Switch jsmol to jupyter-jsmol #30315

mkoeppe · 2020-08-07T18:26:49Z

Currently, jsmol is installed by the jmol spkg and then symlinked into the jupyter notebook directory.

In this ticket, we switch to https://pypi.org/project/jupyter-jsmol/ (https://github.com/fekad/jupyter-jsmol), which can be installed by standard Python tools.

Discussion: https://groups.google.com/g/sage-devel/c/qKqTmLzHAbg/m/6YxQ_qWUBQAJ

See also:

Update jmol to 14.32.35, add spkg-configure for jmol #30316 - Update jmol to 14.31.2, add spkg-configure for jmol
Make jmol optional #31027 - Make jmol optional

Depends on #31002

CC: @kcrisman @novoselt @fchapoton @antonio-rojas @kiwifb @slel @nbruin @paulmasson @egourgoulhon @kwankyu @enriqueartal @jcamp0x2a

Component: packages: standard

Keywords: sd111

Author: Matthias Koeppe

Branch/Commit: 80a3db1

Reviewer: Joshua Campbell

Issue created by migration from https://trac.sagemath.org/ticket/30315

The text was updated successfully, but these errors were encountered:

mkoeppe · 2020-08-08T05:50:17Z

comment:2

(deleted)

mkoeppe · 2020-08-08T05:56:39Z

comment:3

./sage -pip install jupyter-jsmol installs proper nbextensions:

$ jupyter nbextension list
Known nbextensions:
  config dir: /Users/mkoeppe/s/sage/sage-rebasing/local/etc/jupyter/nbconfig
    notebook section
      jupyter_jsmol/extension  enabled 
      - Validating: OK
      jupyter-js-widgets/extension  enabled 
      - Validating: OK

The installed files can be seen in $SAGE_LOCAL/share/jupyter/nbextensions/jupyter_jsmol/

mkoeppe · 2020-11-29T06:58:09Z

Branch: u/mkoeppe/switch_jsmol_to_jupyter_jsmol__make_jmol_optional

mkoeppe · 2020-11-29T07:00:27Z

Commit: ac1ab7c

mkoeppe · 2020-11-29T07:00:27Z

New commits:

`6617f87`	`build/pkgs/jupyter_jsmol: New`
`cbaf661`	`build/pkgs/jmol/spkg-install.in: No longer install jsmol`
`2ca5328`	`sage.repl.display.jsmol_iframe: Adjust path to jsmol`
`ac1ab7c`	`sage.repl.ipython_kernel.install: No longer symlink jsmol`

mkoeppe · 2020-11-29T07:00:27Z

Author: Matthias Koeppe

sagetrac-git · 2020-11-29T07:02:28Z

Branch pushed to git repo; I updated commit sha1. New commits:

`e6ebaf7`	`build/pkgs/jupyter_jsmol: Add dependencies, install-requires.txt`

sagetrac-git · 2020-11-29T07:02:28Z

Changed commit from ac1ab7c to e6ebaf7

mkoeppe · 2020-11-29T07:05:17Z

comment:9

sagetex declares jmol as a dependency - what is it used for?

kcrisman · 2020-11-29T21:11:58Z

comment:10

sagetex declares jmol as a dependency - what is it used for?

I think for generating a 3d image in its documentation, compilation of which is part of its test suite.

mkoeppe · 2020-12-06T18:17:38Z

comment:11

Hoping we can make progress on this ticket this week - https://wiki.sagemath.org/days111

mkoeppe · 2020-12-06T18:17:38Z

Changed keywords from none to sd111

mkoeppe · 2020-12-07T04:07:27Z

Dependencies: #31020

sagetrac-git · 2020-12-07T04:09:29Z

Changed commit from e6ebaf7 to 6a549d9

sagetrac-git · 2020-12-07T04:09:29Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`21259b2`	`build/pkgs/jupyter_jsmol: New`
`b5f5f43`	`build/pkgs/jmol/spkg-install.in: No longer install jsmol`
`a0fe543`	`sage.repl.display.jsmol_iframe: Adjust path to jsmol`
`6e24bc0`	`sage.repl.ipython_kernel.install: No longer symlink jsmol`
`52803b4`	`build/pkgs/jupyter_jsmol: Add dependencies, install-requires.txt`
`7194459`	`build/pkgs/jmol/type: Make it optional`
`0ed256c`	`build/make/Makefile.in: Compute SAGE_CHECK_... earlier, before evaluating dependencies`
`1f714c1`	`build/pkgs/sagetex/dependencies: Conditionalize order-only deps on SAGE_CHECK_sagetex`
`6a549d9`	`Merge branch 't/31020/build_make_makefile_in__fix_sage_check_logic__conditionalize_sagetex_dependencies_on_sage_check' into t/30315/switch_jsmol_to_jupyter_jsmol__make_jmol_optional`

mkoeppe · 2020-12-07T04:10:39Z

comment:14

Replying to @kcrisman:

sagetex declares jmol as a dependency - what is it used for?

