misc (#612)

scverse · Oct 15, 2022 · 90ac001 · 90ac001
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,19 +7,19 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.971
+      rev: v0.982
       hooks:
           - id: mypy
             additional_dependencies:
                 [numpy==1.21.0, scipy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
     - repo: https://github.com/psf/black
-      rev: 22.8.0
+      rev: 22.10.0
       hooks:
           - id: black
             additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.0
+      rev: v3.0.0-alpha.1
       hooks:
           - id: prettier
     - repo: https://github.com/timothycrosley/isort
@@ -68,7 +68,7 @@ repos:
           - id: check-toml
           - id: requirements-txt-fixer
     - repo: https://github.com/myint/autoflake
-      rev: v1.5.3
+      rev: v1.7.3
       hooks:
           - id: autoflake
             args:
@@ -106,7 +106,7 @@ repos:
           - id: blacken-docs
             additional_dependencies: [black==20.8b1]
     - repo: https://github.com/asottile/pyupgrade
-      rev: v2.38.0
+      rev: v3.1.0
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

diff --git a/docs/source/release/changelog/583.bugfix.rst b/docs/source/release/changelog/583.bugfix.rst
@@ -0,0 +1,3 @@
+This PR updates squidpy to accommodate the latest changes made in spaceranger 2.0 which will break
+the released version of squidpy. Will provide backwards compatibility to pre 2.0 releases.
+`@stephenwilliams22 <https://github.com/stephenwilliams22>`__
diff --git a/docs/source/release/notes-dev.rst b/docs/source/release/notes-dev.rst
@@ -1,4 +1,4 @@
-Squidpy dev (2022-08-02)
+Squidpy dev (2022-10-11)
 ========================
 
 Bugfixes
@@ -21,6 +21,200 @@ Bugfixes
   `@michalk8 <https://github.com/michalk8>`__
   `#580 <https://github.com/scverse/squidpy/pull/580>`__
 
+- This PR updates squidpy to accommodate the latest changes made in spaceranger 2.0 which will break
+  the released version of squidpy. Will provide backwards compatibility to pre 2.0 releases.
+  `@stephenwilliams22 <https://github.com/stephenwilliams22>`__
+  `#583 <https://github.com/scverse/squidpy/pull/583>`__
+
+
+Miscellaneous
+-------------
+
+- Better error message for handling palette in  :func:`squidpy.pl.spatial_scatter`.
+  `@giovp <https://github.com/giovp>`__
+  `#562 <https://github.com/scverse/squidpy/pull/562>`__
+
+
+Documentation
+-------------
+
+- Add tutorials on analysis of Vizgen and Nanostring data.
+  Remove reference of ``scanpy.pl.spatial`` plotting in examples.
+  `@dineshpalli <https://github.com/dineshpalli>`__
+  `#569 <https://github.com/scverse/squidpy/pull/569>`__
+
+
+Squidpy dev (2022-10-11)
+========================
+
+Bugfixes
+--------
+
+- Fix plotting non-unique categorical colors in :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#561 <https://github.com/scverse/squidpy/pull/561>`__
+
+- Fixes :func:`squidpy.read.nanostring` . Closes #566 .
+  `@giovp <https://github.com/giovp>`__
+  `#567 <https://github.com/scverse/squidpy/pull/567>`__
+
+- Fix :func:`squidpy.read.vizgen`.
+  `@giovp <https://github.com/giovp>`__
+  `#568 <https://github.com/scverse/squidpy/pull/568>`__
+
+- Fix passing :class:`matplotlib.colors.ListedColorMap` as palette to
+  :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#580 <https://github.com/scverse/squidpy/pull/580>`__
+
+- This PR updates squidpy to accommodate the latest changes made in spaceranger 2.0 which will break
+  the released version of squidpy. Will provide backwards compatibility to pre 2.0 releases.
+  `@stephenwilliams22 <https://github.com/stephenwilliams22>`__
+  `#583 <https://github.com/scverse/squidpy/pull/583>`__
+
+
+Miscellaneous
+-------------
+
+- Better error message for handling palette in  :func:`squidpy.pl.spatial_scatter`.
+  `@giovp <https://github.com/giovp>`__
+  `#562 <https://github.com/scverse/squidpy/pull/562>`__
+
+
+Documentation
+-------------
+
+- Add tutorials on analysis of Vizgen and Nanostring data.
+  Remove reference of ``scanpy.pl.spatial`` plotting in examples.
+  `@dineshpalli <https://github.com/dineshpalli>`__
+  `#569 <https://github.com/scverse/squidpy/pull/569>`__
+
+
+Squidpy dev (2022-10-11)
+========================
+No significant changes.
+
+
+Squidpy dev (2022-10-11)
+========================
+
+Bugfixes
+--------
+
+- Fix plotting non-unique categorical colors in :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#561 <https://github.com/scverse/squidpy/pull/561>`__
+
+- Fixes :func:`squidpy.read.nanostring` . Closes #566 .
+  `@giovp <https://github.com/giovp>`__
+  `#567 <https://github.com/scverse/squidpy/pull/567>`__
+
+- Fix :func:`squidpy.read.vizgen`.
+  `@giovp <https://github.com/giovp>`__
+  `#568 <https://github.com/scverse/squidpy/pull/568>`__
+
+- Fix passing :class:`matplotlib.colors.ListedColorMap` as palette to
+  :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#580 <https://github.com/scverse/squidpy/pull/580>`__
+
+- This PR updates squidpy to accommodate the latest changes made in spaceranger 2.0 which will break
+  the released version of squidpy. Will provide backwards compatibility to pre 2.0 releases.
+  `@stephenwilliams22 <https://github.com/stephenwilliams22>`__
+  `#583 <https://github.com/scverse/squidpy/pull/583>`__
+
+
+Miscellaneous
+-------------
+
+- Better error message for handling palette in  :func:`squidpy.pl.spatial_scatter`.
+  `@giovp <https://github.com/giovp>`__
+  `#562 <https://github.com/scverse/squidpy/pull/562>`__
+
+
+Documentation
+-------------
+
+- Add tutorials on analysis of Vizgen and Nanostring data.
+  Remove reference of ``scanpy.pl.spatial`` plotting in examples.
+  `@dineshpalli <https://github.com/dineshpalli>`__
+  `#569 <https://github.com/scverse/squidpy/pull/569>`__
+
+
+Squidpy dev (2022-10-11)
+========================
+
+Bugfixes
+--------
+
+- Fix plotting non-unique categorical colors in :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#561 <https://github.com/scverse/squidpy/pull/561>`__
+
+- Fixes :func:`squidpy.read.nanostring` . Closes #566 .
+  `@giovp <https://github.com/giovp>`__
+  `#567 <https://github.com/scverse/squidpy/pull/567>`__
+
+- Fix :func:`squidpy.read.vizgen`.
+  `@giovp <https://github.com/giovp>`__
+  `#568 <https://github.com/scverse/squidpy/pull/568>`__
+
+- Fix passing :class:`matplotlib.colors.ListedColorMap` as palette to
+  :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#580 <https://github.com/scverse/squidpy/pull/580>`__
+
+- This PR updates squidpy to accommodate the latest changes made in spaceranger 2.0 which will break
+  the released version of squidpy. Will provide backwards compatibility to pre 2.0 releases.
+  `@stephenwilliams22 <https://github.com/stephenwilliams22>`__
+  `#583 <https://github.com/scverse/squidpy/pull/583>`__
+
+
+Miscellaneous
+-------------
+
+- Better error message for handling palette in  :func:`squidpy.pl.spatial_scatter`.
+  `@giovp <https://github.com/giovp>`__
+  `#562 <https://github.com/scverse/squidpy/pull/562>`__
+
+
+Documentation
+-------------
+
+- Add tutorials on analysis of Vizgen and Nanostring data.
+  Remove reference of ``scanpy.pl.spatial`` plotting in examples.
+  `@dineshpalli <https://github.com/dineshpalli>`__
+  `#569 <https://github.com/scverse/squidpy/pull/569>`__
+
+
+Squidpy dev (2022-10-11)
+========================
+
+Bugfixes
+--------
+
+- Fix plotting non-unique categorical colors in :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#561 <https://github.com/scverse/squidpy/pull/561>`__
+
+- Fixes :func:`squidpy.read.nanostring` . Closes #566 .
+  `@giovp <https://github.com/giovp>`__
+  `#567 <https://github.com/scverse/squidpy/pull/567>`__
+
+- Fix :func:`squidpy.read.vizgen`.
+  `@giovp <https://github.com/giovp>`__
+  `#568 <https://github.com/scverse/squidpy/pull/568>`__
+
+- Fix passing :class:`matplotlib.colors.ListedColorMap` as palette to
+  :func:`squidpy.pl.spatial_scatter`.
+  `@michalk8 <https://github.com/michalk8>`__
+  `#580 <https://github.com/scverse/squidpy/pull/580>`__
+
+- This PR updates squidpy to accommodate the latest changes made in spaceranger 2.0 which will break
+  the released version of squidpy. Will provide backwards compatibility to pre 2.0 releases.
+  `@stephenwilliams22 <https://github.com/stephenwilliams22>`__
+  `#583 <https://github.com/scverse/squidpy/pull/583>`__
+
 
