MAINT: Switch to pip for macOS and minimal jobs (#13882)

Author: larsoner

.github/workflows/tests.yml

@@ -30,7 +30,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: '3.14'
       - uses: pre-commit/action@v3.0.1
       - run: pip install mypy numpy scipy vulture
       - run: mypy
@@ -76,15 +76,12 @@ jobs:
           - os: ubuntu-latest
             python: '3.13'
             kind: conda
-          - os: macos-latest  # arm64 (Apple Silicon): Sequoia
-            python: '3.13'
-            kind: mamba
-          - os: macos-15-intel  # intel: Sequoia
+          - os: macos-latest  # arm64
+            python: '3.14'
+            kind: pip
+          - os: macos-15-intel  # Intel
             python: '3.13'
-            kind: mamba
-          - os: windows-latest
-            python: '3.11'
-            kind: mamba
+            kind: pip
           - os: ubuntu-latest
             python: '3.12'
             kind: minimal
@@ -122,36 +119,21 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
-        if: startswith(matrix.kind, 'pip')
+        if: startswith(matrix.kind, 'pip') || matrix.kind == 'minimal'
+        id: setup-python
+      # Workaround macOS path behavior with login shells (which puts system Python first)
+      - run: echo "export PATH=\"$(dirname ${{ steps.setup-python.outputs.python-path }}):$PATH\"" | tee -a ~/.bash_profile  # zizmor: ignore[template-injection]
+        if: startswith(matrix.kind, 'pip') && startswith(matrix.os, 'macos')
       # Python (if conda)
-      - name: Fixes for conda
-        run: |
-          # For some reason on Linux we get crashes
-          if [[ "$RUNNER_OS" == "Linux" ]]; then
-            sed -i "/numba/d" environment.yml
-          fi
-          # And on Windows and macOS PySide6.9.0 segfaults
-          if [[ "$RUNNER_OS" == "macOS" ]]; then
-            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
-            sed -i "" "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
-
-          else
-            sed -i "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
-            sed -i "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
-            if [[ "$RUNNER_OS" == "Windows" ]]; then
-              echo "MNE_IS_OSMESA=true" | tee -a $GITHUB_ENV
-            fi
-          fi
-        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
       - uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
-          log-level: ${{ runner.debug == '1' && 'debug' || 'info' }}
+          log-level: 'info'
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
             -v
-        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
+        if: matrix.kind == 'conda'
         timeout-minutes: 20
       # Python (if old)
       - uses: astral-sh/setup-uv@v8.1.0
@@ -162,7 +144,9 @@ jobs:
             **/pylock.ci-old.toml
           python-version: ${{ matrix.python }}
         if: matrix.kind == 'old'
+      - run: bash ./tools/github_actions_verify_python.sh "${{ matrix.python }}"
       - run: bash ./tools/github_actions_dependencies.sh
+        timeout-minutes: 10
       - run: python ./tools/github_actions_check_old_env.py
         if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)

azure-pipelines.yml

@@ -82,9 +82,9 @@ stages:
     variables:
       AZURE_CI: 'true'
     jobs:
-      - job: Ultraslow_PG
+      - job: Linux_Ultraslow_PG
         pool:
-          vmImage: 'ubuntu-22.04'
+          vmImage: 'ubuntu-latest'
         variables:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
@@ -93,7 +93,7 @@ stages:
           MNE_BROWSER_PRECOMPUTE: 'false'
         steps:
           - bash: |
-              set -e
+              set -eo pipefail
               ./tools/setup_xvfb.sh
               sudo apt install -yq tcsh
             displayName: 'Install Ubuntu dependencies'
@@ -112,19 +112,19 @@ stages:
               addToPath: true
             displayName: 'Get Python'
           - bash: |
-              set -e
+              set -eo pipefail
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e . --group=test
             displayName: 'Install dependencies with pip'
           - bash: |
-              set -e
+              set -eo pipefail
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .*(PySide6=.*)$"
             displayName: Print config
           - bash: |
-              set -e
+              set -eo pipefail
               LD_DEBUG=libs python -c "from PySide6.QtWidgets import QApplication, QWidget; app = QApplication([]); import matplotlib; matplotlib.use('QtAgg'); import matplotlib.pyplot as plt; plt.figure()"
           - bash: source tools/get_testing_version.sh
             displayName: 'Get testing version'
@@ -141,19 +141,10 @@ stages:
           - bash: bash <(curl -s https://codecov.io/bash)
             displayName: 'Codecov'
             condition: succeededOrFailed()
-          - task: PublishTestResults@2
-            inputs:
-              testResultsFiles: '**/junit-*.xml'
-              testRunTitle: 'Publish test results for $(Agent.JobName)'
-              failTaskOnFailedTests: true
-            condition: succeededOrFailed()
-          - task: PublishCodeCoverageResults@2
-            inputs:
-              summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
 
