[python] Drop support for Python 3.8 (#3021)

* Drop 3.8 support

* lint, update numpy type aliases comment

* Bump R version to `4.3.2`

Co-authored-by: John Kerl <[email protected]>

---------

Co-authored-by: Agisilaos Kounelis <[email protected]>
Co-authored-by: John Kerl <[email protected]>

.github/ISSUE_TEMPLATE/bug_report.md

@@ -15,7 +15,7 @@ Provide a code example and any sample input data (e.g. an H5AD) as an attachment
 
 **Versions (please complete the following information):**
  - TileDB-SOMA version:
- - Language and language version (e.g. Python 3.8, R 4.2.2):
+ - Language and language version (e.g. Python 3.9, R 4.3.2):
  - OS (e.g. MacOS, Ubuntu Linux):
  - Note: you can use `tiledbsoma.show_package_versions()` (Python) or `tiledbsoma::show_package_versions()` (R)
 

.github/workflows/python-ci-full.yml

@@ -25,7 +25,7 @@ jobs:
         # os: [ubuntu-22.04, macos-12, windows-2019]
         # TODO: add 3.12
         # https://github.com/single-cell-data/TileDB-SOMA/issues/1849
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
         include:
           - runs-on: ubuntu-22.04
             cc: gcc-11

.github/workflows/python-ci-minimal.yml

@@ -29,7 +29,7 @@ jobs:
 
       matrix:
         os: [ubuntu-22.04, macos-12]
-        python-version: ['3.8', '3.11']
+        python-version: ['3.9', '3.11']
         include:
           - os: ubuntu-22.04
             cc: gcc-11

apis/python/pyproject.toml

@@ -12,7 +12,7 @@ show_error_codes = true
 ignore_missing_imports = true
 warn_unreachable = true
 strict = true
-python_version = 3.8
+python_version = 3.9
 
 [[tool.mypy.overrides]]
 module = "tiledbsoma._query_condition"

apis/python/setup.py

@@ -288,7 +288,6 @@ def run(self):
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: Microsoft :: Windows",
         "Programming Language :: Python",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
@@ -327,7 +326,7 @@ def run(self):
     setup_requires=["pybind11"],
     install_requires=[
         # Tracked in https://github.com/single-cell-data/TileDB-SOMA/issues/1785
-        "anndata != 0.10.0; python_version>='3.8'",
+        "anndata != 0.10.0",
         "attrs>=22.2",
         "numba>=0.58.0",
         "numpy<2.0",
@@ -343,7 +342,7 @@ def run(self):
     extras_require={
         "dev": open("requirements_dev.txt").read(),
     },
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     cmdclass={"build_ext": build_ext, "bdist_wheel": bdist_wheel},
     version=version.get_version(),
 )

apis/python/src/tiledbsoma/_general_utilities.py

@@ -5,6 +5,7 @@
 
 """General utility functions.
 """
+import importlib.metadata
 import platform
 import sys
 import warnings
@@ -34,20 +35,11 @@ def get_implementation_version() -> str:
 
     Lifecycle: Maturing.
     """
-    if sys.version_info < (3, 8, 0):
-        from pkg_resources import DistributionNotFound, get_distribution
-
-        try:
-            return get_distribution("tiledbsoma").version
-        except DistributionNotFound:
-            return "unknown"
-    else:
-        import importlib.metadata
-
-        try:
-            return importlib.metadata.version("tiledbsoma")
-        except importlib.metadata.PackageNotFoundError:
-            return "unknown"
+
+    try:
+        return importlib.metadata.version("tiledbsoma")
+    except importlib.metadata.PackageNotFoundError:
+        return "unknown"
 
 
 def assert_version_before(major: int, minor: int) -> None:

apis/python/src/tiledbsoma/_types.py

@@ -32,15 +32,14 @@
     PDSeries = pd.Series
     PDIndex = pd.Index
 
-    # Type subscription requires python >= 3.9, and we currently only type-check against 3.11.
-    # TODO: remove these (and unify around subscripted types above) when we drop support for 3.8.
+    # Tests pass `Matrix` (type alias which includes `NPNDArray`, via `DenseMatrix`), as well as other numpy types, to
+    # `isinstance`, which causes error "argument 2 cannot be a parameterized generic" using the typedefs in the
+    # `TYPE_CHECKING` branch above.
     NPInteger = np.integer
     NPFloating = np.floating
-    # This alias likely needs to remain special-cased, even in Python ≥3.11, as tests pass the `Matrix` type alias
-    # (which includes `NPNDArray` via `DenseMatrix`) to `isinstance`, causing error "argument 2 cannot be a
-    # parameterized generic".
     NPNDArray = np.ndarray
 
+
 Path = Union[str, pathlib.Path]
 
 Ids = Union[List[str], List[bytes], List[int]]

apis/python/src/tiledbsoma/io/ingest.py

@@ -2655,11 +2655,11 @@ def _ingest_uns_string_array(
     """
 
     if len(value.shape) == 1:
-        helper = _ingest_uns_1d_string_array  # type:ignore[unreachable]
+        helper = _ingest_uns_1d_string_array
     elif len(value.shape) == 2:
         helper = _ingest_uns_2d_string_array
     else:
-        msg = (  # type:ignore[unreachable]
+        msg = (
             f"Skipped {coll.uri}[{key!r}]"
             f" (uns object): string array is neither one-dimensional nor two-dimensional"
         )

apis/python/tests/test_funcs.py

@@ -1,5 +1,4 @@
 import inspect
-import sys
 import textwrap
 
 import pytest
@@ -26,13 +25,10 @@
             "(__pos_only, *dont_shadow, do_rename: bytes = b'', **kwargs) -> complex",
             "(__pos_only, *dont_shadow_, do_rename: bytes = b'', dont_shadow: int, do_rename_: str, **do_rename__: frozenset) -> complex",
         ),
-        pytest.param(
+        (
             "(pos_only, some_name, /, dst_both_arg, *args, dst_kwarg=1, **dup_dict: complex)",
             "(dst_both_arg, dst_kwarg: int = 10, /, dup_dict: dict = (), **kwargs) -> None",
             "(dst_both_arg_, dst_kwarg_: int = 10, /, dup_dict: dict = (), *, dst_both_arg, dst_kwarg=1, **dup_dict_: complex) -> None",
-            marks=pytest.mark.skipif(
-                sys.version_info < (3, 8), reason="/ is new in 3.8"
-            ),
         ),
     ],
 )

libtiledbsoma/README.md

@@ -3,7 +3,7 @@
 ## System Dependencies
 
 * C++17 compiler
-* Python 3.8+
+* Python 3.9+
 
 Run these commands to setup a fresh Ubuntu 22.04 instance (tested on x86 and Arm):
 ```