docs: Initial docs and JupyterBook setup

[ayushnag]

This pull request includes several changes to improve the documentation setup and configuration for the phylo2vec project. The changes include adding configuration files for Read the Docs and Jupyter Book, updating the table of contents and API reference, and adding necessary dependencies.

Documentation setup and configuration:

• .readthedocs.yaml: Added a configuration file for Read the Docs to specify the build environment and tools required for generating documentation.
• docs/_config.yml: Added a configuration file for Jupyter Book to set book settings, execution options, repository information, and Sphinx extensions.
• docs/_toc.yml: Added a table of contents file for Jupyter Book to define the structure of the documentation.
• docs/api.rst: Added an API reference file to document the functions and modules in the phylo2vec project using Sphinx autosummary.
• docs/requirements.txt: Added a requirement for jupyter-book to ensure the necessary dependencies are installed.

Additionally, the pixi.toml file was updated to include a task for building the documentation using Jupyter Book:

• pixi.toml: Added a build-docs task to the feature.python.tasks section to automate the documentation build process.

Related Issues

Closes #44
Closes #43
Closes #42

[deepsource-io]

Here's the code health analysis summary for commits ec18e9f..386f6ea. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Rust	✅ Success		View Check ↗
Python	✅ Success		View Check ↗

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[lsetiawan]

Looks like the build is failing

[lsetiawan]

Are you able to see the build logs btw?

[ayushnag]

Yes I can see the RTD previews and the log outputs. Somehow jupyter-book is not importing even though it's added to the pixi.toml. I'll take a look

[lsetiawan]

This is because RTD is not using pixi toml to actually install anything, you'll have to modify the .readthedocs to make it so that pixi is used

[lsetiawan]

See readthedocs/readthedocs.org#11548 (comment) for related conversation about this

[lsetiawan]

@ayushnag It works now: https://uw-phylo2vec--66.org.readthedocs.build/en/66/

[ayushnag]

Thanks for the help @lsetiawan!

[lsetiawan]

No problem! Thanks for setting it up! 😄

[lsetiawan]

Good to know we can use pixi to setup jupyterbook!

[lsetiawan]

LGTM

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud