Merge branch 'main' into var_by_distance_clustering

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.6.0
+current_version = 1.6.1
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.github/workflows/lint.yml

@@ -15,10 +15,10 @@ jobs:
             - uses: actions/checkout@v3
               with:
                   submodules: true
-            - name: Set up Python 3.9
+            - name: Set up Python 3.11
               uses: actions/setup-python@v4
               with:
-                  python-version: 3.9
+                  python-version: 3.11
 
             - uses: actions/cache@v3
               with:

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: [3.9, "3.10", "3.11"]
+                python: ["3.10", "3.11", "3.12"]
                 os: [ubuntu-latest]
                 include:
                     - python: "3.12"
@@ -92,7 +92,8 @@ jobs:
                   tox -vv
 
             - name: Upload coverage to Codecov
-              uses: codecov/codecov-action@v3.1.1
+              uses: codecov/codecov-action@v4
               with:
                   name: coverage
                   verbose: true
+                  token: ${{ secrets.CODECOV_TOKEN }} # required

.pre-commit-config.yaml

@@ -6,59 +6,21 @@ default_stages:
     - push
 minimum_pre_commit_version: 2.9.3
 repos:
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.11.0
-      hooks:
-          - id: mypy
-            additional_dependencies: [numpy, 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/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
-      hooks:
-          - id: prettier
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
-      hooks:
-          - id: detect-private-key
-          - id: check-merge-conflict
-          - id: check-ast
-          - id: check-symlinks
-          - id: check-added-large-files
-          - id: check-executables-have-shebangs
-          - id: fix-encoding-pragma
-            args: [--remove]
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: trailing-whitespace
-            exclude: ^.bumpversion.cfg$
-          - id: name-tests-test
-            args: [--django]
-          - id: check-case-conflict
-          - id: check-docstring-first
-          - id: check-yaml
-          - id: check-toml
-          - id: requirements-txt-fixer
-    - repo: https://github.com/jumanjihouse/pre-commit-hooks
-      rev: 3.0.0
-      hooks:
-          - id: script-must-have-extension
-            name: Check executable files use .sh extension
-            types: [shell, executable]
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.4
+      rev: v0.6.3
       hooks:
           - id: ruff
             types_or: [python, pyi, jupyter]
             args: [--fix, --exit-non-zero-on-fix]
           - id: ruff-format
             types_or: [python, pyi, jupyter]
-    - repo: https://github.com/pre-commit/pygrep-hooks
-      rev: v1.10.0
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.18.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.11.2
       hooks:
-          - id: python-no-eval
-          - id: python-use-type-annotations
-          - id: python-check-blanket-noqa
-          - id: rst-backticks
-          - id: rst-directive-colons
-          - id: rst-inline-touching-normal
+          - id: mypy
+            additional_dependencies: [numpy, pandas, types-requests]
+            exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/

.scripts/ci/download_data.py

@@ -30,9 +30,10 @@ def _maybe_download_data(func_name: str, path: Path) -> Any:
 
 
 def main(args: argparse.Namespace) -> None:
-    import squidpy as sq
     from anndata import AnnData
 
+    import squidpy as sq
+
     all_datasets = sq.datasets._dataset.__all__ + sq.datasets._image.__all__
     all_extensions = ["h5ad"] * len(sq.datasets._dataset.__all__) + ["tiff"] * len(sq.datasets._image.__all__)
 

docs/classes.rst

@@ -7,6 +7,6 @@ Classes
     :toctree: classes
 
     im.ImageContainer
-    pl.Interactive
     im.SegmentationWatershed
     im.SegmentationCustom
+    .. pl.Interactive

docs/index.rst

@@ -14,6 +14,17 @@ tissue images if available.
     :align: center
     :target: https://doi.org/10.1038/s41592-021-01358-2
 
+.. warning::
+    🚨🚨🚨 **Warning!** 🚨🚨🚨
+
+    The original napari-plugin of Squidpy has been moved to `napari-spatialdata <https://github.com/scverse/napari-spatialdata>`_.
+
+    All the functionalities previously available are also implemented in the new plugin, which also has many additional new features.
+
+    You can find a rich set of `documentation and examples <https://spatialdata.scverse.org/projects/napari/en/latest/index.html>`_, and we suggest starting with this `tutorial <https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html>`_.
+
+    If you are new to SpatialData, we invite you to take a look at the documentation `here <https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks.html>`_.
+
 Manuscript
 ----------
 Please see our manuscript :cite:`palla:22` in **Nature Methods** to learn more.

