Update CI to match glotzerlab software suite

.github/requirements3.10.txt

@@ -0,0 +1,81 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.10 requirements/requirements-build.txt requirements/requirements-testing.txt requirements/requirements.txt
+attrs==23.2.0
+    # via hypothesis
+bottleneck==1.4.0
+    # via -r requirements/requirements.txt
+coverage==7.6.0
+    # via -r requirements/requirements-testing.txt
+exceptiongroup==1.2.2
+    # via
+    #   hypothesis
+    #   pytest
+freud-analysis==3.1.0
+    # via -r requirements/requirements.txt
+hypothesis==6.108.4
+    # via -r requirements/requirements-testing.txt
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via scikit-learn
+kneed==0.8.5
+    # via -r requirements/requirements.txt
+llvmlite==0.43.0
+    # via numba
+numba==0.60.0
+    # via -r requirements/requirements.txt
+numpy==2.0.1
+    # via
+    #   -r requirements/requirements.txt
+    #   bottleneck
+    #   freud-analysis
+    #   kneed
+    #   numba
+    #   pandas
+    #   rowan
+    #   ruptures
+    #   scikit-learn
+    #   scipy
+    #   xarray
+packaging==24.1
+    # via
+    #   pytest
+    #   xarray
+pandas==2.2.2
+    # via
+    #   -r requirements/requirements.txt
+    #   xarray
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.1
+    # via -r requirements/requirements-testing.txt
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rowan==1.3.0.post1
+    # via freud-analysis
+ruptures==1.1.9
+    # via -r requirements/requirements.txt
+scikit-learn==1.5.1
+    # via -r requirements/requirements.txt
+scipy==1.14.0
+    # via
+    #   freud-analysis
+    #   kneed
+    #   ruptures
+    #   scikit-learn
+setuptools==71.1.0
+    # via -r requirements/requirements-build.txt
+six==1.16.0
+    # via python-dateutil
+sortedcontainers==2.4.0
+    # via hypothesis
+threadpoolctl==3.5.0
+    # via scikit-learn
+tomli==2.0.1
+    # via pytest
+tzdata==2024.1
+    # via pandas
+xarray==2024.6.0
+    # via -r requirements/requirements.txt

.github/requirements3.11.txt

@@ -0,0 +1,75 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.11 requirements/requirements-build.txt requirements/requirements-testing.txt requirements/requirements.txt
+attrs==23.2.0
+    # via hypothesis
+bottleneck==1.4.0
+    # via -r requirements/requirements.txt
+coverage==7.6.0
+    # via -r requirements/requirements-testing.txt
+freud-analysis==3.1.0
+    # via -r requirements/requirements.txt
+hypothesis==6.108.4
+    # via -r requirements/requirements-testing.txt
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via scikit-learn
+kneed==0.8.5
+    # via -r requirements/requirements.txt
+llvmlite==0.43.0
+    # via numba
+numba==0.60.0
+    # via -r requirements/requirements.txt
+numpy==2.0.1
+    # via
+    #   -r requirements/requirements.txt
+    #   bottleneck
+    #   freud-analysis
+    #   kneed
+    #   numba
+    #   pandas
+    #   rowan
+    #   ruptures
+    #   scikit-learn
+    #   scipy
+    #   xarray
+packaging==24.1
+    # via
+    #   pytest
+    #   xarray
+pandas==2.2.2
+    # via
+    #   -r requirements/requirements.txt
+    #   xarray
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.1
+    # via -r requirements/requirements-testing.txt
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rowan==1.3.0.post1
+    # via freud-analysis
+ruptures==1.1.9
+    # via -r requirements/requirements.txt
+scikit-learn==1.5.1
+    # via -r requirements/requirements.txt
+scipy==1.14.0
+    # via
+    #   freud-analysis
+    #   kneed
+    #   ruptures
+    #   scikit-learn
+setuptools==71.1.0
+    # via -r requirements/requirements-build.txt
+six==1.16.0
+    # via python-dateutil
+sortedcontainers==2.4.0
+    # via hypothesis
+threadpoolctl==3.5.0
+    # via scikit-learn
+tzdata==2024.1
+    # via pandas
+xarray==2024.6.0
+    # via -r requirements/requirements.txt