I think for generating a 3d image in its documentation, compilation of which is part of its test suite.

Thanks! I have adjusted the dependencies in #31020 (now a dependency) so that jmol is only treated as a dependency when SAGE_CHECK is active.

sagetrac-git · 2020-12-07T04:34:52Z

Changed commit from 6a549d9 to ae970c2

sagetrac-git · 2020-12-07T04:34:52Z

Branch pushed to git repo; I updated commit sha1. New commits:

`3a45d72`	`build/pkgs/jupyter_jsmol/spkg-install.in: Do not rebuild the javascript file`
`a8e0364`	`Specify bdist temp folder for WSL compatibility`
`a3077c7`	`Use mktemp`
`c5a14a3`	`build/bin/sage-dist-helpers (sdh_setup_bdist_wheel): New`
`fb10429`	`build/pkgs/*/spkg-install.in: Use new function sdh_setup_bdist_wheel`
`32bf463`	`Merge branch 't/31002/public/build/bdist_wsl' into t/30315/switch_jsmol_to_jupyter_jsmol__make_jmol_optional`
`ae970c2`	`build/pkgs/jupyter_jsmol/spkg-install.in: Use new function sdh_setup_bdist_wheel`

mkoeppe · 2020-12-07T04:45:13Z

Changed dependencies from #31020 to #31002, #31020

kcrisman · 2020-12-07T13:12:25Z

comment:18

That is not a good idea. Because we want people to be able to build the documentation for SageTeX, which after all isn't "really" upstream. Instead, we should see if jsmol or some other tool suffices to build 3d pictures in SageTeX, which is a very useful use case for it. Untested = broken, and I don't think that we've ever had a dependency only in SAGE_CHECK before.

kcrisman · 2020-12-07T13:12:53Z

comment:19

and I don't think that we've ever had a dependency only in SAGE_CHECK before.

Though my info on the build system is pretty outdated :-)

novoselt · 2020-12-07T20:32:00Z

comment:22

Replying to @kcrisman:

Interesting. I wonder whether jsmol might be a drop-in replacement for this specific use case though. Or even Tachyon ...

What's the status of generating 3D plots and saving them using threejs? I think for SageTeX it is irrelevant what is producing pictures, just show that it works well. Tachyon is not the best in this regard.

mkoeppe · 2020-12-07T23:35:11Z

comment:23

A discussion has unfolded in https://groups.google.com/g/sage-devel/c/qKqTmLzHAbg/m/6YxQ_qWUBQAJ

sagetrac-git · 2020-12-08T01:50:02Z

Changed commit from ae970c2 to bf3c1dc

sagetrac-git · 2020-12-08T01:50:02Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`e57f927`	`Merge branch 't/31002/public/build/bdist_wsl' into t/30315/switch_jsmol_to_jupyter_jsmol__make_jmol_optional`
`017b816`	`build/pkgs/jupyter_jsmol: New`
`db1b38c`	`build/pkgs/jmol/spkg-install.in: No longer install jsmol`
`95a7131`	`sage.repl.display.jsmol_iframe: Adjust path to jsmol`
`98b83f5`	`sage.repl.ipython_kernel.install: No longer symlink jsmol`
`40a8823`	`build/pkgs/jupyter_jsmol: Add dependencies, install-requires.txt`
`bf3c1dc`	`build/pkgs/jupyter_jsmol/spkg-install.in: Do not rebuild the javascript file`

mkoeppe · 2020-12-08T01:52:26Z

Changed dependencies from #31002, #31020 to #31002

mkoeppe · 2020-12-08T01:52:26Z

comment:26

I have narrowed this ticket to only separating the jmol and jsmol installation.

mkoeppe · 2020-12-08T01:53:17Z

comment:27

Making jmol optional, and the discussion about new technologies to create images from 3d graphics, is now on #31027.

jcamp0x2a · 2020-12-08T18:14:04Z

comment:28

I was able to verify that JSmol still works correctly in both Jupyter and JupyterLab. However, I did notice a test failure in src/sage/repl/ipython_kernel/install.py due to the new deprecation warning:

File "src/sage/repl/ipython_kernel/install.py", line 142, in sage.repl.ipython_kernel.install.SageKernelSpec.use_local_jsmol
Failed example:
    spec.use_local_jsmol()
Expected nothing
Got:
    doctest:warning
      File "/home/joshua/sage/src/bin/sage-runtests", line 182, in <module>
        err = DC.run()
    [...]
    :
    DeprecationWarning: Symlinking jsmol is no longer necessary
    See https://trac.sagemath.org/30315 for details.