-      - job: Qt
+      - job: Linux_Qt_Bindings
         pool:
-          vmImage: 'ubuntu-22.04'
+          vmImage: 'ubuntu-latest'
         variables:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
@@ -169,7 +160,7 @@ stages:
               addToPath: true
             displayName: 'Get Python'
           - bash: |
-              set -e
+              set -eo pipefail
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
               python -c "import vtk"
@@ -223,15 +214,6 @@ stages:
           - bash: bash <(curl -s https://codecov.io/bash)
             displayName: 'Codecov'
             condition: succeededOrFailed()
-          - task: PublishTestResults@2
-            inputs:
-              testResultsFiles: '**/junit-*.xml'
-              testRunTitle: 'Publish test results for $(Agent.JobName)'
-              failTaskOnFailedTests: true
-            condition: succeededOrFailed()
-          - task: PublishCodeCoverageResults@2
-            inputs:
-              summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
 
       - job: Windows
         pool:
@@ -250,9 +232,9 @@ stages:
         strategy:
           maxParallel: 4
           matrix:
-            3.10 pip:
+            3.11 pip:
               TEST_MODE: 'pip'
-              PYTHON_VERSION: '3.10'
+              PYTHON_VERSION: '3.11'
             3.13 pip pre:
               TEST_MODE: 'pip-pre'
               PYTHON_VERSION: '3.13'
@@ -292,12 +274,3 @@ stages:
           - bash: bash <(curl -s https://codecov.io/bash)
             displayName: 'Codecov'
             condition: succeededOrFailed()
-          - task: PublishTestResults@2
-            inputs:
-              testResultsFiles: '**/junit-*.xml'
-              testRunTitle: 'Publish test results for $(Agent.JobName) $(TEST_MODE) $(PYTHON_VERSION)'
-              failTaskOnFailedTests: true
-            condition: succeededOrFailed()
-          - task: PublishCodeCoverageResults@2
-            inputs:
-              summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'

environment.yml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   - python >=3.10
   - antio >=0.5.0
+  - conda
   - curryreader >=0.1.2
   - darkdetect
   - decorator >=5.1
@@ -29,9 +30,11 @@ dependencies:
   - matplotlib >=3.8
   - mffpy >=0.5.7
   - mne-qt-browser
+  - nest-asyncio2
   - nibabel >=2.0
   - nilearn
   - nomkl
+  - noqt5
   - numba >=0.35
   - numpy >=1.26,<3
   - openmeeg >=2.5.7
@@ -43,7 +46,7 @@ dependencies:
   - pyarrow
   - pybv
   - pymatreader
-  - PySide6 !=6.9.1
+  - PySide6 ==6.10.2
   - python-neo
   - python-picard >=0.4
   - pyvista >=0.43
@@ -61,9 +64,8 @@ dependencies:
   - trame
   - trame-vtk
   - trame-vuetify
-  - vtk >=9.2
+  - vtk ==9.6.0
   - xlrd
   - pip:
-      - nest-asyncio2
       - pymef
       - pyobjc-framework-Cocoa >=5.2.0;platform_system=='Darwin'

mne/conftest.py

@@ -213,6 +213,7 @@ def pytest_configure(config: pytest.Config):
     # VTK <-> NumPy 2.5 (https://gitlab.kitware.com/vtk/vtk/-/merge_requests/12796)
     # nitime <-> NumPy 2.5 (https://github.com/nipy/nitime/pull/236)
     ignore:Setting the shape on a NumPy array has been deprecated.*:DeprecationWarning
+    ignore:Implicitly cleaning up.*:ResourceWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

mne/tests/test_source_estimate.py

@@ -1983,7 +1983,7 @@ def test_scale_morph_labels(kind, scale, monkeypatch, tmp_path):
                 min_, max_ = 0.72, 0.76
             else:
                 # min_, max_ = 0.84, 0.855  # zooms='auto' values
-                min_, max_ = 0.46, 0.63
+                min_, max_ = 0.44, 0.63
             assert min_ < corr <= max_, scale
         else:
             assert_allclose(label_tc, label_tc_to_morph, atol=1e-12, rtol=1e-12)

mne/viz/tests/test_evoked.py

@@ -373,6 +373,7 @@ def test_plot_white_rank():
     evoked.plot_white(cov, rank=rank)
 
