ci: Add Python 3.12 to testing to CI as default (#2460)

* Add Python 3.12 to testing in CI.
* Default to using Python 3.12 in GitHub Actions where possible.
* Add ignore of DeprecationWarning for protobuf
* Add Python 3.12 trove classifier to PyPI metadata.

Author: matthewfeickert

.github/workflows/bump-version.yml

@@ -196,11 +196,11 @@ jobs:
         echo "steps.script.outputs.old_tag=v${current_tag}"
         echo "old_tag=v${current_tag}" >> $GITHUB_OUTPUT
 
-    - name: Set up Python 3.11
+    - name: Set up Python 3.12
       if: success()
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install Python dependencies
       run: |

.github/workflows/ci-windows.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/ci.yml

@@ -27,13 +27,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         include:
           - os: macos-latest
-            python-version: '3.11'
+            python-version: '3.12'
           # Apple silicon runner
           - os: macos-14
-            python-version: '3.11'
+            python-version: '3.12'
 
     steps:
     - uses: actions/checkout@v4
@@ -86,7 +86,7 @@ jobs:
         coverage xml
 
     - name: Report contrib coverage with Codecov
-      if: github.event_name != 'schedule' && matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
+      if: github.event_name != 'schedule' && matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: true
@@ -96,17 +96,17 @@ jobs:
 
     - name: Test docstring examples with doctest
       # TODO: Don't currently try to match amd64 and arm64 floating point for docs, but will in the future.
-      if: matrix.python-version == '3.11' && matrix.os != 'macos-14'
+      if: matrix.python-version == '3.12' && matrix.os != 'macos-14'
       run: coverage run --data-file=.coverage-doctest --module pytest src/ README.rst
 
     - name: Coverage report for doctest only
-      if: matrix.python-version == '3.11' && matrix.os != 'macos-14'
+      if: matrix.python-version == '3.12' && matrix.os != 'macos-14'
       run: |
         coverage report --data-file=.coverage-doctest
         coverage xml --data-file=.coverage-doctest -o doctest-coverage.xml
 
     - name: Report doctest coverage with Codecov
-      if: github.event_name != 'schedule' && matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
+      if: github.event_name != 'schedule' && matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: true
@@ -115,6 +115,6 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Run benchmarks
-      if: github.event_name == 'schedule' && matrix.python-version == '3.11'
+      if: github.event_name == 'schedule' && matrix.python-version == '3.12'
       run: |
         pytest --benchmark-sort=mean tests/benchmarks/test_benchmark.py

.github/workflows/dependencies-head.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -47,7 +47,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -77,7 +77,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -103,7 +103,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -128,7 +128,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -165,7 +165,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/docs.yml

@@ -24,7 +24,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install Python dependencies
       run: |

.github/workflows/notebooks.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/publish-package.yml

@@ -36,10 +36,10 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Set up Python 3.11
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install python-build and twine
       run: |

.github/workflows/release_tests.yml

@@ -18,10 +18,10 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         include:
           - os: macos-latest
-            python-version: '3.11'
+            python-version: '3.12'
 
     steps:
     - uses: actions/checkout@v4

pyproject.toml

@@ -39,6 +39,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: Implementation :: CPython",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Physics",
@@ -106,7 +107,7 @@ test = [
     "pytest-mpl",
     "ipympl>=0.3.0",
     "pydocstyle",
-    "papermill~=2.3.4",
+    "papermill~=2.5.0",
     "scrapbook~=0.5.0",
     "jupyter",
     "graphviz",
@@ -225,6 +226,7 @@ filterwarnings = [
     "ignore:ml_dtypes.float8_e4m3b11 is deprecated.",  #FIXME: Can remove when jaxlib>=0.4.12
     "ignore:jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the:DeprecationWarning",  # Issue #2139
     "ignore:Skipping device Apple Paravirtual device that does not support Metal 2.0:UserWarning",  # Can't fix given hardware/virtualized device
+    'ignore:Type google._upb._message.[A-Z]+ uses PyType_Spec with a metaclass that has custom:DeprecationWarning',  # protobuf via tensorflow
 ]
 
 [tool.coverage.run]