Merge branch 'main' into dark/spatial-datatypes

.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

@@ -25,7 +25,7 @@ dependencies = [
   "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"]
 
@@ -44,7 +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
@@ -55,7 +55,7 @@ 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).
 #

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/src/somacore/coordinates.py

@@ -26,9 +26,7 @@ class Axis:
 
 
 @attrs.define(frozen=True)
-class CoordinateSpace(
-    collections.abc.Sequence
-):  # Change to Sequence[Axis] after 3.8 is dropped.
+class CoordinateSpace(collections.abc.Sequence[Axis]):
     """A coordinate space for spatial data.
 
     Args:

python-spec/src/somacore/types.py

@@ -57,7 +57,7 @@ def str_or_seq_length(obj: Union[str, Sequence[str]]) -> int:
 class Slice(Protocol[_T_co]):
     """A slice which stores a certain type of object.
 
-    This protocol describes the built in ``slice`` type, with a hint to callers
+    This protocol describes the built-in ``slice`` type, with a hint to callers
     about what type they should put *inside* the slice.  It is for type
     annotations only and is not runtime-checkable (i.e., you can't do
     ``isinstance(thing, Slice)``), because ``range`` objects also have
@@ -86,7 +86,7 @@ def stop(self) -> Optional[_T_co]: ...
     def step(self) -> Optional[_T_co]: ...
 
     if sys.version_info < (3, 10) and not TYPE_CHECKING:
-        # Python 3.9 and below have a bug where any Protocol with an @property
+        # Python 3.9 and below have a bug where any Protocol with a @property
         # was always regarded as runtime-checkable.
         @classmethod
         def __subclasscheck__(cls, __subclass: type) -> NoReturn:

python-spec/testing/test_coordinates.py

@@ -2,6 +2,8 @@
 import pytest
 
 from somacore import AffineTransform
+from somacore import Axis
+from somacore import CoordinateSpace
 from somacore import CoordinateTransform
 from somacore import IdentityTransform
 from somacore import ScaleTransform
@@ -28,6 +30,15 @@ def check_transform_is_equal(
         assert False
 
 
+def test_coordinate_space():
+    coord_space = CoordinateSpace(
+        (Axis("x", unit="nanometer"), Axis("y", unit="nanometer"))  # type: ignore[arg-type]
+    )
+    assert len(coord_space) == 2
+    assert coord_space.axis_names == ("x", "y")
+    assert coord_space[0] == Axis("x", unit="nanometer")
+
+
 @pytest.mark.parametrize(
     ("input", "expected"),
     [

python-spec/update-requirements-txt

@@ -10,9 +10,9 @@ TEMPDIR="$(mktemp -d)"
 trap "trash $TEMPDIR" EXIT
 
 # The version of Python we want to run lints under.
-LINTVER=3.8
+LINTVER=3.9
 
-for PYVER in 3.8 3.9 3.10 3.11 3.12; do
+for PYVER in 3.9 3.10 3.11 3.12; do
   CONDIR="$TEMPDIR/py-$PYVER"
   conda create -y -p "$CONDIR" "python=$PYVER"
   (