Make some improvements to documentation

[Marius1311]

This PR improves the readme.rst file to give a better overview of the moscot software.

Closes #772

[Marius1311]

I'm not sure how to fix

docs/index.rst:23: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:23: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:23: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:23: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:23: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:23: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:26: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:26: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:27: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:27: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:28: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:28: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:29: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:29: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:33: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:33: (ERROR/3) Unknown interpreted text role "doc".
docs/index.rst:34: (INFO/1) No role entry for "doc" in module "docutils.parsers.rst.languages.en".
docs/index.rst:34: (ERROR/3) Unknown interpreted text role "doc".

The links work fine after building the docs locally, would appreciate some help here.

[Marius1311]

@MUCDK, feel free to modify this PR to your liking, it's meant as a starting point.

[MUCDK]

Looks good thanks!

The error is due to wrong links to notebooks, e.g. do

- :doc:`Trajectory inference <notebooks/moscot_notebooks/tutorials/200_temporal_problem>`

instead of

- :doc:`Trajectory inference <notebooks/tutorials/200_temporal_problem>`

[MUCDK]

Once we have links to the notebooks I think that looks great. We can merge, and then see whether we want further adaptations.

[Marius1311]

notebooks/moscot_notebooks/tutorials/

Unfortunately that change does not fix the issue, and additionally, it gives

/Users/mlange/Projects/moscot/docs/index.rst:23: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/200_temporal_problem' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:23: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/500_spatiotemporal' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:23: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/100_lineage' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:26: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/400_spatial_mapping' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:27: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/300_spatial_alignment' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:28: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/600_tutorial_translation' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:34: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/index' [ref.doc]
/Users/mlange/Projects/moscot/docs/index.rst:72: WARNING: unknown document: 'notebooks/moscot_notebooks/tutorials/index' [ref.doc]
/Users/mlange/Projects/moscot/docs/notebooks/examples/problems/200_custom_cost_matrices.ipynb:80004: WARNING: py:attr reference target not found: moscot.problems.generic.FGWProblem.prepare.cost [ref.attr]