spatialdata-io 0.1.5__tar.gz → 0.1.6__tar.gz

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/.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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/.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:
@@ -52,7 +52,7 @@ 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
@@ -60,7 +60,7 @@ jobs:
                   path: ./data
 
             - name: List the data directory
-              if: matrix.python == '3.10'
+              if: matrix.python == '3.12'
               run: |
                   ls -l ./data
                   pwd

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/.mypy.ini

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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/.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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/.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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/CHANGELOG.md

@@ -8,6 +8,12 @@ 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
 
+## [0.1.6] - 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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: spatialdata-io
-Version: 0.1.5
+Version: 0.1.6
 Summary: SpatialData IO for common techs
 Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/spatialdata-io
@@ -36,8 +36,7 @@ License: BSD 3-Clause License
         CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-License-File: LICENSE
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Requires-Dist: anndata
 Requires-Dist: dask-image
 Requires-Dist: h5py
@@ -48,7 +47,7 @@ Requires-Dist: pyarrow
 Requires-Dist: readfcs
 Requires-Dist: scanpy
 Requires-Dist: scikit-image
-Requires-Dist: spatialdata>=0.2.2
+Requires-Dist: spatialdata>=0.2.6
 Requires-Dist: tifffile>=2023.8.12
 Provides-Extra: dev
 Requires-Dist: bump2version; extra == 'dev'

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.5'
-__version_tuple__ = version_tuple = (0, 1, 5)
+__version__ = version = '0.1.6'
+__version_tuple__ = version_tuple = (0, 1, 6)

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/docs/conf.py

@@ -90,6 +90,7 @@ source_suffix = {
 }
 
 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),

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/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 = '''
 (

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/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):

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/_utils.py

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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/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 @@ from spatialdata._logging import logger
 
 
 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:

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/_utils/_utils.py

@@ -3,9 +3,8 @@ from __future__ import annotations
 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
 
@@ -13,19 +12,11 @@ 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)

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/cosmx.py

@@ -5,7 +5,7 @@ import re
 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 @@ __all__ = ["cosmx"]
 @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({}),

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/dbit.py

@@ -4,7 +4,6 @@ import os
 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:

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/merscope.py

@@ -2,10 +2,10 @@ from __future__ import annotations
 
 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

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/steinbock.py

@@ -4,7 +4,7 @@ import os
 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)

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/stereoseq.py

@@ -5,7 +5,7 @@ import re
 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 @@ __all__ = ["stereoseq"]
 @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({}),

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/visium_hd.py

@@ -79,7 +79,7 @@ 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
     -------
@@ -107,7 +107,6 @@ def visium_hd(
         )
 
     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(
@@ -347,6 +346,7 @@ def visium_hd(
             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")

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/src/spatialdata_io/readers/xenium.py

@@ -10,7 +10,7 @@ import zipfile
 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
@@ -22,7 +22,6 @@ import zarr
 from anndata import AnnData
 from dask.dataframe import read_parquet
 from dask_image.imread import imread
-from datatree.datatree import DataTree
 from geopandas import GeoDataFrame
 from joblib import Parallel, delayed
 from pyarrow import Table
@@ -38,7 +37,7 @@ from spatialdata.models import (
     TableModel,
 )
 from spatialdata.transformations.transformations import Affine, Identity, Scale
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata_io._constants._constants import XeniumKeys
 from spatialdata_io._docs import inject_docs
@@ -364,7 +363,7 @@ def _decode_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
 
 
 def _get_polygons(
-    path: Path, file: str, specs: dict[str, Any], n_jobs: int, idx: Optional[ArrayLike] = None
+    path: Path, file: str, specs: dict[str, Any], n_jobs: int, idx: ArrayLike | None = None
 ) -> GeoDataFrame:
     def _poly(arr: ArrayLike) -> Polygon:
         return Polygon(arr[:-1])

{spatialdata_io-0.1.5 → spatialdata_io-0.1.6}/tests/test_xenium.py

@@ -46,7 +46,7 @@ def test_roundtrip_with_data_limits() -> None:
 # pointing to "data".
 # The GitHub workflow "prepare_test_data.yaml" takes care of downloading the datasets and uploading an artifact for the
 # tests to use
-@pytest.mark.skipif(sys.version_info < (3, 10), reason="Test requires Python 3.10 or higher")
+@pytest.mark.skipif(sys.version_info < (3, 12), reason="Test requires Python 3.10 or higher")
 @pytest.mark.parametrize(
     "dataset,expected",
     [