Merge branch 'master' into dask-utils

Author: flying-sheep

.github/workflows/publish.yml

@@ -0,0 +1,21 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write # to authenticate as Trusted Publisher to pypi.org
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -1,13 +1,10 @@
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.10.0
-    hooks:
-    -   id: black
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.1
+    rev: v0.1.3
     hooks:
     -   id: ruff
         args: ["--fix"]
+    -   id: ruff-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:

docs/conf.py

@@ -179,7 +179,7 @@ def setup(app: Sphinx):
 # -- Suppress link warnings ----------------------------------------------------
 
 qualname_overrides = {
-    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
+    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.metrics.DistanceMetric",
     # If the docs are built with an old version of numpy, this will make it work:
     "numpy.random.RandomState": "numpy.random.mtrand.RandomState",
     "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
@@ -192,8 +192,10 @@ def setup(app: Sphinx):
     # Will probably be documented
     ("py:class", "scanpy._settings.Verbosity"),
     ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
-    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
+    # Currently undocumented
+    # https://github.com/mwaskom/seaborn/issues/1810
     ("py:class", "seaborn.ClusterGrid"),
+    ("py:class", "samalg.SAM"),
     # Won’t be documented
     ("py:class", "scanpy.plotting._utils._AxesSubplot"),
     ("py:class", "scanpy._utils.Empty"),

docs/dev/index.md

@@ -11,8 +11,8 @@ getting-set-up
 testing
 documentation
 ci
-release
 versioning
+release
 ```
 
 Parts of the guidelines have been adapted from the [pandas](https://pandas.pydata.org/pandas-docs/stable/development/index.html) and [MDAnalysis](https://userguide.mdanalysis.org/stable/contributing.html) guides.

docs/dev/release.md

@@ -1,62 +1,70 @@
 # Making a release
 
-This is a guide on how to make a release of scanpy for maintainers.
+First, check out {doc}`versioning` to see which kind of release you want to make.
+That page also explains concepts like *pre-releases* and applications thereof.
 
-## Checking that PyPI will accept it
+## Actually making the release
 
-Sometimes PyPI will reject a build.
-You can locally check whether the build is acceptable with `twine check`.
+1. Go to GitHub’s [releases][] page
+2. Click “Draft a new release”
+3. Click “Choose a tag” and type the version of the tag you want to release, such as `1.9.6`
+4. Click “**+ Create new tag: 1.\<minor>.\<patch>** on publish”
+5. If the version is a *pre-release* version, such as `1.7.0rc1` or `1.10.0a1`, tick the “Set as a pre-release” checkbox
 
-```shell
-# First, make a build
-python -m build
+[releases]: https://github.com/scverse/scanpy/releases
 
-# Now check that build
-twine check dist/*  # Assuming dist is otherwise empty
-```
+## After making a release
 
-## Actually making release
+After *any* release has been made:
 
-First, make sure you're working repository is clean and is on the commit you'd like to release from.
-Then follow these steps:
+- Create a new release notes file for the next bugfix release.
+  This should be included in both dev and stable branches.
+- Create a milestone for the next release (in case you made a bugfix release) or releases (in case of a major/minor release).
+  For bugfix releases, this should have `on-merge: backport to 0.<minor>.x`,
+  so the [meeseeksdev][] bot will create a backport PR. See {doc}`versioning` for more info.
+- Clear out and close the milestone you just made a release for.
 
-```shell
-# Tag the commit with version info
-git tag {version}  # where version is a version number like "1.7.0"
+After a *major* or *minor* release has been made:
+
+- Tweet about it! Announce it on Zulip! Announce it on Discourse! Think about making a bot for this! Maybe actually do that?
+- Create a new release notes file for the next minor release. This should only be added to the dev branch.
+- Tag the development branch. If you just released `1.7.0`, this would be `1.8.0.dev0`.
+- Create a new branch for this release series, like `1.7.x`. This should get a new release notes file.
+
+[meeseeksdev]: https://meeseeksbox.github.io
+
+## Debugging the build process
+
+If you changed something about the build process (e.g. [Hatchling’s build configuration][hatch-build]),
+or something about the package’s structure,
+you might want to manually check if the build and upload process behaves as expected:
 
+```shell
 # Clear out old distributions
 rm -r dist
 
-# Build distributions and wheel
+# Build source distribution and wheel both
 python -m build
-# you can check that the previous step worked by installing from it's results
-# e.g. pip install dist/scanpy-{version}-py3-none-any.whl
-
-# Once you're confident the build looks good, push the tag to github
-git push upstream {version}
-
-# Upload wheel and code distribution to pypi
-twine upload dist/scanpy-{version}
-```
 
-### Checking the distributions
+# Now check those build artifacts
+twine check dist/*
 
-If you're feeling cautious, you can:
+# List the wheel archive’s contents
+bsdtar -tf dist/*.whl
 
-- List the contents of a wheel with: `unzip -l dist/*.whl`
-- Make a release candidate. Tag these with `{version}rc1` (e.g. `1.7.0rc1`)
-- Upload them to <test.pypi.org> ([tutorial](https://packaging.python.org/en/latest/tutorials/packaging-projects/#uploading-the-distribution-archives))
+```
 
-## After making a release
+You can also upload the package to <test.pypi.org> ([tutorial][testpypi tutorial])
 
-After a major or minor release has been made:
+[testpypi tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#uploading-the-distribution-archives
 
-- Tweet about it! Announce it on Zulip! Announce it on Discourse! Think about making a bot for this! Maybe actually do that?
-- Create a new release notes file for the next minor release. This should only be added to the dev branch.
-- Tag the development branch. If you just released `1.7.0`, this would be `1.8.0.dev0`.
-- Create a new branch for this release series, like `1.7.x`. This should get a new release notes file.
+```
+twine upload --repository testpypi dist/*
+```
 
-After any release has been made:
+The above approximates what the [publish workflow][] does automatically for us.
+If you want to replicate the process more exactly, make sure you are careful,
+and create a version tag before building (make sure you delete it after uploading to TestPyPI!).
 
-- Create a new release notes file for the next bugfix release. This should be included in both dev and stable branches `release-latest.md`
-- Create a milestone for the next release(s). For bugfix releases, this should have `on-merge: backport to 0.8.x` so [meeseeksdev](https://meeseeksbox.github.io) bot will create a backport PR. See {doc}`versioning` for more info.
+[hatch-build]: https://hatch.pypa.io/latest/config/build/
+[publish workflow]: https://github.com/scverse/scanpy/tree/master/.github/workflows/publish.yml

docs/dev/versioning.md

@@ -17,8 +17,10 @@ At a `point` release, there should be no changes beyond bug fixes.
 
 Valid version numbers are described in [PEP 440](https://peps.python.org/pep-0440/).
 
-[Release candidates](https://peps.python.org/pep-0440/#pre-releases) should have versions like `1.7.0rc1`, `1.7.0rc2`.
-[Development versions](https://peps.python.org/pep-0440/#developmental-releases) should look like `1.8.0.dev0`, with a commit hash optionally appended as a local version identifier (e.g. `1.8.0.dev2+g00ad77b`).
+[Pre-releases](https://peps.python.org/pep-0440/#pre-releases)
+:   should have versions like `1.7.0rc1` or `1.7.0rc2`.
+[Development versions](https://peps.python.org/pep-0440/#developmental-releases)
+:   should look like `1.8.0.dev0`, with a commit hash optionally appended as a local version identifier (e.g. `1.8.0.dev2+g00ad77b`).
 
 ## Tooling
 

docs/extensions/typed_returns.py

@@ -16,6 +16,10 @@ def process_return(lines):
 
 def scanpy_parse_returns_section(self, section):
     lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
+    if lines_raw[0] == ":":
+        # Remove the “:” inserted by sphinx-autodoc-typehints
+        # https://github.com/tox-dev/sphinx-autodoc-typehints/blob/a5c091f725da8374347802d54c16c3d38833d41c/src/sphinx_autodoc_typehints/patches.py#L66
+        lines_raw.pop(0)
     lines = self._format_block(":returns: ", lines_raw)
     if lines and lines[-1]:
         lines.append("")

docs/release-notes/1.10.0.md

@@ -14,14 +14,15 @@
 
