Merge branch 'master' into dp/shareparams

PlasmaControl · Feb 13, 2025 · d9943d6 · d9943d6
2 parents d159675 + f4cb154
commit d9943d6
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,44 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    groups:
+      # group similar dependencies together into fewer PRs
+      docs:
+        patterns:
+          - "sphinx"
+      linting:
+        patterns:
+          - "flake8"
+          - "black"
+          - "pre-commit"
+      testing:
+        patterns:
+          - "pytest"
+          - "qic"
+          - "qsc"
+          - "shapely"
+      minor_packages:
+        patterns:
+          - "colorama"
+          - "nvgpu"
+          - "psutil"
+          - "pylatexenc"
+          - "termcolor"
+      jax:
+        patterns:
+          - "jax"
+          - "diffrax"
+          - "interpax"
+          - "orthax"
+          - "quadax"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -58,30 +58,45 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Check full Python version
+        run: |
+          python --version
+          python_version=$(python --version 2>&1 | cut -d' ' -f2)
+          echo "Python version: $python_version"
+          echo "version=$python_version" >> $GITHUB_ENV
+
       - name: Restore Python environment cache
         if: env.has_changes == 'true'
         id: restore-env
         uses: actions/cache/restore@v4
         with:
-          path: .venv-${{ matrix.python-version }}
-          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+          path: .venv-${{ env.version }}
+          key: ${{ runner.os }}-venv-${{ env.version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
 
       - name: Set up virtual environment if not restored from cache
         if: steps.restore-env.outputs.cache-hit != 'true' && env.has_changes == 'true'
         run: |
           gh cache list
-          python -m venv .venv-${{ matrix.python-version }}
-          source .venv-${{ matrix.python-version }}/bin/activate
+          python -m venv .venv-${{ env.version }}
+          source .venv-${{ env.version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
           pip install matplotlib==3.9.2
 
-      - name: Benchmark with pytest-benchmark (PR)
+      - name: Action Details
         if: env.has_changes == 'true'
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
+          source .venv-${{ env.version }}/bin/activate
+          which python
+          python --version
           pwd
           lscpu
+          pip list
+
+      - name: Benchmark with pytest-benchmark (PR)
+        if: env.has_changes == 'true'
+        run: |
+          source .venv-${{ env.version }}/bin/activate
           cd tests/benchmarks
           python -m pytest benchmark_cpu_small.py -vv \
             --benchmark-save='Latest_Commit' \
@@ -105,9 +120,7 @@ jobs:
       - name: Benchmark with pytest-benchmark (MASTER)
         if: env.has_changes == 'true'
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
-          pwd
-          lscpu
+          source .venv-${{ env.version }}/bin/activate
           cd tests/benchmarks
           python -m pytest benchmark_cpu_small.py -vv \
             --benchmark-save='master' \
@@ -120,7 +133,7 @@ jobs:
       - name: Put benchmark results in same folder
         if: env.has_changes == 'true'
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
+          source .venv-${{ env.version }}/bin/activate
           pwd
           cd tests/benchmarks
           find .benchmarks/ -type f -printf "%T@ %p\n" | sort -n | cut -d' ' -f 2- | tail -n 1 > temp1
@@ -141,20 +154,20 @@ jobs:
       - name: Compare latest commit results to the master branch results
         if: env.has_changes == 'true'
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
+          source .venv-${{ env.version }}/bin/activate
           cd tests/benchmarks
           pwd
           python compare_bench_results.py
           cat commit_msg.txt
 
       - name: Comment PR with the results
         if: env.has_changes == 'true'
-        uses: thollander/actions-comment-pull-request@v2
+        uses: thollander/actions-comment-pull-request@v3
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
         with:
-          filePath: tests/benchmarks/commit_msg.txt
-          comment_tag: benchmark
+          file-path: tests/benchmarks/commit_msg.txt
+          comment-tag: benchmark
 
       - name: Upload benchmark data
         if: always() && env.has_changes == 'true'

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -19,25 +19,32 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Check full Python version
+        run: |
+          python --version
+          python_version=$(python --version 2>&1 | cut -d' ' -f2)
+          echo "Python version: $python_version"
+          echo "version=$python_version" >> $GITHUB_ENV
+
       - name: Restore Python environment cache
         id: restore-env
         uses: actions/cache/restore@v4
         with:
-          path: .venv-${{ matrix.python-version }}
-          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+          path: .venv-${{ env.version }}
+          key: ${{ runner.os }}-venv-${{ env.version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
 
       - name: Set up virtual environment if not restored from cache
         if: steps.restore-env.outputs.cache-hit != 'true'
         run: |
           gh cache list
-          python -m venv .venv-${{ matrix.python-version }}
-          source .venv-${{ matrix.python-version }}/bin/activate
+          python -m venv .venv-${{ env.version }}
+          source .venv-${{ env.version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
 
       - name: Check files using the black formatter
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
+          source .venv-${{ env.version }}/bin/activate
           black --version
           black --check desc/ tests/ || black_return_code=$?
           echo "BLACK_RETURN_CODE=$black_return_code" >> $GITHUB_ENV

diff --git a/.github/workflows/cache_dependencies.yml b/.github/workflows/cache_dependencies.yml
@@ -24,21 +24,28 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Check full Python version
+        run: |
+          python --version
+          python_version=$(python --version 2>&1 | cut -d' ' -f2)
+          echo "Python version: $python_version"
+          echo "version=$python_version" >> $GITHUB_ENV
+
       - name: Delete old cached file with same python version
         run: |
           echo "Current Cached files list"
           gh cache list
-          echo "Deleting cached files with pattern: ${{ runner.os }}-venv-${{ matrix.python-version }}-"
-          for cache_key in $(gh cache list --json key -q ".[] | select(.key | startswith(\"${{ runner.os }}-venv-${{ matrix.python-version }}-\")) | .key"); do
+          echo "Deleting cached files with pattern: ${{ runner.os }}-venv-${{ env.version }}-"
+          for cache_key in $(gh cache list --json key -q ".[] | select(.key | startswith(\"${{ runner.os }}-venv-${{ env.version }}-\")) | .key"); do
             echo "Deleting cache with key: $cache_key"
             gh cache delete "$cache_key"
           done
 
       # Update the matplotlib version if needed later
       - name: Set up virtual environment
         run: |
-          python -m venv .venv-${{ matrix.python-version }}
-          source .venv-${{ matrix.python-version }}/bin/activate
+          python -m venv .venv-${{ env.version }}
+          source .venv-${{ env.version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
           pip install matplotlib==3.9.2
@@ -47,12 +54,13 @@ jobs:
         id: cache-env
         uses: actions/cache@v4
         with:
-          path: .venv-${{ matrix.python-version }}
-          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+          path: .venv-${{ env.version }}
+          key: ${{ runner.os }}-venv-${{ env.version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
 
       - name: Verify virtual environment activation
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
+          source .venv-${{ env.version }}/bin/activate
+          which python
           python --version
           pip --version
           pip list
diff --git a/.github/workflows/jax_tests.yml b/.github/workflows/jax_tests.yml
@@ -15,10 +15,11 @@ jobs:
         jax-version: [0.4.12, 0.4.13, 0.4.14, 0.4.16, 0.4.17,
                       0.4.18, 0.4.19, 0.4.20, 0.4.21, 0.4.22, 0.4.23,
                       0.4.24, 0.4.25, 0.4.26, 0.4.27, 0.4.28, 0.4.29,
-                      0.4.30, 0.4.31, 0.4.33, 0.4.34, 0.4.35]
+                      0.4.30, 0.4.31, 0.4.33, 0.4.34, 0.4.35, 0.4.37]
                       # 0.4.32 is not available on PyPI
                       # earlier jax versions are not compatible with other
                       # dependencies as of 2024-10-04
+                      # 0.4.36 has a bug that causes tests to fail
         group: [1, 2]
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/mpl_tests.yml b/.github/workflows/mpl_tests.yml
@@ -12,29 +12,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        mpl-version: [3.0.0]
+        mpl-version: [3.5.0]
         include:
-          - mpl-version: 3.0.0
-          - mpl-version: 3.0.1
-          - mpl-version: 3.0.2
-          - mpl-version: 3.0.3
-          - mpl-version: 3.1.0
-          - mpl-version: 3.1.1
-          - mpl-version: 3.1.2
-          - mpl-version: 3.1.3
-          - mpl-version: 3.2.0
-          - mpl-version: 3.2.1
-          - mpl-version: 3.2.2
-          - mpl-version: 3.3.0
-          - mpl-version: 3.3.1
-          - mpl-version: 3.3.2
-          - mpl-version: 3.3.3
-          - mpl-version: 3.3.4
-          - mpl-version: 3.4.0
-          - mpl-version: 3.4.1
-          - mpl-version: 3.4.2
-          - mpl-version: 3.4.3
-          - mpl-version: 3.5.0
           - mpl-version: 3.5.1
           - mpl-version: 3.5.2
           - mpl-version: 3.5.3
@@ -55,6 +34,8 @@ jobs:
           - mpl-version: 3.8.4
           - mpl-version: 3.9.0
           - mpl-version: 3.9.2
+          - mpl-version: 3.9.3
+          - mpl-version: 3.10.0
 
     steps:
       - uses: actions/checkout@v4
@@ -63,13 +44,19 @@ jobs:
         with:
           python-version: '3.10'
           cache: pip
-      - name: Install dependencies
+      - name: Install dependencies with given Matplotlib version
         run: |
-          python -m pip install --upgrade pip
-          pip install -r devtools/dev-requirements.txt
-          pip install "matplotlib==${{ matrix.mpl-version }}"
-      - name: Test with pytest
+          sed -i '/matplotlib/d' ./requirements.txt
+          sed -i '1i\matplotlib == ${{ matrix.mpl-version }}' ./requirements.txt
+          cat ./requirements.txt
+          pip install -r ./devtools/dev-requirements.txt
+
+      - name: Action Details
         run: |
           pwd
           lscpu
+          pip list
+
+      - name: Test with pytest
+        run: |
           python -m pytest tests/test_plotting.py --durations=0 --mpl --maxfail=1
diff --git a/.github/workflows/notebook_tests.yml b/.github/workflows/notebook_tests.yml
@@ -51,30 +51,45 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Check full Python version
+        run: |
+          python --version
+          python_version=$(python --version 2>&1 | cut -d' ' -f2)
+          echo "Python version: $python_version"
+          echo "version=$python_version" >> $GITHUB_ENV
+
       - name: Restore Python environment cache
         if: env.has_changes == 'true'
         id: restore-env
         uses: actions/cache/restore@v4
         with:
-          path: .venv-${{ matrix.python-version }}
-          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+          path: .venv-${{ env.version }}
+          key: ${{ runner.os }}-venv-${{ env.version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
 
       - name: Set up virtual environment if not restored from cache
         if: steps.restore-env.outputs.cache-hit != 'true' && env.has_changes == 'true'
         run: |
           gh cache list
-          python -m venv .venv-${{ matrix.python-version }}
-          source .venv-${{ matrix.python-version }}/bin/activate
+          python -m venv .venv-${{ env.version }}
+          source .venv-${{ env.version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
           pip install matplotlib==3.9.2
 
-      - name: Test notebooks with pytest and nbmake
+      - name: Action Details
         if: env.has_changes == 'true'
         run: |
-          source .venv-${{ matrix.python-version }}/bin/activate
+          source .venv-${{ env.version }}/bin/activate
+          which python
+          python --version
           pwd
           lscpu
+          pip list
+
+      - name: Test notebooks with pytest and nbmake
+        if: env.has_changes == 'true'
+        run: |
+          source .venv-${{ env.version }}/bin/activate
           export PYTHONPATH=$(pwd)
           pytest -v --nbmake "./docs/notebooks" \
             --nbmake-timeout=2000 \