Switch from provision to setup micromamba (#4197)

* switch from provision to setup micromamba * Switch fully to pytest-xdist auto in gh actions
MDAnalysis · Jul 30, 2023 · ac30c88 · ac30c88
1 parent 439435e
commit ac30c88
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Showing 5 changed files with 68 additions and 43 deletions.
diff --git a/.github/actions/setup-os/action.yaml b/.github/actions/setup-os/action.yaml
@@ -24,7 +24,6 @@ runs:
         echo "CXX=clang++" >> $GITHUB_ENV
         gfortran-9 -v
         echo "FC=gfortran-9" >> $GITHUB_ENV
-        echo "numprocs=3" >> $GITHUB_ENV
         echo "ENABLE_HIGH_MEM_UNIT_TESTS=true" >> $GITHUB_ENV
 
     - name: setup_linux
@@ -39,4 +38,3 @@ runs:
         echo "CXX=g++" >> $GITHUB_ENV
         gfortran -v
         echo "FC=gfortran" >> $GITHUB_ENV
-        echo "numprocs=2" >> $GITHUB_ENV
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -220,14 +220,19 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: setup_micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: False
           environment-name: mda
-          extra-specs: |
-            python==${{ matrix.python-version }}
+          create-args: >-
+            python=${{ matrix.python-version }}
             pip
-          channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+          # jaime's shim to avoid pulling down the cudatoolkit
+          # bioconda for clustalw things
+          condarc: |
+            channels:
+              - jaimergp/label/unsupported-cudatoolkit-shim
+              - conda-forge
+              - bioconda
 
       - name: install_full_deps
         uses: ./.github/actions/setup-deps

diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml
@@ -34,14 +34,18 @@ jobs:
         os-type: "ubuntu"
 
     - name: setup_micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: False
         environment-name: mda
-        extra-specs: |
-          python=="3.11"
+        create-args: >-
+          python=3.11
           pip
-        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+        # using jaime's shim to avoid pulling down the cudatoolkit
+        condarc: |
+          channels:
+            - jaimergp/label/unsupported-cudatoolkit-shim
+            - conda-forge
+            - bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps
@@ -68,7 +72,7 @@ jobs:
 
     - name: run_tests
       run: |
-        pytest -n $numprocs testsuite/MDAnalysisTests --durations=50 -W error::FutureWarning
+        pytest -n auto testsuite/MDAnalysisTests --durations=50 -W error::FutureWarning
 
 
   # Issue #3442
@@ -86,14 +90,17 @@ jobs:
         os-type: "ubuntu"
 
     - name: setup_micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: False
         environment-name: mda
-        extra-specs: |
-          python=="3.11"
+        create-args: >-
+          python=3.11
           pip
-        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+        condarc: |
+          channels:
+            - jaimergp/label/unsupported-cudatoolkit-shim
+            - conda-forge
+            - bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps
@@ -113,7 +120,7 @@ jobs:
 
     - name: run_tests
       run: |
-        pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
+        pytest -n auto testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
 
 
   old_ubuntu_macos:
@@ -134,14 +141,17 @@ jobs:
         os-type: ${{ matrix.os }}
 
     - name: setup_micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: False
         environment-name: mda
-        extra-specs: |
-          python=="3.9"
+        create-args: >-
+          python=3.9
           pip
-        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+        condarc: |
+          channels:
+            - jaimergp/label/unsupported-cudatoolkit-shim
+            - conda-forge
+            - bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps
@@ -157,7 +167,7 @@ jobs:
 
     - name: run_tests
       run: |
-        pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
+        pytest -n auto testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
 
 
   # Issue 1727
@@ -195,7 +205,7 @@ jobs:
 
     - name: run_tests
       run: |
-        pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
+        pytest -n auto testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
         
   # Issue 4208
   conda-latest-release:

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -22,7 +22,7 @@ jobs:
   main_tests:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 60
+    timeout-minutes: 120
     strategy:
         fail-fast: false
         matrix:
@@ -61,14 +61,18 @@ jobs:
         os-type: ${{ matrix.os }}
 
     - name: setup_micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: False
         environment-name: mda
-        extra-specs: |
-          python==${{ matrix.python-version }}
+        create-args: >-
+          python=${{ matrix.python-version }}
           pip
-        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+        # using jaime's shim to avoid pulling down the cudatoolkit
+        condarc: |
+          channels:
+            - jaimergp/label/unsupported-cudatoolkit-shim
+            - conda-forge
+            - bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps
@@ -93,7 +97,7 @@ jobs:
           PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"
         fi
         echo $PYTEST_FLAGS
-        pytest -n $numprocs testsuite/MDAnalysisTests $PYTEST_FLAGS
+        pytest -n auto testsuite/MDAnalysisTests $PYTEST_FLAGS
 
     - name: run_asv
       if: contains(matrix.name, 'asv_check')
@@ -123,14 +127,18 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: setup_micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: False
         environment-name: mda
-        extra-specs: |
-          python=="3.9"
+        create-args: >-
+          python=3.9
           pip
-        channels: conda-forge, bioconda
+        # using jaime's shim to avoid pulling down the cudatoolkit
+        condarc: |
+          channels:
+            - jaimergp/label/unsupported-cudatoolkit-shim
+            - conda-forge
+            - bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps

diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml
@@ -127,14 +127,18 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: setup_micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: False
           environment-name: mda
-          extra-specs: |
-            python=="3.9"
+          create-args: >-
+            python=3.9
             pip
-          channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+          # using jaime's shim to avoid pulling down the cudatoolkit
+          condarc: |
+            channels:
+              - jaimergp/label/unsupported-cudatoolkit-shim
+              - conda-forge
+              - bioconda
 
       - name: install_deps
         uses: ./.github/actions/setup-deps