Merge branch 'main' of https://github.com/scverse/spatialdata-io into…

… visium_hd

.flake8

@@ -38,6 +38,8 @@ ignore =
     D400
     # First line should be in imperative mood; try rephrasing
     D401
+    # Abstract base class without abstractmethod.
+    B024
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
     tests/*: D

.github/workflows/test.yaml

@@ -18,7 +18,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: ["3.9", "3.10"]
+                python: ["3.10", "3.12"]
                 os: [ubuntu-latest]
 
         env:
@@ -52,15 +52,15 @@ jobs:
                   pip install --pre -e ".[dev,test]"
 
             - name: Download artifact of test data
-              if: matrix.python == '3.10'
+              if: matrix.python == '3.12'
               uses: dawidd6/action-download-artifact@v2
               with:
                   workflow: prepare_test_data.yaml
                   name: data
                   path: ./data
 
             - name: List the data directory
-              if: matrix.python == '3.10'
+              if: matrix.python == '3.12'
               run: |
                   ls -l ./data
                   pwd

.mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
@@ -73,7 +73,7 @@ repos:
       rev: v3.17.0
       hooks:
           - id: pyupgrade
-            args: [--py3-plus, --py39-plus, --keep-runtime-typing]
+            args: [--py3-plus, --py310-plus, --keep-runtime-typing]
     - repo: local
       hooks:
           - id: forbid-to-commit

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
     os: ubuntu-20.04
     tools:
-        python: "3.9"
+        python: "3.10"
 sphinx:
     configuration: docs/conf.py
     fail_on_warning: true

CHANGELOG.md

@@ -8,7 +8,13 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.1.4] - xxxx-xx-xx
+## [0.1.6] - 2024-11-26
+
+-   (MERSCOPE) added `feature_key` attribute for points (i.e., the `'gene'` column) #210
+-   (Visium HD) get transformation matrices even when only images are parsed #215
+-   Support for `xarray.DataTree` (which was moved from `datatree.DataTree`) #232
+
+## [0.1.5] - 2024-09-25
 
 ### Added
 
@@ -18,6 +24,8 @@ and this project adheres to [Semantic Versioning][].
 
 -   Passing `rgb=None` to image model parser for both visium and visiumhd, leading to 3-4 channel images being
     interpreted as RGB(A)
+-   Fix header bug Visium data #200
+-   (Visium HD) Fix path parsing when images are missing #204 #206
 
 ## [0.1.4] - 2024-08-07
 

docs/conf.py

@@ -90,6 +90,7 @@
 }
 
 intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "spatialdata": ("https://scverse-spatialdata.readthedocs.io/en/latest/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),

pyproject.toml

@@ -10,7 +10,7 @@ dynamic= [
 ]
 description = "SpatialData IO for common techs"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 authors = [
     {name = "scverse"},
@@ -25,7 +25,7 @@ dependencies = [
     "anndata",
     "numpy",
     "scanpy",
-    "spatialdata>=0.2.2",
+    "spatialdata>=0.2.6",
     "scikit-image",
     "h5py",
     "joblib",
@@ -83,7 +83,7 @@ skip_glob = ["docs/*"]
 
 [tool.black]
 line-length = 120
-target-version = ['py39']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 (

src/spatialdata_io/_constants/_constants.py

@@ -322,6 +322,7 @@ class MerscopeKeys(ModeEnum):
     GLOBAL_Z = "global_z"
     Z_INDEX = "ZIndex"
     REGION_KEY = "cells_region"
+    GENE_KEY = "gene"
 
 
 @unique

src/spatialdata_io/_constants/_enum.py

@@ -1,7 +1,8 @@
 from abc import ABC, ABCMeta
+from collections.abc import Callable
 from enum import Enum, EnumMeta
 from functools import wraps
-from typing import Any, Callable
+from typing import Any
 
 
 class PrettyEnum(Enum):

src/spatialdata_io/_docs.py

@@ -1,7 +1,8 @@
 from __future__ import annotations
 
+from collections.abc import Callable
 from textwrap import dedent
-from typing import Any, Callable
+from typing import Any
 
 
 def inject_docs(**kwargs: Any) -> Callable[..., Any]:  # noqa: D103

src/spatialdata_io/_utils.py

@@ -2,7 +2,8 @@
 
 import functools
 import warnings
-from typing import Any, Callable, TypeVar
+from collections.abc import Callable
+from typing import Any, TypeVar
 
