Update documentation

[schmoelder]

• Add backlinks in documentation from parameters to model
• Consistent binding model order in documentation
• Consistent model/config tags in documentation
• Fix inline issue in documentation
• Update badges for README
• Add citing section to README
• Update copyright to 2023 (@sleweke how is that currently done?)

[schmoelder]

@sleweke Do you know why appveyor is still trying to build CADET?

[schmoelder]

I'm not opposed to having the "Citing" section in the README but I just wanted to comment that at some point @lieres and I had decided to leave the Github REAMDE as clean as possible and move all relevant information to the website where we already have a citing section. Background was that we didn't want to clutter information everywhere and instead have a single point of entry for CADET (i.e. cadet.github.io).

For comparison, the CADET-Process Github page and entry on readthedocs are identical (which I also like).

[jbreue16]

Makes sense to me, maybe we should just edit the citing section on the website. On the other hand, things may have changed now that we have the zenodo doi linked in the github readme.

[lieres]

Having identical content will not be possible for CADET-Core and cadet.github.io, as the latter serves as central landing page for the whole CADET multiverse. Hence, it might be useful to copy some but not all information, and I think citing section is important.

[schmoelder]

Having identical content will not be possible for CADET-Core and cadet.github.io, as the latter serves as central landing page for the whole CADET multiverse. Hence, it might be useful to copy some but not all information, and I think citing section is important.

I agree, but that was also the reason why removed the citing section (311d626) from this page to focus on code-releated things and and instead refer to https://cadet.github.io

I'm fine if we reinstate it here. Just wanted to mention it.

[schmoelder]

please write every sentence on a single line

[schmoelder]

clarify usage of Zenodo DOI vs other publications

[schmoelder]

This is almost ready to merge. However, documentation seems to be breaking currently. I suspect m2r. If I remember correctly, @ronald-jaepel added this. However, it does not seem to be maintained any more (https://github.com/miyakogi/m2r).

Also, @sleweke, updating the copyright I had to touch 358 files. To keep sanity, I used sed for this purpose but is there another way to do that? Do we really need that copyright notice in every file or is it enough to have one central location for it?

[ronald-jaepel]

I can't reproduce the error locally, but based on the error we get here, I don't think it's m2r.

Extension error:
Could not import extension sphinxcontrib.bibtex (exception: No module named 'pkg_resources')
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.12.2/x64/bin/sphinx-multiversion", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.2/x64/lib/python3.12/site-packages/sphinx_multiversion/main.py", line 338, in main
    subprocess.check_call(cmd, cwd=current_cwd)
  File "/opt/hostedtoolcache/Python/3.12.2/x64/lib/python3.12/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '('/opt/hostedtoolcache/Python/3.12.2/x64/bin/python', '-R', '-m', 'sphinx', '-D', 'smv_metadata_path=/tmp/tmpw2okj78f/versions.json', '-D', 'smv_latest_version=v4.4.0', '-D', 'smv_current_version=master', '-c', '/home/runner/work/CADET-Website/CADET-Website/CADET/doc', '/tmp/tmpw2okj78f/0fcdbbf017b99712287c435cb4006cef85e11b8e/doc', '/home/runner/work/CADET-Website/CADET-Website/build/master')' returned non-zero exit status 2.

Google turned up this for

"no module named 'pkg-resources'"

which suggests that the fault may lie in a missing/outdated installation of setuptools, so I've added that to the 'requirements.txt' to test if that helps at all.

[ronald-jaepel]

¯_(ツ)_/¯ I don't know why, but putting setuptools into the requirements.txt doesn't actually install setuptools. Adding pip install setuptools to the workflow file does and fixes the error. ᓚᘏᗢ

Docs build now

[sleweke-bayer]

To keep sanity, I used sed for this purpose but is there another way to do that?

I don't think there is another way.

Do we really need that copyright notice in every file or is it enough to have one central location for it?

As far as I know, we do not need the years in the copyright statement. For example, curl recently removed them: https://daniel.haxx.se/blog/2023/01/08/copyright-without-years/
So my proposal is to just get rid of the years in the copyright statement. This would avoid changing them every year.