Update docs (#1279)

* Update `conf.py`

Update to latest sphinx version.

* Update vignette index

* Update docstrings

Replace `Arguments:` by `Parameters`

* Remove redundant import

Removes `pca` which is merely imported from and defined in Scanpy.

* Update `perspectives/index.rst`

Fix notebook linking.

* Update index page

- Remove reference to veloVI.
- Update bibtex references

* Update references

- Update list of references.
- Use consistent ID `AuthorYY` for references.
- Properly cite papers in docstrings.

* Update `docs/api.rst`

- Remove `pca`.
- Add empty line for consistent formatting.

* Update `conf.py`

Refactor sphinx config.

* Update `set_figure_params`

Update type hint of argument `format`.

* Fix unit tests

Fix import of removed `pca` function.

* Update `getting_started.rst`

Update docs according to latest changes; The syntax `scv.read` no longer
works and needs to be used with Scanpy directly.

* Update `pyproject.toml`

docs/source/api.rst

@@ -33,7 +33,6 @@ Preprocessing (pp)
 .. autosummary::
    :toctree: .
 
-   pp.pca
    pp.neighbors
    pp.moments
 
@@ -86,6 +85,7 @@ Tools (tl)
    tl.velocity_confidence
    tl.score_genes_cell_cycle
 
+
 Inference from metabolic labeling information
 ---------