.github/requirements3.12.txt

@@ -0,0 +1,75 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.12 requirements/requirements-build.txt requirements/requirements-testing.txt requirements/requirements.txt
+attrs==23.2.0
+    # via hypothesis
+bottleneck==1.4.0
+    # via -r requirements/requirements.txt
+coverage==7.6.0
+    # via -r requirements/requirements-testing.txt
+freud-analysis==3.1.0
+    # via -r requirements/requirements.txt
+hypothesis==6.108.4
+    # via -r requirements/requirements-testing.txt
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via scikit-learn
+kneed==0.8.5
+    # via -r requirements/requirements.txt
+llvmlite==0.43.0
+    # via numba
+numba==0.60.0
+    # via -r requirements/requirements.txt
+numpy==2.0.1
+    # via
+    #   -r requirements/requirements.txt
+    #   bottleneck
+    #   freud-analysis
+    #   kneed
+    #   numba
+    #   pandas
+    #   rowan
+    #   ruptures
+    #   scikit-learn
+    #   scipy
+    #   xarray
+packaging==24.1
+    # via
+    #   pytest
+    #   xarray
+pandas==2.2.2
+    # via
+    #   -r requirements/requirements.txt
+    #   xarray
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.1
+    # via -r requirements/requirements-testing.txt
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rowan==1.3.0.post1
+    # via freud-analysis
+ruptures==1.1.9
+    # via -r requirements/requirements.txt
+scikit-learn==1.5.1
+    # via -r requirements/requirements.txt
+scipy==1.14.0
+    # via
+    #   freud-analysis
+    #   kneed
+    #   ruptures
+    #   scikit-learn
+setuptools==71.1.0
+    # via -r requirements/requirements-build.txt
+six==1.16.0
+    # via python-dateutil
+sortedcontainers==2.4.0
+    # via hypothesis
+threadpoolctl==3.5.0
+    # via scikit-learn
+tzdata==2024.1
+    # via pandas
+xarray==2024.6.0
+    # via -r requirements/requirements.txt

.github/requirements3.9.txt

@@ -0,0 +1,81 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.9 requirements/requirements-build.txt requirements/requirements-testing.txt requirements/requirements.txt
+attrs==23.2.0
+    # via hypothesis
+bottleneck==1.4.0
+    # via -r requirements/requirements.txt
+coverage==7.6.0
+    # via -r requirements/requirements-testing.txt
+exceptiongroup==1.2.2
+    # via
+    #   hypothesis
+    #   pytest
+freud-analysis==3.1.0
+    # via -r requirements/requirements.txt
+hypothesis==6.108.4
+    # via -r requirements/requirements-testing.txt
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via scikit-learn
+kneed==0.8.5
+    # via -r requirements/requirements.txt
+llvmlite==0.43.0
+    # via numba
+numba==0.60.0
+    # via -r requirements/requirements.txt
+numpy==2.0.1
+    # via
+    #   -r requirements/requirements.txt
+    #   bottleneck
+    #   freud-analysis
+    #   kneed
+    #   numba
+    #   pandas
+    #   rowan
+    #   ruptures
+    #   scikit-learn
+    #   scipy
+    #   xarray
+packaging==24.1
+    # via
+    #   pytest
+    #   xarray
+pandas==2.2.2
+    # via
+    #   -r requirements/requirements.txt
+    #   xarray
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.1
+    # via -r requirements/requirements-testing.txt
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rowan==1.3.0.post1
+    # via freud-analysis
+ruptures==1.1.9
+    # via -r requirements/requirements.txt
+scikit-learn==1.5.1
+    # via -r requirements/requirements.txt
+scipy==1.13.1
+    # via
+    #   freud-analysis
+    #   kneed
+    #   ruptures
+    #   scikit-learn
+setuptools==71.1.0
+    # via -r requirements/requirements-build.txt
+six==1.16.0
+    # via python-dateutil
+sortedcontainers==2.4.0
+    # via hypothesis
+threadpoolctl==3.5.0
+    # via scikit-learn
+tomli==2.0.1
+    # via pytest
+tzdata==2024.1
+    # via pandas
+xarray==2024.6.0
+    # via -r requirements/requirements.txt

.github/workflows/run-pytest.yml

@@ -30,22 +30,21 @@ jobs:
           - os: 'macos-latest'
             python: '3.12'
     steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: "recursive"
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
       with:
         python-version: ${{ matrix.python }}
-    - name: Update pip/build packages
-      run: |
-        pip install setuptools --upgrade
-    - name: Install dependencies
-      run: |
-        pip install -r .github/workflows/requirements-test.txt
-    - name: Install the package
+    - name: Set up Python environment
+      uses: glotzerlab/workflows/setup-uv@3573ddaebf3290e00bfb150b82a46412192a61d3
+      with:
+        only-binary: ":none:"
+        lockfile: ".github/requirements${{ matrix.python }}.txt"
+    - name: Install package
       run: |
-        pip install -e .
+        python --version
+        uv pip install . --no-build-isolation --no-deps --system -v
     - name: Test with pytest
       run: |
         python -m pytest -v

requirements/requirements-build.txt

@@ -0,0 +1 @@
+setuptools

requirements/requirements-testing.txt

@@ -1,2 +1,3 @@
-pytest>6.2.1
-hypothesis>6.30.0
+pytest
+hypothesis
+coverage

requirements/requirements.txt

@@ -1,7 +1,9 @@
-bottleneck>=1.3.4
-freud-analysis>=2.7.0
-kneed>=0.8.2
-numpy>=1.21
-ruptures>=1.1.5
-scikit-learn>=0.24.0
-pandas>=1.1.3
+bottleneck
+freud-analysis
+kneed
+numba
+numpy
+ruptures
+scikit-learn
+pandas
+xarray