1.9.5

Remove use of AnnData constructor dtype kwarg (#2658) (#2659)

* Remove use of AnnData constructor dtype kwarg (#2658)

* Remove use of AnnData constructor dtype kwarg

* release note

* Fix release note

(cherry picked from commit 0b49eebbcf6007e2fa742763e382d99e6a151a78)

* Fix test

* Set release date

* Add release notes to index

1.9.4

Backport PR #2639: Prepare 1.9.4 release (#2641)

1.9.3

Backport of Prepare for pandas 2.0 (#2434) onto 1.9.x (#2435)

* Prepare for pandas 2.0 (#2434)

* is_categorical -> is_categorical_dtype

* cat.replace(to_remove, np.nan) -> cat.remove_categories(to_remove)

* df1.append(df2) -> pd.concat([df1, df2])

* Series.iteritems -> Series.items

* Fix indexing a pandas object with a set in score genes

* Release notes

(cherry picked from commit 0692ef9ea30335b95f7e7f9aab7be856469d9f35)

* Fix anndata-dev test

* anndata-dev compatibility

* Prep 1.9.3

* Fix pr reference

1.9.2

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]>

Backport PR #2219: Finalize docs for 1.9.1 (#2221)

Co-authored-by: Isaac Virshup <[email protected]>

1.10.0.dev0

Release notes (#2197)

1.9.0: Prep release notes (#2196)

* Update release notes (including some old ones)

* More updates to release notes

* Tutorial links + zulip link

* Tutorial links + zulip link

* Fix up doc index page

* Group release notes

* Update news

* Update ecosystem (+ add release notes)

* Expand on 100 contributors

* More rewording of contributor milestone

* dammit

Backport PR #2037: Prep 1.8.2 release (#2038)

Co-authored-by: Isaac Virshup <[email protected]>

Backport PR #1937: Prep 1.8.1 (#1938)

Co-authored-by: Isaac Virshup <[email protected]>

1.9.0.dev0

Start release notes for 1.9.0 (#1906)