WIP: Various improvements to the CLI endpoints

[cwognum]

Changelogs

• Added fine-tuning through Optuna, using the Optuna Sweeper Plugin for Hydra.
• Migrated the CLI from Click to Typer.
• Made it possible to specify a pre-trained model with a .ckpt path, instead of always relying on a manually defined mapping in the spaces.py.
• Added some utilities for saving essential results in case there is no logger.
• Removed the graphium-prepare-data command in favor of a new subcommand at: graphium data prepare.
• Added graphium finetune fingerprint to easily extract fingerprints from a model.
• (WIP: Added a notebook to investigate the correlation between pre-training and fine-tuning performance.)

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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.
• 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

[codecov]

Codecov Report

Merging #441 (3c9e327) into main (e424f21) will decrease coverage by 0.76%.
Report is 2 commits behind head on main.
The diff coverage is 25.25%.

@@            Coverage Diff             @@
##             main     #441      +/-   ##
==========================================
- Coverage   65.37%   64.61%   -0.76%     
==========================================
  Files          92       93       +1     
  Lines        8253     8404     +151     
==========================================
+ Hits         5395     5430      +35     
- Misses       2858     2974     +116     

Flag	Coverage Δ
unittests	64.61% <25.25%> (-0.76%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
ipu	49.14% <ø> (ø)

[DomInvivo]

Only a comment about the CLI for fingerprinting. Seems to miss the ability to chose a dataset?? Or does that come from the config?

[DomInvivo]

How do you specify which dataset you want to generate the fingerprints on?

[cwognum]

Comes from the config! It uses the predict_dataloader() of the datamodule, which in Graphium has been implemented to fallback to the test_dataloader if not explicitly specified.