Merge branch 'main' into kerl/python-3.12

.github/workflows/python-somacore.yaml

@@ -12,19 +12,19 @@ jobs:
   format-check:
     runs-on: ubuntu-latest
     env:
-      PYTHON_VERSION: "3.8"
+      PYTHON_VERSION: "3.9"
     steps:
       - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           cache: pip
-          cache-dependency-path: python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
+          cache-dependency-path: "python-spec/requirements-py${{ env.PYTHON_VERSION }}*.txt"
 
       - name: Install static analysis packages
-        run: |
-          pip install -r python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
+        working-directory: python-spec
+        run: pip install -r requirements-py${PYTHON_VERSION}.txt -r requirements-py${PYTHON_VERSION}-lint.txt
 
       - name: Restore pre-commit cache
         uses: actions/cache@v3
@@ -45,14 +45,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # setuptools-scm needs a deep clone so it can look through history
           # to find a relevant tag.
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
@@ -78,8 +78,8 @@ jobs:
       && startsWith(github.event.release.tag_name, 'python-')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           cache: pip
           cache-dependency-path: python-spec/requirements-py3.10.txt

pyproject.toml

@@ -22,9 +22,10 @@ dependencies = [
   # Remove this once we can specify a recent pyarrow.
   "pyarrow-hotfix",
   "scipy",
+  "shapely",
   "typing-extensions>=4.1", # For LiteralString (py3.11)
 ]
-requires-python = "~=3.8"
+requires-python = ">=3.9"
 urls = { repository = "https://github.com/single-cell-data/SOMA.git" }
 classifiers = ["License :: OSI Approved :: MIT License"]
 
@@ -43,7 +44,7 @@ tag_regex = '^python-(?P<version>[vV]?\d+(?:\.\d+){0,2}[^\+]*)(?:\+.*)?$'
 
 [tool.ruff]
 lint.extend-select = ["I"]
-target-version = "py38"
+target-version = "py39"
 
 [tool.ruff.lint.isort]
 force-single-line = true
@@ -54,13 +55,13 @@ single-line-exclusions = ["typing", "typing_extensions"]
 check_untyped_defs = true
 enable_error_code = ["ignore-without-code"]
 warn_redundant_casts = true
-python_version = 3.8
+python_version = 3.9
 # We want to enable this but it won't work when running locally due to the
 # presence of _version.py (which invalidates the ignore, which causes an error).
 #
 #     warn_unused_ignores = true
 
 [[tool.mypy.overrides]]
 # These dependencies do not currently have canonical type stubs.
-module = ["anndata", "pyarrow", "pyarrow_hotfix", "scipy"]
+module = ["anndata", "pyarrow", "pyarrow.compute", "pyarrow_hotfix", "scipy", "shapely"]
 ignore_missing_imports = true

python-spec/requirements-py3.10.txt

@@ -14,6 +14,7 @@ pyarrow-hotfix==0.6
 python-dateutil==2.9.0.post0
 pytz==2024.1
 scipy==1.13.1
+shapely==2.0.4
 six==1.16.0
 typing_extensions==4.12.2
 tzdata==2024.1

python-spec/requirements-py3.11.txt

@@ -12,6 +12,7 @@ pyarrow==16.1.0
 pyarrow-hotfix==0.6
 python-dateutil==2.9.0.post0
 pytz==2024.1
+shapely==2.0.4
 scipy==1.13.1
 six==1.16.0
 typing_extensions==4.12.2

python-spec/requirements-py3.12.txt

@@ -14,6 +14,7 @@ python-dateutil==2.9.0.post0
 pytz==2024.1
 scipy==1.13.1
 setuptools==70.0.0
+shapely==2.0.4
 six==1.16.0
 typing_extensions==4.12.2
 tzdata==2024.1

python-spec/requirements-py3.9-lint.txt

@@ -0,0 +1,3 @@
+mypy==1.11.2
+pandas-stubs==2.2.2.240807  # last version which supports Python 3.9
+pre-commit==3.8.0

python-spec/requirements-py3.9.txt

@@ -18,6 +18,7 @@ pytz==2024.1
 rsa==4.7.2
 s3transfer==0.6.0
 scipy==1.13.1
+shapely==2.0.4
 six==1.16.0
 typing_extensions==4.12.2
 tzdata==2024.1

python-spec/src/somacore/__init__.py

@@ -16,6 +16,13 @@
 
 from .base import SOMAObject
 from .collection import Collection
+from .coordinates import AffineTransform
+from .coordinates import Axis
+from .coordinates import CoordinateSpace
+from .coordinates import CoordinateTransform
+from .coordinates import IdentityTransform
+from .coordinates import ScaleTransform
+from .coordinates import UniformScaleTransform
 from .data import DataFrame
 from .data import DenseNDArray
 from .data import NDArray
@@ -30,6 +37,12 @@
 from .query import AxisColumnNames
 from .query import AxisQuery
 from .query import ExperimentAxisQuery
+from .scene import Scene
+from .spatial import GeometryDataFrame
+from .spatial import ImageProperties
+from .spatial import MultiscaleImage
+from .spatial import PointCloudDataFrame
+from .spatial import SpatialRead
 from .types import ContextBase
 
 try:
@@ -52,13 +65,26 @@
     "ReadIter",
     "SparseNDArray",
     "SparseRead",
+    "SpatialRead",
     "Experiment",
     "Measurement",
+    "Scene",
+    "ImageProperties",
+    "MultiscaleImage",
+    "GeometryDataFrame",
+    "PointCloudDataFrame",
     "BatchSize",
     "IOfN",
     "ResultOrder",
     "AxisColumnNames",
     "AxisQuery",
     "ExperimentAxisQuery",
     "ContextBase",
+    "Axis",
+    "CoordinateSpace",
+    "CoordinateTransform",
+    "AffineTransform",
+    "ScaleTransform",
+    "UniformScaleTransform",
+    "IdentityTransform",
 )

python-spec/src/somacore/collection.py

@@ -1,5 +1,14 @@
 import abc
-from typing import Any, MutableMapping, Optional, Sequence, Type, TypeVar, overload
+from typing import (
+    Any,
+    MutableMapping,
+    Optional,
+    Sequence,
+    Tuple,
+    Type,
+    TypeVar,
+    overload,
+)
 
 import pyarrow as pa
 from typing_extensions import Final, Self
@@ -145,6 +154,7 @@ def add_new_dataframe(
         uri: Optional[str] = None,
         schema: pa.Schema,
         index_column_names: Sequence[str] = (options.SOMA_JOINID,),
+        domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
         platform_config: Optional[options.PlatformConfig] = None,
     ) -> data.DataFrame:
         """Creates a new DataFrame as a child of this collection.