 RT = TypeVar("RT")
 

src/spatialdata_io/readers/_utils/_read_10x_h5.py

@@ -31,7 +31,7 @@
 # code below taken from https://github.com/scverse/scanpy/blob/master/scanpy/readwrite.py
 
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any
 
 import h5py
 import numpy as np
@@ -40,8 +40,8 @@
 
 
 def _read_10x_h5(
-    filename: Union[str, Path],
-    genome: Optional[str] = None,
+    filename: str | Path,
+    genome: str | None = None,
     gex_only: bool = True,
 ) -> AnnData:
     """
@@ -96,7 +96,7 @@ def _read_10x_h5(
     return adata
 
 
-def _read_v3_10x_h5(filename: Union[str, Path], *, start: Optional[Any] = None) -> AnnData:
+def _read_v3_10x_h5(filename: str | Path, *, start: Any | None = None) -> AnnData:
     """Read hdf5 file from Cell Ranger v3 or later versions."""
     with h5py.File(str(filename), "r") as f:
         try:

src/spatialdata_io/readers/_utils/_utils.py

@@ -3,29 +3,20 @@
 import os
 from collections.abc import Mapping
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Union
 
-import numpy as np
 from anndata import AnnData, read_text
 from h5py import File
 
 from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
 
 PathLike = Union[os.PathLike, str]  # type:ignore[type-arg]
 
-try:
-    from numpy.typing import NDArray
-
-    NDArrayA = NDArray[Any]
-except (ImportError, TypeError):
-    NDArray = np.ndarray
-    NDArrayA = np.ndarray
-
 
 def _read_counts(
     path: str | Path,
     counts_file: str,
-    library_id: Optional[str] = None,
+    library_id: str | None = None,
     **kwargs: Any,
 ) -> tuple[AnnData, str]:
     path = Path(path)

src/spatialdata_io/readers/cosmx.py

@@ -5,7 +5,7 @@
 from collections.abc import Mapping
 from pathlib import Path
 from types import MappingProxyType
-from typing import Any, Optional
+from typing import Any
 
 import dask.array as da
 import numpy as np
@@ -38,7 +38,7 @@
 @inject_docs(cx=CosmxKeys)
 def cosmx(
     path: str | Path,
-    dataset_id: Optional[str] = None,
+    dataset_id: str | None = None,
     transcripts: bool = True,
     imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),

src/spatialdata_io/readers/dbit.py

@@ -4,7 +4,6 @@
 import re
 from pathlib import Path
 from re import Pattern
-from typing import Optional, Union
 
 import anndata as ad
 import numpy as np
@@ -27,9 +26,9 @@ def _check_path(
     path: Path,
     pattern: Pattern[str],
     key: DbitKeys,
-    path_specific: Optional[str | Path] = None,
+    path_specific: str | Path | None = None,
     optional_arg: bool = False,
-) -> tuple[Union[Path, None], bool]:
+) -> tuple[Path | None, bool]:
     """
     Check that the path is valid and match a regex pattern.
 
@@ -218,11 +217,11 @@ def _xy2edges(xy: list[int], scale: float = 1.0, border: bool = True, border_sca
 
 @inject_docs(vx=DbitKeys)
 def dbit(
-    path: Optional[str | Path] = None,
-    anndata_path: Optional[str] = None,
-    barcode_position: Optional[str] = None,
-    image_path: Optional[str] = None,
-    dataset_id: Optional[str] = None,
+    path: str | Path | None = None,
+    anndata_path: str | None = None,
+    barcode_position: str | None = None,
+    image_path: str | None = None,
+    dataset_id: str | None = None,
     border: bool = True,
     border_scale: float = 1,
 ) -> SpatialData:

src/spatialdata_io/readers/merscope.py

@@ -2,10 +2,10 @@
 
 import re
 import warnings
-from collections.abc import Mapping
+from collections.abc import Callable, Mapping
 from pathlib import Path
 from types import MappingProxyType
-from typing import Any, Callable, Literal
+from typing import Any, Literal
 
 import anndata
 import dask.dataframe as dd
@@ -303,6 +303,7 @@ def _get_points(transcript_path: Path, transformations: dict[str, BaseTransforma
         transcript_df,
         coordinates={"x": MerscopeKeys.GLOBAL_X, "y": MerscopeKeys.GLOBAL_Y},
         transformations=transformations,
+        feature_key=MerscopeKeys.GENE_KEY,
     )
     transcripts["gene"] = transcripts["gene"].astype("category")
     return transcripts

src/spatialdata_io/readers/steinbock.py

@@ -4,7 +4,7 @@
 from collections.abc import Mapping
 from pathlib import Path
 from types import MappingProxyType
-from typing import Any, Literal, Union
+from typing import Any, Literal
 
 import anndata as ad
 from dask_image.imread import imread
@@ -95,7 +95,7 @@ def _get_images(
     sample: str,
     imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
-) -> Union[SpatialImage, MultiscaleSpatialImage]:
+) -> SpatialImage | MultiscaleSpatialImage:
     image = imread(path / SteinbockKeys.IMAGES_DIR / f"{sample}{SteinbockKeys.IMAGE_SUFFIX}", **imread_kwargs)
     return Image2DModel.parse(data=image, transformations={sample: Identity()}, rgb=None, **image_models_kwargs)
 
@@ -106,6 +106,6 @@ def _get_labels(
     labels_kind: str,
     imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
-) -> Union[SpatialImage, MultiscaleSpatialImage]:
+) -> SpatialImage | MultiscaleSpatialImage:
     image = imread(path / labels_kind / f"{sample}{SteinbockKeys.LABEL_SUFFIX}", **imread_kwargs).squeeze()
     return Labels2DModel.parse(data=image, transformations={sample: Identity()}, **image_models_kwargs)

src/spatialdata_io/readers/stereoseq.py

@@ -5,7 +5,7 @@
 from collections.abc import Mapping
 from pathlib import Path
 from types import MappingProxyType
-from typing import Any, Union
+from typing import Any
 
 import anndata as ad
 import h5py
@@ -29,7 +29,7 @@
 @inject_docs(xx=SK)
 def stereoseq(
     path: str | Path,
-    dataset_id: Union[str, None] = None,
+    dataset_id: str | None = None,
     read_square_bin: bool = True,
     optional_tif: bool = False,
     imread_kwargs: Mapping[str, Any] = MappingProxyType({}),

src/spatialdata_io/readers/visium_hd.py

@@ -84,7 +84,7 @@ def visium_hd(
     image_models_kwargs
         Keyword arguments for :class:`spatialdata.models.Image2DModel`.
     anndata_kwargs
-        Keyword arguments for :func:`anndata.read_h5ad`.
+        Keyword arguments for :func:`anndata.io.read_h5ad`.
 
     Returns
     -------
@@ -113,7 +113,6 @@ def load_image(path: Path, suffix: str, scale_factors: list[int] | None = None)
         )
 
     metadata, hd_layout = _parse_metadata(path, filename_prefix)
-    transform_matrices = _get_transform_matrices(metadata, hd_layout)
     file_format = hd_layout[VisiumHDKeys.FILE_FORMAT]
     if file_format != "1.0":
         warnings.warn(
@@ -338,6 +337,8 @@ def _get_bins(path: Path) -> list[str]:
             fullres_image_paths = [path_fullres / image_filename for image_filename in fullres_image_filenames]
         elif list((path_fullres := (path / f"{filename_prefix}tissue_image")).parent.glob(f"{path_fullres.name}.*")):
             fullres_image_paths = list(path_fullres.parent.glob(f"{path_fullres.name}.*"))
+        else:
+            fullres_image_paths = []
         if len(fullres_image_paths) > 1:
             warnings.warn(
                 f"Multiple files found in {path_fullres}, using the first one: {fullres_image_paths[0].stem}. Please"
@@ -411,6 +412,7 @@ def _get_bins(path: Path) -> list[str]:
             suffix="_cytassist_image",
         )
         image = images[dataset_id + "_cytassist_image"]
+        transform_matrices = _get_transform_matrices(metadata, hd_layout)
         affine0 = transform_matrices["cytassist_colrow_to_spot_colrow"]
         affine1 = transform_matrices["spot_colrow_to_microscope_colrow"]
         set_transformation(image, Sequence([affine0, affine1]), "global")