Use uv and caching in CI

.github/actions/build-test-environment/action.yml

@@ -8,22 +8,22 @@ runs:
       run: |
         git config --global user.email "CI@example.com"
         git config --global user.name "CI Almighty"
-        pip install tabulate  # This produces summaries at the end
-        pip install -e .[test,extractors,streaming_extractors,test_extractors,full]
+        uv pip install --system tabulate  # This produces summaries at the end
+        uv pip install --system -e .[test,extractors,streaming_extractors,test_extractors,full]
       shell: bash
     - name: Install git-annex
       shell: bash
       run: |
-        pip install datalad-installer
+        uv pip install --system datalad-installer
         datalad-installer --sudo ok git-annex --method datalad/packages
         git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
     - name: Force installation of latest dev from key-packages when running dev (not release)
       run: |
         spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
         if [ $spikeinterface_is_dev_version = "True" ]; then
           echo "Running spikeinterface dev version"
-          pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo
-          pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface
+          uv pip install --system git+https://github.com/NeuralEnsemble/python-neo
+          uv pip install --system git+https://github.com/SpikeInterface/probeinterface
         fi
           echo "Running tests for release, using pyproject.toml versions of neo and probeinterface"
       shell: bash

.github/workflows/all-tests.yml

@@ -29,9 +29,13 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
 
       - name: Free space
         if: runner.os == 'Linux'
@@ -83,20 +87,20 @@ jobs:
 
       - name: Install packages
         run: |
-          pip install -e .[test_core]
+          uv pip install --system -e .[test_core]
         shell: bash
 
       - name: Pip list
-        run: pip list
+        run: uv pip list --system
 
       - name: Test core
         run: pytest -m "core"
         shell: bash
 
       - name: Install Dependencies for Timing Display
         run: |
-          pip install tabulate
-          pip install pandas
+          uv pip install --system tabulate
+          uv pip install --system pandas
         shell: bash
 
       - name: Get current hash (SHA) of the ephy_testing_data repo
@@ -117,7 +121,7 @@ jobs:
         shell: bash
         if: env.RUN_EXTRACTORS_TESTS == 'true' || env.RUN_PREPROCESSING_TESTS == 'true'
         run: |
-          pip install datalad-installer
+          uv pip install --system datalad-installer
           if [ ${{ runner.os }} = 'Linux' ]; then
             datalad-installer --sudo ok git-annex --method datalad/packages
           elif [ ${{ runner.os }} = 'macOS' ]; then
@@ -141,78 +145,78 @@ jobs:
           HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell
         if: env.RUN_EXTRACTORS_TESTS == 'true'
         run: |
-          pip install -e .[extractors,streaming_extractors,test_extractors]
-          pip list
+          uv pip install --system -e .[extractors,streaming_extractors,test_extractors]
+          uv pip list --system
           ./.github/run_tests.sh "extractors and not streaming_extractors" --no-virtual-env
 
       - name: Test streaming extractors
         shell: bash
         if: env.RUN_STREAMING_EXTRACTORS_TESTS == 'true'
         run: |
-          pip install -e .[streaming_extractors,test_extractors]
-          pip list
+          uv pip install --system -e .[streaming_extractors,test_extractors]
+          uv pip list --system
           ./.github/run_tests.sh "streaming_extractors" --no-virtual-env
 
       - name: Test preprocessing
         shell: bash
         if: env.RUN_PREPROCESSING_TESTS == 'true'
         run: |
-          pip install -e .[preprocessing,test_preprocessing]
-          pip list
+          uv pip install --system -e .[preprocessing,test_preprocessing]
+          uv pip list --system
           ./.github/run_tests.sh "preprocessing and not deepinterpolation" --no-virtual-env
 
       - name: Install remaining testing dependencies # TODO: Remove this step once we have better modularization
         shell: bash
         run: |
-          pip install -e .[test]
-          pip list
+          uv pip install --system -e .[test]
+          uv pip list --system
 
       - name: Test postprocessing
         shell: bash
         if: env.RUN_POSTPROCESSING_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh postprocessing --no-virtual-env
 
       - name: Test metrics
         shell: bash
         if: env.RUN_METRICS_TESTS == 'true'
         run: |
-          pip install -e .[metrics]
-          pip list
+          uv pip install --system -e .[metrics]
+          uv pip list --system
           ./.github/run_tests.sh metrics --no-virtual-env
 
       - name: Test comparison
         shell: bash
         if: env.RUN_COMPARISON_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh comparison --no-virtual-env
 
       - name: Test core sorters
         shell: bash
         if: env.RUN_SORTERS_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh sorters --no-virtual-env
 
       - name: Test internal sorters
         shell: bash
         if: env.RUN_INTERNAL_SORTERS_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh sorters_internal --no-virtual-env
 
       - name: Test curation
         shell: bash
         if: env.RUN_CURATION_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh curation --no-virtual-env
 
       - name: Test widgets
@@ -221,24 +225,24 @@ jobs:
         env:
           KACHERY_ZONE: "scratch"
         run: |
-          pip install -e .[full,widgets]
-          pip list
+          uv pip install --system -e .[full,widgets]
+          uv pip list --system
           ./.github/run_tests.sh widgets --no-virtual-env -s
 
       - name: Test exporters
         shell: bash
         if: env.RUN_EXPORTERS_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh exporters --no-virtual-env
 
       - name: Test sortingcomponents
         shell: bash
         if: env.RUN_SORTINGCOMPONENTS_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
 
           # Internal shell check for platform and env var
           if [[ "$RUNNER_OS" == "macOS" ]]; then
@@ -258,6 +262,6 @@ jobs:
         shell: bash
         if: env.RUN_GENERATION_TESTS == 'true'
         run: |
-          pip install -e .[full]
-          pip list
+          uv pip install --system -e .[full]
+          uv pip list --system
           ./.github/run_tests.sh generation --no-virtual-env