 
+@pytest.mark.slowtest
 def test_plot_white():
     """Test plot_white."""
     cov = read_cov(cov_fname)

tools/environment_minimal.yml

@@ -79,4 +79,3 @@ which mne_surf2bem
 mne_surf2bem --version
 which mri_average
 mri_average --version
-set +x

tools/get_minimal_commands.sh

@@ -3,31 +3,27 @@
 set -eo pipefail
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ONLY_BINARY_ARG="--only-binary=numpy,scipy,matplotlib,numba,llvmlite,antio"
 STD_ARGS="--progress-bar off --upgrade"
 INSTALL_ARGS="-e"
 if [ ! -z "$CONDA_ENV" ]; then
 	echo "Uninstalling MNE for CONDA_ENV=${CONDA_ENV}"
-	# This will fail if mne-base is not in the env (like in our minimal env, so ||true them):
 	echo "::group::Uninstalling MNE"
-	conda remove -c conda-forge --force -yq mne-base || true
-	python -m pip uninstall -y mne || true
+	conda remove -c conda-forge --force -y mne-base
 	echo "::endgroup::"
-	# If using bare environment.yml and not on windows, do a non-editable install
-	if [[ "${RUNNER_OS}" != "Windows" ]] && [[ "${CONDA_ENV}" != "environment_"* ]]; then
+	# If not on windows, do a non-editable install
+	if [[ "${CI_OS_NAME}" != "windows"* ]]; then
 		INSTALL_ARGS=""
 	fi
-	# If on minimal, just install testing deps
-	if [[ "${MNE_CI_KIND}" == "minimal" ]]; then
-		GROUP="test"
-		EXTRAS=""
-		STD_ARGS="--progress-bar off ${MNE_QT_BACKEND}"
-		echo "::group::Upgrading pip installation"
-		python -m pip install --upgrade pip  # upgrade pip to support --group
-		echo "::endgroup::"
-	else
-		GROUP="test_extra"
-		EXTRAS="[hdf5]"
-	fi
+	GROUP="test_extra"
+	EXTRAS="[hdf5]"
+elif [[ "${MNE_CI_KIND}" == "minimal" ]]; then
+	GROUP="test"
+	EXTRAS=""
+	STD_ARGS="--progress-bar off ${MNE_QT_BACKEND}"
+	echo "::group::Upgrading pip installation"
+	python -m pip install --upgrade pip setuptools
+	echo "::endgroup::"
 elif [[ "${MNE_CI_KIND}" == "old" ]]; then
 	GROUP=""  # group "test" already included when pylock file generated
 	EXTRAS=""
@@ -39,10 +35,12 @@ elif [[ "${MNE_CI_KIND}" == "old" ]]; then
 elif [[ "${MNE_CI_KIND}" == "pip" ]]; then
 	GROUP="test_extra"
 	EXTRAS="[full-pyside6]"
+	python -m pip install --upgrade pip setuptools
 else
 	test "${MNE_CI_KIND}" == "pip-pre"
+	python -m pip install $STD_ARGS pip setuptools
 	STD_ARGS="$STD_ARGS --pre"
-	${SCRIPT_DIR}/install_pre_requirements.sh || exit 1
+	${SCRIPT_DIR}/install_pre_requirements.sh
 	GROUP="test_extra"
 	EXTRAS=""
 fi
@@ -61,6 +59,5 @@ else
 	echo "::group::Installing MNE in development mode using pip"
 fi
 set -x
-python -m pip install $STD_ARGS $INSTALL_ARGS .$EXTRAS $GROUP_ARG
-set +x
+python -m pip install $STD_ARGS $ONLY_BINARY_ARG $INSTALL_ARGS .$EXTRAS $GROUP_ARG
 echo "::endgroup::"