Backport PR #1373: Test against and list support for python 3.12 (#1377)

Co-authored-by: Isaac Virshup <[email protected]>

.azure-pipelines.yml

@@ -15,14 +15,14 @@ jobs:
       vmImage: "ubuntu-22.04"
     strategy:
       matrix:
-        Python3.11:
-          python.version: "3.11"
+        Python3.12:
+          python.version: "3.12"
           RUN_COVERAGE: yes
           TEST_TYPE: "coverage"
         Python3.9:
           python.version: "3.9"
         PreRelease:
-          python.version: "3.11"
+          python.version: "3.12"
           DEPENDENCIES_VERSION: "pre-release"
           TEST_TYPE: "strict-warning"
         minimum_versions:
@@ -105,8 +105,8 @@ jobs:
     steps:
       - task: UsePythonVersion@0
         inputs:
-          versionSpec: "3.11"
-        displayName: "Use Python 3.11"
+          versionSpec: "3.12"
+        displayName: "Use Python 3.12"
 
       - script: |
           python -m pip install --upgrade pip

.github/workflows/benchmark.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.11"]
+        python: ["3.12"]
         os: [ubuntu-latest]
 
     env:

.readthedocs.yml

@@ -2,7 +2,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.11"
+    python: "3.12"
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: true # do not change or you will be fired

anndata/tests/test_layers.py

@@ -81,7 +81,12 @@ def test_readwrite_loom(tmp_path):
     adata = AnnData(X=X, layers=dict(L=L.copy()))
 
     with warnings.catch_warnings():
-        warnings.simplefilter("ignore", NumbaDeprecationWarning)
+        warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
+        warnings.filterwarnings(
+            "ignore",
+            message=r"datetime.datetime.utcnow\(\) is deprecated",
+            category=DeprecationWarning,
+        )
         adata.write_loom(loom_path)
     adata_read = read_loom(loom_path, X_name="")
 

anndata/tests/test_readwrite.py

@@ -392,7 +392,12 @@ def test_readwrite_loom(typ, obsm_mapping, varm_mapping, tmp_path):
     adata_src.varm["X_b"] = np.zeros((adata_src.n_vars, 3))
 
     with warnings.catch_warnings():
-        warnings.simplefilter("ignore", NumbaDeprecationWarning)
+        warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
+        warnings.filterwarnings(
+            "ignore",
+            message=r"datetime.datetime.utcnow\(\) is deprecated",
+            category=DeprecationWarning,
+        )
         adata_src.write_loom(tmp_path / "test.loom", write_obsm_varm=True)
 
     adata = ad.read_loom(
@@ -427,7 +432,15 @@ def test_readwrite_loom(typ, obsm_mapping, varm_mapping, tmp_path):
 def test_readloom_deprecations(tmp_path):
     loom_pth = tmp_path / "test.loom"
     adata_src = gen_adata((5, 10), obsm_types=[np.ndarray], varm_types=[np.ndarray])
-    adata_src.write_loom(loom_pth, write_obsm_varm=True)
+
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
+        warnings.filterwarnings(
+            "ignore",
+            message=r"datetime.datetime.utcnow\(\) is deprecated",
+            category=DeprecationWarning,
+        )
+        adata_src.write_loom(loom_pth, write_obsm_varm=True)
 
     # obsm_names -> obsm_mapping
     obsm_mapping = {"df": adata_src.obs.columns}
@@ -536,7 +549,13 @@ def test_readwrite_empty(read, write, name, tmp_path):
 
 
 def test_read_excel():
-    adata = ad.read_excel(HERE / "data/excel.xlsx", "Sheet1", dtype=int)
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            message=r"datetime.datetime.utcnow\(\) is deprecated",
+            category=DeprecationWarning,
+        )
+        adata = ad.read_excel(HERE / "data/excel.xlsx", "Sheet1", dtype=int)
     assert adata.X.tolist() == X_list
 
 

docs/release-notes/0.10.6.md

@@ -17,3 +17,4 @@
 ```
 
 * `anndata`'s CI now tests against minimum versions of it's dependencies. As a result, several dependencies had their minimum required version bumped. See diff for details {pr}`1314` {user}`ivirshup`
+* `anndata` now tests against Python 3.12 {pr}`1373` {user}`ivirshup`

pyproject.toml

@@ -32,6 +32,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Visualization",
 ]