Small improvements

[Luthaf]

Fix #392

[bernstei]

Great - I thought I tried scale, but maybe not (or maybe I did it wrong)

[ceriottm]

LGTM and works locally on my side

[bernstei]

FWIW, I have no easy way of testing this because when I try to install from the repo I get errors about missing rust, but when I edit ~/.local/.../chemiscope/sphinx/static/chemiscope.min.js, find the JS code that saves the PNG chemiscope map and add a scale:3 argument I don't actually get saved bitmaps larger than 600x600 (after restarting both the jupyter server and the notebook kernel).

[ceriottm]

It's very strange that you get errors about rust - it might be needed for the optional dependency metatensor, but not for just pip install . checked more thoroughly and it does save at 1800px minimum size from firefox and chrome, both with the web interface and jupyter. @Luthaf can check on safari, I cannot ^_^

[Luthaf]

Rust should not even be needed for metatensor, since pip should use the pre-built wheels and not build from source.

[Luthaf]

@bernstei you could also try to install the wheel built by CI for this PR by downloading https://github.com/lab-cosmo/chemiscope/actions/runs/11822592226/artifacts/2183374870, unziping and then running pip install ./<path/to>/chemiscope*.whl.

[bernstei]

I thought I had a rust issue earlier, but now the error is just complaining about npm. I'll try the wheel. Is there also always a wheel built for the main branch whenever a PR is merged?

tin 1751 : python3 -m pip install --user git+https://github.com/lab-cosmo/chemiscope
Collecting git+https://github.com/lab-cosmo/chemiscope
  Cloning https://github.com/lab-cosmo/chemiscope to /tmp/pip-req-build-4j40egx_
  Running command git clone --filter=blob:none --quiet https://github.com/lab-cosmo/chemiscope /tmp/pip-req-build-4j40egx_
  Resolved https://github.com/lab-cosmo/chemiscope to commit f493599581cf5ea27c0f7a8200392d972fc48ea1
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [23 lines of output]
      /bin/sh: npm: command not found
      ==== rebuilding the JS code with npm, this might take a while ...
      Traceback (most recent call last):
        File "/home/Software/python/miniconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/Software/python/miniconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/Software/python/miniconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-4386fyd6/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-4386fyd6/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-4386fyd6/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 130, in <module>
        File "<string>", line 84, in run_npm_build
        File "/home/Software/python/miniconda3/lib/python3.11/subprocess.py", line 571, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command 'npm ci' returned non-zero exit status 127.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[bernstei]

I can confirm that the prebuilt PR wheel works, and I get a much better resolution image. It'd be even better for that resolution to be settable, but that's not at all urgent.

[Luthaf]

An error on npm makes sense, we need it to build the JS part of the code.

Is there also always a wheel built for the main branch whenever a PR is merged?

Even before it is merged, you can find the link by looking at the "build-wheels" CI job, and then "Summary" and "Artifacts" at the bottom.

[bernstei]

OK, I can install now that I added npm. Is there a faster way of doing debugging than just modifying the typescript source in the repo dir and doing pip install --user .? That operation takes quite a few minutes. Do I need to learn about the javascript console in the browser?

[Luthaf]

So if you are debugging the juptyter extension, that's the main way. If you want to work with the website, npm start will start a debug version of the code (which will compile a lot faster) which you can open. It will also automatically rebuild and reload when the code changes. See also https://github.com/lab-cosmo/chemiscope/blob/main/Contributing.md for more information about the development workflow

[bernstei]

Thanks. I guess since the problem shows up in both, I can try to debug it in the web server context. Now I just have to figure out how to get information out of the typescript code (without knowing much about it).