Merge branch 'main' into autodiff-uncerts

scikit-hep · Apr 23, 2024 · 5d3d3d6 · 5d3d3d6
2 parents d3142fc + 64ab264
commit 5d3d3d6
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Showing 86 changed files with 866 additions and 430 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,6 +5,10 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
     labels:
       - "github-actions"
       - "dependencies"

diff --git a/.github/workflows/bump-version.yml b/.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@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install Python dependencies
       run: |

diff --git a/.github/workflows/ci-windows.yml b/.github/workflows/ci-windows.yml
@@ -0,0 +1,46 @@
+name: CI on Windows
+
+on:
+  # Run daily at 1:23 UTC
+  schedule:
+  - cron:  '23 1 * * *'
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade '.[all,test]'
+
+    - name: List installed Python packages
+      run: python -m pip list
+
+    - name: Test with pytest and coverage
+      # FIXME: ignore tests/test_scripts.py as runner breaks on Windows currently
+      run: |
+        coverage run --module pytest --ignore tests/test_scripts.py --ignore tests/contrib --ignore tests/benchmarks --ignore tests/test_notebooks.py
+
+    - name: Coverage report for core project
+      run: |
+        coverage report
+        coverage xml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -27,23 +27,26 @@ 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: '3.12'
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install --upgrade .[test]
+        python -m pip install --upgrade ".[all,test]"
 
     - name: List installed Python packages
       run: python -m pip list
@@ -66,10 +69,12 @@ jobs:
       if: >-
         github.event_name != 'schedule' &&
         matrix.os == 'ubuntu-latest'
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
+        fail_ci_if_error: true
         files: ./coverage.xml
         flags: unittests-${{ matrix.python-version }}
+        token: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Test Contrib module with pytest
       run: |
@@ -81,30 +86,35 @@ jobs:
         coverage xml
 
     - name: Report contrib coverage with Codecov
-      if: github.event_name != 'schedule' && matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
-      uses: codecov/codecov-action@v3
+      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
         files: ./coverage.xml
         flags: contrib
+        token: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Test docstring examples with doctest
-      if: matrix.python-version == '3.11'
+      # TODO: Don't currently try to match amd64 and arm64 floating point for docs, but will in the future.
+      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'
+      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'
-      uses: codecov/codecov-action@v3
+      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
         files: doctest-coverage.xml
         flags: doctest
+        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
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -26,7 +26,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: python
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -35,4 +35,4 @@ jobs:
         # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/dependencies-head.yml b/.github/workflows/dependencies-head.yml
@@ -17,20 +17,20 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade --pre .[test]
+        python -m pip --no-cache-dir --quiet install --upgrade --pre ".[all,test]"
         python -m pip list
 
     - name: List release candidates, alpha, and beta releases
@@ -47,13 +47,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -62,7 +62,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
+        python -m pip --no-cache-dir --quiet install --upgrade ".[all,test]"
         python -m pip uninstall --yes scipy
         python -m pip install --upgrade --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy
         python -m pip list
@@ -77,18 +77,18 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
+        python -m pip --no-cache-dir --quiet install --upgrade ".[all,test]"
         python -m pip uninstall --yes iminuit
         python -m pip install --upgrade cython
         python -m pip install --upgrade git+https://github.com/scikit-hep/iminuit.git
@@ -103,18 +103,18 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
+        python -m pip --no-cache-dir --quiet install --upgrade ".[all,test]"
         python -m pip uninstall --yes uproot
         python -m pip install --upgrade git+https://github.com/scikit-hep/uproot5.git
         python -m pip list
@@ -128,20 +128,20 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
+        python -m pip --no-cache-dir --quiet install --upgrade ".[all,test]"
         python -m pip uninstall --yes matplotlib
         # Need to use --extra-index-url as dependencies aren't on scientific-python-nightly-wheels package index.
         # Need to use --pre as dev releases will need priority over stable releases.
@@ -165,18 +165,18 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
+        python -m pip --no-cache-dir --quiet install --upgrade ".[all,test]"
         python -m pip uninstall --yes pytest
         python -m pip install --upgrade git+https://github.com/pytest-dev/pytest.git
         python -m pip list

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -22,9 +22,9 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install Python dependencies
       run: |
@@ -91,7 +91,7 @@ jobs:
         done
 
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v2
+      uses: actions/upload-pages-artifact@v3
       with:
         path: 'docs/_build/html'
 
@@ -113,8 +113,8 @@ jobs:
 
     steps:
     - name: Setup Pages
-      uses: actions/configure-pages@v3
+      uses: actions/configure-pages@v5
 
     - name: Deploy to GitHub Pages
       id: deployment
-      uses: actions/deploy-pages@v2
+      uses: actions/deploy-pages@v4
diff --git a/.github/workflows/lower-bound-requirements.yml b/.github/workflows/lower-bound-requirements.yml
@@ -20,14 +20,14 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies and force lowest bound
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir install --constraint tests/constraints.txt .[test]
+        python -m pip --no-cache-dir install --constraint tests/constraints.txt ".[all,test]"
 
     - name: List installed Python packages
       run: python -m pip list

diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml
@@ -16,21 +16,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
         # FIXME: c.f. https://github.com/scikit-hep/pyhf/issues/2104
-        python -m pip install --upgrade .[test] 'jupyter-client<8.0.0'
+        python -m pip install --upgrade ".[all,test]" 'jupyter-client<8.0.0'
 
     - name: List installed Python packages
       run: python -m pip list