Modularize CI test and runtime dependencies per module

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

@@ -9,7 +9,7 @@ runs:
         git config --global user.email "CI@example.com"
         git config --global user.name "CI Almighty"
         uv pip install --system tabulate  # This produces summaries at the end
-        uv pip install --system -e .[test,extractors,streaming_extractors,test_extractors,full]
+        uv pip install --system -e .[extractors,streaming_extractors,full] --group test-all
       shell: bash
     - name: Install git-annex
       shell: bash

.github/workflows/all-tests.yml

@@ -87,7 +87,7 @@ jobs:
 
       - name: Install packages
         run: |
-          uv pip install --system -e .[test_core]
+          uv pip install --system -e . --group test-core
         shell: bash
 
       - name: Pip list
@@ -145,77 +145,71 @@ jobs:
           HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell
         if: env.RUN_EXTRACTORS_TESTS == 'true'
         run: |
-          uv pip install --system -e .[extractors,streaming_extractors,test_extractors]
+          uv pip install --system -e .[extractors,streaming_extractors] --group 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: |
-          uv pip install --system -e .[streaming_extractors,test_extractors]
+          uv pip install --system -e .[streaming_extractors] --group test-streaming-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: |
-          uv pip install --system -e .[preprocessing,test_preprocessing]
+          uv pip install --system -e .[preprocessing] --group 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: |
-          uv pip install --system -e .[test]
-          uv pip list --system
-
       - name: Test postprocessing
         shell: bash
         if: env.RUN_POSTPROCESSING_TESTS == 'true'
         run: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[postprocessing] --group test-postprocessing
           uv pip list --system
           ./.github/run_tests.sh postprocessing --no-virtual-env
 
       - name: Test metrics
         shell: bash
         if: env.RUN_METRICS_TESTS == 'true'
         run: |
-          uv pip install --system -e .[metrics]
+          uv pip install --system -e .[metrics] --group test-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: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[comparison] --group test-comparison
           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: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[sorters] --group test-sorters
           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: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[sorters_internal] --group test-sorters-internal
           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: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[curation] --group test-curation
           uv pip list --system
           ./.github/run_tests.sh curation --no-virtual-env
 
@@ -225,23 +219,23 @@ jobs:
         env:
           KACHERY_ZONE: "scratch"
         run: |
-          uv pip install --system -e .[full,widgets]
+          uv pip install --system -e .[widgets] --group test-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: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[exporters] --group test-exporters
           uv pip list --system
           ./.github/run_tests.sh exporters --no-virtual-env
 
       - name: Test sortingcomponents
         shell: bash
         if: env.RUN_SORTINGCOMPONENTS_TESTS == 'true'
         run: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[sortingcomponents] --group test-sortingcomponents
           uv pip list --system
 
           # Internal shell check for platform and env var
@@ -262,6 +256,6 @@ jobs:
         shell: bash
         if: env.RUN_GENERATION_TESTS == 'true'
         run: |
-          uv pip install --system -e .[full]
+          uv pip install --system -e .[generation] --group test-generation
           uv pip list --system
           ./.github/run_tests.sh generation --no-virtual-env

.github/workflows/core-test.yml

@@ -31,7 +31,7 @@ jobs:
         run: |
           git config --global user.email "CI@example.com"
           git config --global user.name "CI Almighty"
-          uv pip install --system -e .[test_core]
+          uv pip install --system -e . --group 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

.github/workflows/deepinterpolation.yml

@@ -46,7 +46,7 @@ jobs:
           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]
+          uv pip install --system -e .[full] --group test-core
       - name: Pip list
         if: ${{ steps.modules-changed.outputs.DEEPINTERPOLATION_CHANGED == 'true' }}
         run: |

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

@@ -25,7 +25,7 @@ jobs:
           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]
+          uv pip install --system -e . --group test-core
       - name: Test core with pytest
         run: |
           pytest -v src/spikeinterface/core

.github/workflows/test_kilosort4.yml

@@ -69,7 +69,7 @@ jobs:
 
       - name: Install SpikeInterface
         run: |
-          uv pip install --system -e .[test]
+          uv pip install --system -e .[full] --group test-sorters
         shell: bash
 
       - name: Install legacy setuptools for KS4 < 4.0.19

doc/development/development.rst

@@ -65,9 +65,9 @@ Note that you should install spikeinterface before running the tests. You can do
 
 .. code-block:: bash
 
-    pip install -e .[test,extractors,full]
+    pip install -e .[extractors,full] --group test-all
 
-You can change the :code:`[test,extractors,full]` to install only the dependencies you need. The dependencies are specified in the :code:`pyproject.toml` file in the root of the repository.
+You can change the :code:`[extractors,full]` extras to install only the runtime dependencies you need, and swap :code:`--group test-all` for a per-module test group (for example :code:`--group test-postprocessing`). Both lists are defined in :code:`pyproject.toml`: feature extras live under :code:`[project.optional-dependencies]` and test groups under :code:`[dependency-groups]` (PEP 735). Note that :code:`--group` requires pip 25.1+ or uv.
 
 The specific environment for the CI is specified in the :code:`.github/actions/build-test-environment/action.yml` and you can
 find the full tests in the :code:`.github/workflows/full_test.yml` file.