docs/release/notes-1.6.1.rst

@@ -0,0 +1,12 @@
+Squidpy 1.6.1 (2024-08-23)
+==========================
+
+Maintenance
+-----------
+
+- The Squidpy `interactive` module has been removed. Please use the ``napari-spatialdata`` plugin instead. You can find it `here <https://spatialdata.scverse.org/projects/napari/en/latest/index.html>`__  `@giovp <https://github.com/giovp>`__
+  `#877 <https://github.com/scverse/squidpy/pull/877>`__
+- Drop support for Python 3.9 `@giovp <https://github.com/giovp>`__
+  `#881 <https://github.com/scverse/squidpy/pull/881>`__
+- Add Xenium tutorial with spatialdata `@LLehner <https://github.com/LLehner>`__
+  `#125 <https://github.com/scverse/squidpy_notebooks/pull/125>`__

pyproject.toml

@@ -18,8 +18,9 @@ classifiers = [
     "Operating System :: MacOS :: MacOS X",
     "Typing :: Typed",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Environment :: Console",
     "Framework :: Jupyter",
     "Intended Audience :: Science/Research",
@@ -76,10 +77,6 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-interactive = [
-    "napari[pyqt5]==0.4.15",
-    "pydantic==1.10.13"
-]
 dev = [
     "pre-commit>=3.0.0",
     "tox>=4.0.0",
@@ -214,10 +211,11 @@ required-imports = ["from __future__ import annotations"]
 "*/__init__.py" = ["D104", "F401"]
 "tests/*"= ["D"]
 "docs/*"= ["D","B"]
-"squidpy/pl/_ligrec.py"= ["D","B"]
-"squidpy/_constants/_pkg_constants.py"= ["D101","D102","D106"]
-"squidpy/_constants/_constants.py"= ["D101"]
-"squidpy/pl/_interactive/_widgets.py"= ["D"]
+"src/squidpy/pl/_ligrec.py"= ["D","B"]
+"src/squidpy/_constants/_pkg_constants.py"= ["D101","D102","D106"]
+"src/squidpy/_constants/_constants.py"= ["D101"]
+"src/squidpy/pl/_interactive/_widgets.py"= ["D"]
+"src/squidpy/pl/_interactive/interactive.py"= ["F","E"]
 ".scripts/ci/download_data.py"= ["D","B"]
 # "squidpy/*.py"= ["RST303"]
 

src/squidpy/_utils.py

@@ -37,20 +37,18 @@ def wrapper(*args: Any, **kw: Any) -> Any:
         return wrapper
 
 
-try:
-    from numpy.typing import NDArray
+from numpy.typing import NDArray
 
-    NDArrayA = NDArray[Any]
-except (ImportError, TypeError):
-    NDArray = np.ndarray  # type: ignore[misc]
-    NDArrayA = np.ndarray  # type: ignore[misc]
+NDArrayA = NDArray[Any]
 
 
 class SigQueue(Queue["Signal"] if TYPE_CHECKING else Queue):  # type: ignore[misc]
     """Signalling queue."""
 
 
-def _unique_order_preserving(iterable: Iterable[Hashable]) -> tuple[list[Hashable], set[Hashable]]:
+def _unique_order_preserving(
+    iterable: Iterable[Hashable],
+) -> tuple[list[Hashable], set[Hashable]]:
     """Remove items from an iterable while preserving the order."""
     seen: set[Hashable] = set()
     seen_add = seen.add
@@ -124,7 +122,12 @@ def parallelize(
     else:
         tqdm = None
 
-    def runner(iterable: Iterable[Any], *args: Any, queue: SigQueue | None = None, **kwargs: Any) -> list[Any]:
+    def runner(
+        iterable: Iterable[Any],
+        *args: Any,
+        queue: SigQueue | None = None,
+        **kwargs: Any,
+    ) -> list[Any]:
         result: list[Any] = []
 
         for it in iterable:
@@ -200,7 +203,10 @@ def wrapper(*args: Any, **kwargs: Any) -> Any:
         col_len = len(collection)
         step = int(np.ceil(len(collection) / n_split))
         collections = list(
-            filter(len, (collection[i * step : (i + 1) * step] for i in range(int(np.ceil(col_len / step)))))
+            filter(
+                len,
+                (collection[i * step : (i + 1) * step] for i in range(int(np.ceil(col_len / step)))),
+            )
         )
 