 Miscellaneous
 -------------

diff --git a/docs/source/spelling_wordlist.txt b/docs/source/spelling_wordlist.txt
@@ -92,6 +92,7 @@ segmentations
 semibold
 seqFISH
 seqV
+spaceranger
 Squidpy
 StarDist
 stromal

diff --git a/setup.py b/setup.py
@@ -37,8 +37,8 @@
     zip_safe=False,
     install_requires=[l.strip() for l in Path("requirements.txt").read_text("utf-8").splitlines()],
     extras_require=dict(
-        dev=["pre-commit>=2.9.0", "towncrier>=21.3.0"],
-        test=["tox>=3.20.1"],
+        dev=["pre-commit>=2.9.0", "towncrier>=22.8.0"],
+        test=["tox>=3.26.0"],
         docs=[
             l.strip()
             for l in (Path("docs") / "requirements.txt").read_text("utf-8").splitlines()

diff --git a/squidpy/datasets/_utils.py b/squidpy/datasets/_utils.py
@@ -14,7 +14,7 @@
 Function_t = Callable[..., Union[AnnData, Any]]
 
 
-@dataclass(frozen=True)  # type: ignore[misc]
+@dataclass(frozen=True)
 class Metadata(ABC):
     """Base class handling metadata."""
 

diff --git a/squidpy/im/_container.py b/squidpy/im/_container.py
@@ -1071,7 +1071,7 @@ def interactive(
         blending: Literal["opaque", "translucent", "additive"] = "opaque",
         symbol: Literal["disc", "square"] = "disc",
         key_added: str = "shapes",
-    ) -> Interactive:
+    ) -> Interactive:  # type: ignore[type-var]
         """
         Launch :mod:`napari` viewer.
 

diff --git a/tests/plotting/test_spatial_static.py b/tests/plotting/test_spatial_static.py
@@ -154,7 +154,7 @@ def test_plot_spatial_segment(self, adata_mibitof: AnnData):
             na_color="lightgrey",
         )
 
-    def test_plot_spatial_segment_group(self, adata_mibitof: AnnData):
+    def test_tol_plot_spatial_segment_group(self, adata_mibitof: AnnData):
         pl.spatial_segment(
             adata_mibitof,
             color=["Cluster"],
@@ -168,6 +168,7 @@ def test_plot_spatial_segment_group(self, adata_mibitof: AnnData):
             scalebar_dx=2.0,
             scalebar_kwargs={"scale_loc": "bottom", "location": "lower right"},
         )
+        self.compare("SpatialStatic_spatial_segment_group", tolerance=60)
 
     def test_plot_spatial_segment_crop(self, adata_mibitof: AnnData):
         pl.spatial_segment(