MAINT: Fix docker (#548)

mne-tools · Apr 2, 2024 · 191ca41 · 191ca41
1 parent 27dd2fe
commit 191ca41
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Showing 7 changed files with 42 additions and 45 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/Docker_Release_Tags.yml b/.github/workflows/Docker_Release_Tags.yml
@@ -18,33 +18,21 @@ on:
 
 jobs:
   version:
-
     runs-on: ubuntu-latest
-
     steps:
-
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-
+      - uses: actions/checkout@v4
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
-
       - name: Build docker image
         run: docker-compose build --build-arg mne_python_v=${{ github.event.inputs.mne_python }} --build-arg mne_nirs_v=${{ github.event.inputs.mne_nirs }} --build-arg nilearn_v=${{ github.event.inputs.nilearn }} base
-
-      - name: List docker images
-        run: docker images
-
+      - run: docker images
       - name: Rename base image tag for release
         run: docker tag mne-tools/mne-nirs ghcr.io/mne-tools/mne-nirs:${{ github.event.inputs.mne_nirs }}
-
       - name: Push image to github
         run: docker push ghcr.io/mne-tools/mne-nirs:${{ github.event.inputs.mne_nirs }}
-
       - name: System info
         run: docker run ghcr.io/mne-tools/mne-nirs:${{ github.event.inputs.mne_nirs }} python -c "import mne_nirs; print(mne_nirs.__version__)"
diff --git a/.github/workflows/Docker_Tests.yml b/.github/workflows/Docker_Tests.yml
@@ -13,28 +13,21 @@ concurrency:
 
 jobs:
   latest:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
-
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-
-      - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+      - uses: actions/checkout@v4
+      - uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Build docker image
-        run: docker-compose build worker
-
+      - run: docker-compose build worker
       - name: System info
         run: docker run mne-tools/mne-nirs python -c "import mne; mne.sys_info()"
-
       - name: MNE-NIRS info
         run: docker run mne-tools/mne-nirs python -c "import mne_nirs; print(mne_nirs.__version__)"
-
       - name: Run visualisation test
         run: docker run -v `pwd`:/opt/app/examples mne-tools/mne-nirs ipython /opt/app/examples/.github/workflows/docker_tests.py
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -13,27 +13,19 @@ concurrency:
 jobs:
   # PIP + non-default stim channel + log level info
   job:
-    name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.mne}}'
-    runs-on: ubuntu-20.04
+    name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.mne }}'
+    runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -el {0}
-    env:
-      DISPLAY: ':99.0'
-      MNE_LOGGING_LEVEL: 'info'
-      MNE_STIM_CHANNEL: 'STI101'
-      OPENBLAS_NUM_THREADS: '1'
-      PYTHONUNBUFFERED: '1'
-      PYTHON_VERSION: '3.10'
-      MNEPYTHON: ${{ matrix.mne }}
     strategy:
       fail-fast: false
       matrix:
         include:
           - os: ubuntu-latest
             mne: stable
             kind: pip
-            python: "3.8"  # oldest
+            python: "3.9"  # oldest
           - os: ubuntu-latest
             mne: dev
             kind: pip
@@ -45,12 +37,12 @@ jobs:
           - os: windows-latest
             mne: dev
             kind: conda
-            python: "3.9"
+            python: "3.10"
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version: ${{ matrix.python }}
         if: matrix.kind == 'pip'
       - uses: pyvista/setup-headless-display-action@main
         with:
@@ -61,12 +53,25 @@ jobs:
           environment-file: environment.yml
           environment-name: mne-nirs
           create-args: >-
-            python=${{ env.PYTHON_VERSION }}
+            python=${{ matrix.python }}
         if: matrix.kind == 'conda'
       - run: pip install -r requirements_testing.txt
+      - run: git clone https://github.com/mne-tools/mne-python
+      - run: pip install --upgrade --pre -e ./mne-python git+https://github.com/nilearn/nilearn
+        if: matrix.mne == 'dev'
+        name: Install MNE and nilearn dev
+      # - run: pip install --upgrade --pre --force --only-binary=":all:" --index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0rc1" scipy h5py matplotlib pandas scikit-learn statsmodels "tables>=3.9.3.dev0"
+      #   if: matrix.mne == 'dev' && startsWith(matrix.os, 'ubuntu')
+      #   name: Install numpy, scipy, nilearn pre
       - run: pip install -ve .
       - run: mne sys_info
+      - run: ./tools/get_testing_version.sh
+        working-directory: mne-python
+      - uses: actions/cache@v4
+        with:
+          key: ${{ env.TESTING_VERSION }}
+          path: ~/mne_data
       - run: ./tools/github_actions_download.sh
       - run: pytest --cov=mne_nirs --cov-report xml -vv -m "not examples" "mne_nirs/"
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         if: success()
diff --git a/mne_nirs/conftest.py b/mne_nirs/conftest.py
@@ -63,6 +63,10 @@ def pytest_configure(config):
     ignore:Mesa version 10\.2\.4 is too old.*:RuntimeWarning
     # Pandas
     ignore:np\.find_common_type is deprecated.*:DeprecationWarning
+    # statsmodels
+    ignore:The numpy\.linalg\.linalg has been made private.*:DeprecationWarning
+    # sklearn
+    ignore:KMeans is known to have a memory leak on Windows with MKL.*:UserWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

diff --git a/mne_nirs/io/fold/_fold.py b/mne_nirs/io/fold/_fold.py
@@ -307,7 +307,7 @@ def _source_detector_fold_table(raw, cidx, reference, fold_tbl, interpolate):
     if len(tbl) == 0 and interpolate:
         # Try something hopefully not too terrible: pick the one with the
         # smallest net distance
-        good = np.in1d(fold_tbl["Source"], reference["label"]) & np.in1d(
+        good = np.isin(fold_tbl["Source"], reference["label"]) & np.isin(
             fold_tbl["Detector"], reference["label"]
         )
         assert good.any()

diff --git a/tools/github_actions_download.sh b/tools/github_actions_download.sh
@@ -7,3 +7,4 @@ fi
 python -c 'from mne_nirs.datasets import fnirs_motor_group; fnirs_motor_group.data_path(force_update=True)'
 python -c 'from mne_nirs.datasets import block_speech_noise; block_speech_noise.data_path(force_update=True)'
 python -c 'from mne_nirs.datasets import audio_or_visual_speech; audio_or_visual_speech.data_path(force_update=True)'
+python -c "from mne.datasets import fnirs_motor; fnirs_motor.data_path(force_update=True)"