement date: #:measurement data.date#
Measurement parameter: #:measurement data.param1#
You can use inline blocks as follows. Note that the source block needs
to be evaluated to ensure that the variables exist in the session (hence
the :exports results header)
--8---cut here---start-8---
#+srcname: measurement
#+begin_src python :session :exports results
date = 12.03.2148
param1 = 19.7
perf = 77
#+end_src
Measurement date: src_python[:session]{date}
Measurement parameter: src_python[:session]{param1}
--8---cut here---end---8---
13.3.2148: Scotty
Spoke told me it could be better by performing a new warp-core calibration...
However, I could write the abstract already:
#+srcname: paper_for_star_fleet_physics_journal
#+begin_src LaTeX
\begin{abstract}
the new set-up shows a $#:measurement perf#,/%$ better perfomance then
the old warp drive...
\end{abstract}
#+end_src
The inline code blocks will not be processed inside source blocks. I'm
not sure how to achieve what you want with the current machinery, but
have you read the recent posts by Thomas Dye describing how he uses
latex blocks with org-babel? In particular you should look at the noweb
reference expansions. These are also documented on the Worg page. In
general of course, the more you can write in org rather than latex, the
more functionality you'll get out of org-babel. Is it possible write the
abstract in org and defer export to latex?
...
I hope this gives an idea of what I like to do. :)
Export should allow selections like export all (including comment texts and
source code blocks), export without source code blocks and export results
only. The last one would produce the native LaTeX code ready for submission.
This would allow to process the file with any standard LaTeX environment.
The Worg page says
,
| exports
|