 ```{rubric} Docs
 ```
+* Fixed a lot of broken usage examples {pr}`2605` {smaller}`P Angerer`
 
 ```{rubric} Bug fixes
 ```
 
 * Updated {func}`~scanpy.read_visium` such that it can read spaceranger 2.0 files {smaller}`L Lehner`
 * Fix {func}`~scanpy.pp.normalize_total` {pr}`2466` {smaller}`P Angerer`
 * Fix testing package build {pr}`2468` {smaller}`P Angerer`
-
+* Fix setting `sc.settings.verbosity` in some cases {pr}`2605` {smaller}`P Angerer`
 
 ```{rubric} Ecosystem
 ```

docs/release-notes/1.9.6.md

@@ -1,4 +1,4 @@
-### 1.9.6 {small}`the future`
+### 1.9.6 {small}`2023-10-31`
 
 ```{rubric} Bug fixes
 ```
@@ -8,3 +8,4 @@
 - Fix {func}`scanpy.pl.pca` when `return_fig=True` and `annotate_var_explained=True` {pr}`2682` {smaller}`J Wagner`
 - Temp fix for {issue}`2680` by skipping `seaborn` version 0.13.0 {pr}`2661` {smaller}`P Angerer`
 - Fix {func}`scanpy.pp.highly_variable_genes` to not modify the used layer when `flavor=seurat` {pr}`2698` {smaller}`E Roellin`
+- Prevent pandas from causing infinite recursion when setting a slice of a categorical column {pr}`2719` {smaller}`P Angerer`

docs/release-notes/1.9.7.md

@@ -0,0 +1,4 @@
+### 1.9.7 {small}`the future`
+
+```{rubric} Bug fixes
+```