save plot in python babel

save plot in python babel

[Jeremie Juste]

Hello,

I've barely use python with org-mode and I would need some help with the
python setup. I somehow have some trouble saving python plots. Is this the right way
to do it?


#+begin_src python :results output file link :file myfig1.pdf :session *Python*
  import matplotlib
  import numpy as np
  import matplotlib.pyplot as plt
  e_values = np.random.randn(100)
  plt.plot(e_values)
#+end_src


In R things seems to be smoother.

#+begin_src R :results output graphics  :file myfig1.pdf :session *R*
plot(1)
#+end_src

I tried to look around and noticed that the documentation regarding
python with org-mode is aging a bit and there are ob-* all over the
place. [1] ob-ipython does not seem to be maintained, [2] ein on top of ob-python

[1]: https://github.com/gregsexton/ob-ipython
[2]: https://github.com/millejoh/emacs-ipython-notebook


Any help will be appreciated. I'll be ready to improve the documentation of
org-babel python setup as soon as I'm more familiar with it myself.

Best regards,
Jeremie

Re: save plot in python babel

[Jack Kamm]

Hi Jeremie,

> I tried to look around and noticed that the documentation regarding
> python with org-mode is aging a bit...  Any help will be
> appreciated. I'll be ready to improve the documentation of org-babel
> python setup as soon as I'm more familiar with it myself.

Historically ob-python has been a bit broken, especially
sessions. Earlier this year, I started taking care of ob-python and
implemented some fixes [1], which will land in 9.4. When that's
released, I plan to update the outdated worg documentation [2].

> I've barely use python with org-mode and I would need some help with
> the python setup. I somehow have some trouble saving python plots. Is
> this the right way to do it?

This part of the documentation [2], at the bottom of the page, is still
up-to-date. Basically, you need to manually call plt.savefig(), then
return the filename.

> In R things seems to be smoother.

Yes, ob-R is in much better shape. In addition to plotting, returning
dataframes works (pandas DataFrames are not yet supported in
ob-python). I also much prefer the way ob-R returns lists as a column
vector instead of a row vector.

> there are ob-* all over the place. [1] ob-ipython does not seem to be
> maintained

For serious work these days, I'm using ob-jupyter [3], which works
really well. Scimax [4] also has a maintained fork of ob-ipython, though
I haven't tried it.

My goal is to make ob-python a serious alternative to these external
ob-* packages eventually. Here are some of the improvements I have in
mind:

- Improved plotting
- Support for pandas DataFrames and numpy Arrays
- Async session evaluation [5]

I've been delayed working on this as I've gotten very busy due to the
pandemic (I am a bioinformaticist working on SARS-CoV-2 sequencing). But
I'm hoping to make a bit of progress this week, as I'm on vacation and
unable to go outside due to the smoke from the California fires.

It's unclear to me if we're in a feature freeze, so I'm currently
pushing ob-python development to a separate branch [6], which I'll
cherry pick into master after the Org 9.4 release.

[1] https://orgmode.org/list/87pnfdo88v.fsf@gmail.com/
[2] https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html
[3] https://github.com/nnicandro/emacs-jupyter
[4] https://github.com/jkitchin/scimax
[5] https://github.com/jackkamm/ob-session-async
[6] https://code.orgmode.org/jackkamm/org-mode/src/python-develop

Re: save plot in python babel

[Jeremie Juste]

Hello Jack,

Many thanks for having taken the time to reply.
I'll definitely try ob-jupyter. 

>
> My goal is to make ob-python a serious alternative to these external
> ob-* packages eventually. Here are some of the improvements I have in
> mind:
>
> - Improved plotting
> - Support for pandas DataFrames and numpy Arrays
> - Async session evaluation 
yes these improvements would be great. My elisp skills are poor but I'll
be sure to give you feedback on these features.


> I've been delayed working on this as I've gotten very busy due to the
> pandemic (I am a bioinformaticist working on SARS-CoV-2 sequencing). But
> I'm hoping to make a bit of progress this week, as I'm on vacation and
> unable to go outside due to the smoke from the California fires.
>
> It's unclear to me if we're in a feature freeze, so I'm currently
> pushing ob-python development to a separate branch [6], which I'll
> cherry pick into master after the Org 9.4 release.
In your own time will be just fine. I've been only an enthusiastic user
of org-mode until now. I'll go through the manual again and I'll try to
give back what I can.

Stay safe,
Jeremie