.github/workflows/caches_cron_job.yml

@@ -17,9 +17,13 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.11'
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.11'
+          enable-cache: true
       - name: Create the directory to store the data
         run: |
           mkdir -p  ~/spikeinterface_datasets/ephy_testing_data/
@@ -45,16 +49,15 @@ jobs:
         run: |
           git config --global user.email "CI@example.com"
           git config --global user.name "CI Almighty"
-          python -m pip install -U pip  # Official recommended way
-          pip install datalad-installer
+          uv pip install --system datalad-installer
           if [ ${{ runner.os }} == 'Linux' ]; then
             datalad-installer --sudo ok git-annex --method datalad/packages
           elif [ ${{ runner.os }} == 'macOS' ]; then
             datalad-installer --sudo ok git-annex --method brew
           elif [ ${{ runner.os }} == 'Windows' ]; then
             datalad-installer --sudo ok git-annex --method datalad/git-annex:release
           fi
-          pip install datalad
+          uv pip install --system datalad
           git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
         shell: bash
       - name: Download dataset

.github/workflows/core-test.yml

@@ -20,23 +20,26 @@ jobs:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.11'
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.11'
+          enable-cache: true
       - name: Install dependencies
         run: |
           git config --global user.email "CI@example.com"
           git config --global user.name "CI Almighty"
-          python -m pip install -U pip  # Official recommended way
-          pip install -e .[test_core]
+          uv pip install --system -e .[test_core]
       - name: Test core with pytest
         run: |
           pytest -m "core" -vv -ra --durations=0 --durations-min=0.001 | tee report.txt; test $? -eq 0 || exit 1
         shell: bash  # Necessary for pipeline to work on windows
       - name: Build test summary
         run: |
-          pip install pandas
-          pip install tabulate
+          uv pip install --system pandas
+          uv pip install --system tabulate
           echo "# Timing profile of core tests in ${{matrix.os}}" >> $GITHUB_STEP_SUMMARY
           # Outputs markdown summary to standard output
           python ./.github/scripts/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY

.github/workflows/deepinterpolation.yml

@@ -20,9 +20,13 @@ jobs:
         os: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.10'
+          enable-cache: false
       - name: Get changed files
         id: changed-files
         uses: tj-actions/changed-files@v46.0.1
@@ -38,16 +42,15 @@ jobs:
       - name: Install dependencies
         if: ${{ steps.modules-changed.outputs.DEEPINTERPOLATION_CHANGED == 'true' }}
         run: |
-          python -m pip install -U pip  # Official recommended way
           # install deepinteprolation
-          pip install tensorflow==2.8.4
-          pip install deepinterpolation@git+https://github.com/AllenInstitute/deepinterpolation.git
-          pip install numpy==1.26.4
-          pip install -e .[full,test_core]
+          uv pip install --system tensorflow==2.8.4
+          uv pip install --system deepinterpolation@git+https://github.com/AllenInstitute/deepinterpolation.git
+          uv pip install --system numpy==1.26.4
+          uv pip install --system -e .[full,test_core]
       - name: Pip list
         if: ${{ steps.modules-changed.outputs.DEEPINTERPOLATION_CHANGED == 'true' }}
         run: |
-          pip list
+          uv pip list --system
       - name: Test DeepInterpolation with pytest
         if: ${{ steps.modules-changed.outputs.DEEPINTERPOLATION_CHANGED == 'true' }}
         run: |

.github/workflows/full-test-with-codecov.yml

@@ -20,9 +20,13 @@ jobs:
         os: ["ubuntu-latest", ]
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.12'
+          enable-cache: true
       - name: Free space
         run: |
           sudo rm -rf /usr/local/lib/android
@@ -50,7 +54,7 @@ jobs:
       - name: Install packages
         uses: ./.github/actions/build-test-environment
       - name: Pip list
-        run: pip list
+        run: uv pip list --system
       - name: run tests
         env:
           HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell

.github/workflows/installation-tips-test.yml

@@ -5,9 +5,6 @@ on:
   schedule:
     - cron: "0 12 * * 0"  # Weekly at noon UTC on Sundays
 
-env:
-  UV_SYSTEM_PYTHON: 1
-
 jobs:
   installation-tips-testing:
     name: Test uv installation on ${{ matrix.os }} OS
@@ -21,14 +18,17 @@ jobs:
           - os: windows-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: '3.12'
     - name: Install uv
-      uses: astral-sh/setup-uv@v6
+      uses: astral-sh/setup-uv@v7
+      with:
+        python-version: '3.12'
+        enable-cache: true
 
     - name: Install requirements
-      run: uv pip install -r ./installation_tips/beginner_requirements_stable.txt
+      run: uv pip install --system -r ./installation_tips/beginner_requirements_stable.txt
     - name: Check Installation Tips (mac)
       if: ${{ matrix.os == 'macos-latest' }}
       run: python ./installation_tips/check_your_install.py --ci --short --skip-kilosort4 # ci flag turns off gui

.github/workflows/publish-to-pypi.yml

@@ -13,16 +13,19 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.12'
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.12'
+          enable-cache: true
       - name: Install dependencies for testing
         run: |
-          python -m pip install -U pip  # Official recommended way
-          pip install pytest
-          pip install zarr
-          pip install setuptools wheel twine build
-          pip install -e .[test_core]
+          uv pip install --system pytest
+          uv pip install --system zarr
+          uv pip install --system setuptools wheel twine build
+          uv pip install --system -e .[test_core]
       - name: Test core with pytest
         run: |
           pytest -v src/spikeinterface/core