Also, after removing the local/share/jsmol folder since it is no longer needed (and wouldn't be present on a clean install), I get a couple more test failures in the same file:

File "src/sage/repl/ipython_kernel/install.py", line 144, in sage.repl.ipython_kernel.install.SageKernelSpec.use_local_jsmol
Failed example:
    os.path.isdir(jsmol)
Expected:
    True
Got:
    False

and

File "src/sage/repl/ipython_kernel/install.py", line 146, in sage.repl.ipython_kernel.install.SageKernelSpec.use_local_jsmol
Failed example:
    os.path.isfile(os.path.join(jsmol, "JSmol.min.js"))
Expected:
    True
Got:
    False

sagetrac-git · 2020-12-09T00:53:26Z

Branch pushed to git repo; I updated commit sha1. New commits:

`f2a02d9`	`Get rid of JSMOL_DIR`
`7732e2e`	`build/pkgs/jmol/SPKG.rst: Update`

sagetrac-git · 2020-12-09T00:53:26Z

Changed commit from bf3c1dc to 7732e2e

mkoeppe · 2020-12-09T00:55:15Z

comment:30

Thanks. This function, after all, does not make sense any more, so there's no point in trying to go through deprecation. I have now removed it completely (alongside with the variable JSMOL_DIR).

jcamp0x2a · 2020-12-09T16:41:36Z

comment:31

Looks good. JSmol still works in Jupyter and JupyterLab.

jcamp0x2a · 2020-12-09T16:41:36Z

Reviewer: Joshua Campbell

mkoeppe · 2020-12-09T19:59:21Z

comment:32

Thank you!

sagetrac-git · 2020-12-10T00:56:37Z

Changed commit from 7732e2e to 80a3db1

sagetrac-git · 2020-12-10T00:56:37Z

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

`80a3db1`	`build/pkgs/jupyter_jsmol/spkg-install.in: Use sdh_setup_bdist_wheel`

mkoeppe · 2020-12-10T00:57:13Z

comment:34

Forgot to actually use #31002 - this change is necessary for correct installation on WSL

jcamp0x2a · 2020-12-10T02:01:03Z

comment:35

Replying to @mkoeppe:

Forgot to actually use #31002 - this change is necessary for correct installation on WSL

Ok. I tested this on Ubuntu WSL earlier without any installation issues. If I understand #31002 correctly, the problem was occurring due to mounting Windows folders, which I'm not doing, so that's probably why I didn't run into it.

I've gone ahead and re-verified that JSmol still works in Jupyter and JupyterLab.

mkoeppe · 2020-12-10T03:16:51Z

comment:36

Thanks again!

vbraun · 2020-12-13T20:30:50Z

Changed branch from u/mkoeppe/switch_jsmol_to_jupyter_jsmol__make_jmol_optional to 80a3db1

mkoeppe added this to the sage-9.2 milestone Aug 7, 2020

mkoeppe added c: packages: standard labels Aug 7, 2020

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mkoeppe modified the milestones: sage-9.2, sage-9.3 Aug 13, 2020

mkoeppe added the s: needs review label Nov 29, 2020

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mkoeppe changed the title ~~Switch jsmol to jupyter-jsmol, make jmol optional~~ Switch jsmol to jupyter-jsmol Dec 8, 2020

jcamp0x2a mannequin added s: positive review and removed s: needs review labels Dec 9, 2020

sagetrac-git mannequin added s: needs review and removed s: positive review labels Dec 10, 2020

jcamp0x2a mannequin added s: positive review and removed s: needs review labels Dec 10, 2020

vbraun removed the s: positive review label Dec 13, 2020

vbraun closed this as completed in 6bde0c0 Dec 13, 2020

Switch jsmol to jupyter-jsmol #30315

Switch jsmol to jupyter-jsmol #30315

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