     if use_runner:
@@ -289,7 +295,9 @@ def decorator(func1: Callable[..., Any]) -> Callable[..., Any]:
             def new_func1(*args: Any, **kwargs: Any) -> Any:
                 warnings.simplefilter("always", DeprecationWarning)
                 warnings.warn(
-                    fmt1.format(name=func1.__name__, reason=reason), category=DeprecationWarning, stacklevel=2
+                    fmt1.format(name=func1.__name__, reason=reason),
+                    category=DeprecationWarning,
+                    stacklevel=2,
                 )
                 warnings.simplefilter("default", DeprecationWarning)
                 return func1(*args, **kwargs)
@@ -317,7 +325,11 @@ def new_func1(*args: Any, **kwargs: Any) -> Any:
         @functools.wraps(func2)
         def new_func2(*args: Any, **kwargs: Any) -> Any:
             warnings.simplefilter("always", DeprecationWarning)
-            warnings.warn(fmt2.format(name=func2.__name__), category=DeprecationWarning, stacklevel=2)
+            warnings.warn(
+                fmt2.format(name=func2.__name__),
+                category=DeprecationWarning,
+                stacklevel=2,
+            )
             warnings.simplefilter("default", DeprecationWarning)
             return func2(*args, **kwargs)
 

src/squidpy/gr/_build.py

@@ -233,11 +233,11 @@ def spatial_neighbors(
 
     if library_key is not None:
         mats: list[tuple[spmatrix, spmatrix]] = []
-        ixs = []  # type: ignore[var-annotated]
+        ixs: list[int] = []
         for lib in libs:
             ixs.extend(np.where(adata.obs[library_key] == lib)[0])
             mats.append(_build_fun(adata[adata.obs[library_key] == lib]))
-        ixs = np.argsort(ixs)  # type: ignore[assignment] # invert
+        ixs = np.argsort(ixs)  # invert
         Adj = block_diag([m[0] for m in mats], format="csr")[ixs, :][:, ixs]
         Dst = block_diag([m[1] for m in mats], format="csr")[ixs, :][:, ixs]
     else:

src/squidpy/gr/_nhood.py

@@ -190,7 +190,15 @@ def nhood_enrichment(
         n_jobs=n_jobs,
         backend=backend,
         show_progress_bar=show_progress_bar,
-    )(callback=_test, indices=indices, indptr=indptr, int_clust=int_clust, libraries=libraries, n_cls=n_cls, seed=seed)
+    )(
+        callback=_test,
+        indices=indices,
+        indptr=indptr,
+        int_clust=int_clust,
+        libraries=libraries,
+        n_cls=n_cls,
+        seed=seed,
+    )
     zscore = (count - perms.mean(axis=0)) / perms.std(axis=0)
 
     if copy:
@@ -293,7 +301,13 @@ def centrality_scores(
 
     if copy:
         return df
-    _save_data(adata, attr="uns", key=Key.uns.centrality_scores(cluster_key), data=df, time=start)
+    _save_data(
+        adata,
+        attr="uns",
+        key=Key.uns.centrality_scores(cluster_key),
+        data=df,
+        time=start,
+    )
 
 
 @d.dedent
@@ -345,7 +359,7 @@ def interaction_matrix(
 
     g_data = g.data if weights else np.broadcast_to(1, shape=len(g.data))
     dtype = int if pd.api.types.is_bool_dtype(g.dtype) or pd.api.types.is_integer_dtype(g.dtype) else float
-    output = np.zeros((n_cats, n_cats), dtype=dtype)  # type: ignore[var-annotated]
+    output: NDArrayA = np.zeros((n_cats, n_cats), dtype=dtype)
 
     _interaction_matrix(g_data, g.indices, g.indptr, cats.cat.codes.to_numpy(), output)
 
@@ -360,7 +374,11 @@ def interaction_matrix(
 
 @njit
 def _interaction_matrix(
-    data: NDArrayA, indices: NDArrayA, indptr: NDArrayA, cats: NDArrayA, output: NDArrayA
+    data: NDArrayA,
+    indices: NDArrayA,
+    indptr: NDArrayA,
+    cats: NDArrayA,
+    output: NDArrayA,
 ) -> NDArrayA:
     indices_list = np.split(indices, indptr[1:-1])
     data_list = np.split(data, indptr[1:-1])