Packaging of Graphium 3.0

[Andrewq11]

Changelogs

• Updated setup.py to build graphium_cpp as part of the graphium build process.
• Small changes to setup.py to allow proper graphium_cpp compilation.
• Addition of doxygen for graphium_cpp doc building. Configured to integrate into existing docs deployment.(@DomInvivo I would pull this branch and run mkdocs serve to ensure it all looks good to you. There is a nav menu button named "Graphium C++").
• env.yml file updated with dependencies/versions that are compatible with graphium and graphium_cpp.
• Updated README.md to reflect how to install 3.0.0. A note was added about PyPi version limitation.

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Checklist:

• Was this PR discussed in an issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR. Graphium 3.0 #519
• Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
• Update the API documentation is a new function is added, or an existing one is deleted.
• Write concise and explanatory changelogs above.
• If possible, assign one of the following labels to the PR: feature, fix or test (or ask a maintainer to do it for you).

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discussion related to that PR

Important Notes

• The conda-forge recipe for Graphium 3.0 is essentially ready-to-go. I just need to open a PR into the main feedstock when we are getting closer to deployment and test cross-platform builds. Branch is here - https://github.com/Andrewq11/graphium-feedstock/tree/release/graphium-3.0
• @WenkelF is going to update the graphium documentation given that he has the most context about what features are available and not in the package. We looked today and some work was needed.
• @WenkelF I noticed there were still some references to IPUs in graphium/trainer/metrics.py. Is this correct?
• @DomInvivo we can only support Python versions 3.9, 3.10 and 3.11 right now. Because pyg is pinning us to numpy version 1.25.0, we cannot use 3.12 (not compatible with that version of numpy). Once pyg makes a new release, I will update our conda-forge recipe to build for 3.12.
• Please note the changes in tests/test_datamodule.py. I had to update two assert statements to get passing tests. Was this update correct or did I just make a failing test pass?
• This PR looks much bigger than it is. >90% of the files changed are auto-generated by doxygen.

[DomInvivo]

I have made a few minor requests.
Also, I feel that the Graphium-cpp main page should not be empty. Perhaps a text stating:

Welcome to the documentation for the C++ API of the graphium library. For the python API, go to this linkhttps://graphium-docs.datamol.io/stable/). The C++ API is used to significantly accelerate the computation of positional and structural encodings, but also the caching of the supervised labels into very light and optimized files. This significantly accelerates the dataloading and removes the need for long pre-processing of large datasets.

[DomInvivo]

Suggested change

	conda install graphium
	mamba install graphium -c conda-forge

[DomInvivo]

Suggested change

	- numpy=1.25.0
	- numpy <= 1.25.0

Too strict

[DomInvivo]

Too strict. Can you do <= or >=?

[Andrewq11]

I'll run a test build with <= and report back.

[Andrewq11]

@DomInvivo applied your suggestions and got the tests running for all operating systems we'll support. It's ready for another quick round of review. Please remember to build the docs and checkout the changes I made to the C++ API docs.