From 63c7ba8d00f21970e2970e6f4a7e8c63c36d9685 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.williams@tiledb.com>
Date: Mon, 23 Sep 2024 16:04:54 -0400
Subject: [PATCH] drop Python 3.8 support (#224)

---
 .github/workflows/python-somacore.yaml  |  4 ++--
 pyproject.toml                          |  6 +++---
 python-spec/requirements-py3.8-lint.txt |  3 ---
 python-spec/requirements-py3.8.txt      | 19 -------------------
 python-spec/requirements-py3.9-lint.txt |  3 +++
 python-spec/src/somacore/coordinates.py |  3 +--
 python-spec/update-requirements-txt     |  4 ++--
 7 files changed, 11 insertions(+), 31 deletions(-)
 delete mode 100644 python-spec/requirements-py3.8-lint.txt
 delete mode 100644 python-spec/requirements-py3.8.txt
 create mode 100644 python-spec/requirements-py3.9-lint.txt

diff --git a/.github/workflows/python-somacore.yaml b/.github/workflows/python-somacore.yaml
index b6611425..a23d6773 100644
--- a/.github/workflows/python-somacore.yaml
+++ b/.github/workflows/python-somacore.yaml
@@ -12,7 +12,7 @@ jobs:
   format-check:
     runs-on: ubuntu-latest
     env:
-      PYTHON_VERSION: "3.8"
+      PYTHON_VERSION: "3.9"
     steps:
       - uses: actions/checkout@v3
 
@@ -45,7 +45,7 @@ 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@v4
         with:
diff --git a/pyproject.toml b/pyproject.toml
index 1cf68cc6..63c415fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
   "scipy",
   "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 +43,7 @@ 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
@@ -54,7 +54,7 @@ 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).
 #
diff --git a/python-spec/requirements-py3.8-lint.txt b/python-spec/requirements-py3.8-lint.txt
deleted file mode 100644
index 5b1ec208..00000000
--- a/python-spec/requirements-py3.8-lint.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-mypy==1.11.2
-pandas-stubs==2.0.3.230814  # last version that supports Python 3.8
-pre-commit==3.5.0
diff --git a/python-spec/requirements-py3.8.txt b/python-spec/requirements-py3.8.txt
deleted file mode 100644
index 7da2b9f5..00000000
--- a/python-spec/requirements-py3.8.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-anndata==0.9.2
-attrs==23.2.0
-h5py==3.11.0
-importlib_metadata==7.1.0
-llvmlite==0.41.1
-natsort==8.4.0
-numba==0.58.1
-numpy==1.24.4
-packaging==24.1
-pandas==2.0.3
-pyarrow==16.1.0
-pyarrow-hotfix==0.6
-python-dateutil==2.9.0.post0
-pytz==2024.1
-scipy==1.10.1
-six==1.16.0
-typing_extensions==4.12.2
-tzdata==2024.1
-zipp==3.19.2
diff --git a/python-spec/requirements-py3.9-lint.txt b/python-spec/requirements-py3.9-lint.txt
new file mode 100644
index 00000000..aef1a068
--- /dev/null
+++ b/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
diff --git a/python-spec/src/somacore/coordinates.py b/python-spec/src/somacore/coordinates.py
index 727dac3d..83555e88 100644
--- a/python-spec/src/somacore/coordinates.py
+++ b/python-spec/src/somacore/coordinates.py
@@ -35,8 +35,7 @@ class CoordinateSpace(collections.abc.Sequence):
     Lifecycle: experimental
     """
 
-    # Change to Sequence[Axis] after 3.8 is dropped.
-    axes: Tuple[Axis, ...] = attrs.field(converter=tuple)
+    axes: Sequence[Axis] = attrs.field(converter=tuple)
 
     @axes.validator
     def _validate(self, _, axes: Tuple[Axis, ...]) -> None:
diff --git a/python-spec/update-requirements-txt b/python-spec/update-requirements-txt
index 172bee02..42f9b88a 100755
--- a/python-spec/update-requirements-txt
+++ b/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"
   (