Backport PR #2414 on branch 1.9.x (matplotlib 3.7 compat) (#2419)
* Backport PR #2414: matplotlib 3.7 compat
* fix scrublet
* Update visium default plot for matplotlib 3.7
* Update hashsolo docstrings
* skip plotting test that changed on mpl 3.7 if mpl < 3.7 is installed
* Fix hashsolo docs (again)
* update anndata-dev tests to install anndata test deps
* Temporarily set warnings as errors to False for doc builds
* Release notes
* Fix using custom layer with highly_variable_genes (#2302)
* Fix using custom layer with highly_variable_genes
* Add tests
* Add release note
* Move release note to correct section
* Format release notes
* Add check for number of normalized dispersions (#2231)
* Add check for number of normalized dispersions
In sc.pp.highly_variable_genes() when flavor='cell_ranger' and
n_top_genes is set check that enough normalized dispersions have been
calculated and if not raise a warning and set n_top_genes to the number
of calculated dispersions.
Fixes #2230
* Use .size instead of len()
* Add test for n_top_genes warning
* Add release note
* Remove blank line
Co-authored-by: Isaac Virshup <[email protected]>
---------
Co-authored-by: Isaac Virshup <[email protected]>
Co-authored-by: adamgayoso <[email protected]>
Co-authored-by: Dries Schaumont <[email protected]>
Co-authored-by: Luke Zappia <[email protected]>
