✨ basic docs

[enryH]

Add documentation of module

• add local builds of documentation in action
• optional dependencies in poetry - does it later work with build python package?
• figure out how to have relative links from README.

[enryH]

documentation is build now using an action for testing. quarto-cli seems to work fine at least on Ubuntu.

[enryH]

@sayalaruano test it locally, and see some of my commit messages for some things I changed:)

[sayalaruano]

I tested locally in a new environment installing the dependencies with pip and it works. I got errors because of unknown paths using the report_config_micw2graph.yaml, but solved it by adding "docs/" into the paths of the config.

With respect to the docs, I tried to build it using this command, but did not work:

sphinx-build -n -W --keep-going -b html ./ ./_build/

Got this error:

updating environment: [new config] 4 added, 0 changed, 0 removed
/Users/asaru/Downloads/vuegen-mk_docs/docs/vuegen_demo.ipynb: Executing notebook using local CWD [mystnb]
/Users/asaru/Downloads/vuegen-mk_docs/docs/example_data/MicW2Graph/1_Exploratory_Data_Analysis/3_Extra_info/1_test_md.md.rst:1: WARNING: Document headings start at H3, not H1 [myst.header]
/Users/asaru/Downloads/vuegen-mk_docs/docs/index.md:17: WARNING: toctree contains reference to nonexisting document 'reference/vuegen' [toc.not_readable]

Exception occurred:
  File "/Users/asaru/Library/Caches/pypoetry/virtualenvs/vuegen-4Ofs6PX7-py3.12/lib/python3.12/site-packages/myst_nb/core/execute/direct.py", line 50, in start_client
    raise ExecutionError(str(self.path)) from result.err
myst_nb.core.execute.base.ExecutionError: /Users/asaru/Downloads/vuegen-mk_docs/docs/vuegen_demo.ipynb
The full traceback has been saved in /var/folders/64/3nt358294s9cjcj1qbtv1g_h0000gp/T/sphinx-err-1jfm0r8b.log, if you want to report the issue to the developers.```



Should I do something else?

[sayalaruano]

In the README, should we just keep one of the ways of loading the images, either the md or html?

[enryH]

yes, we can if that is okay with you. I did not yet wanted to delete it, but I could not get it to work with the div section. You can try to find out if you want

[enryH]

I tested locally in a new environment installing the dependencies with pip and it works. I got errors because of unknown paths using the report_config_micw2graph.yaml, but solved it by adding "docs/" into the paths of the config.

With respect to the docs, I tried to build it using this command, but did not work:

sphinx-build -n -W --keep-going -b html ./ ./_build/

Got this error:

updating environment: [new config] 4 added, 0 changed, 0 removed
/Users/asaru/Downloads/vuegen-mk_docs/docs/vuegen_demo.ipynb: Executing notebook using local CWD [mystnb]
/Users/asaru/Downloads/vuegen-mk_docs/docs/example_data/MicW2Graph/1_Exploratory_Data_Analysis/3_Extra_info/1_test_md.md.rst:1: WARNING: Document headings start at H3, not H1 [myst.header]
/Users/asaru/Downloads/vuegen-mk_docs/docs/index.md:17: WARNING: toctree contains reference to nonexisting document 'reference/vuegen' [toc.not_readable]

Exception occurred:
  File "/Users/asaru/Library/Caches/pypoetry/virtualenvs/vuegen-4Ofs6PX7-py3.12/lib/python3.12/site-packages/myst_nb/core/execute/direct.py", line 50, in start_client
    raise ExecutionError(str(self.path)) from result.err
myst_nb.core.execute.base.ExecutionError: /Users/asaru/Downloads/vuegen-mk_docs/docs/vuegen_demo.ipynb
The full traceback has been saved in /var/folders/64/3nt358294s9cjcj1qbtv1g_h0000gp/T/sphinx-err-1jfm0r8b.log, if you want to report the issue to the developers.```



Should I do something else?

You need to create the reference folder from your source files (in vuegen) using the command above:)

[sayalaruano]

I ran the previous command, and now it's working fine.