Switched from miniconda-setup to micromamba-setup for mypy workflow (#…

…781) * Switched from miniconda to micromamba for mypy workflow * setup-micromamba for test.yml * Specified environment-name for test.yml * Changed mamba to micromamba for test.yml
pymc-devs · Jun 11, 2024 · 75a9fd2 · 75a9fd2
1 parent 6857517
commit 75a9fd2
Show file tree

Hide file tree

Showing 2 changed files with 81 additions and 90 deletions.
diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
@@ -10,35 +10,22 @@ jobs:
     runs-on: ubuntu-latest
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
     steps:
       - uses: actions/checkout@v4
-      - name: Cache conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if environment.yml has not changed
-          CACHE_NUMBER: 0
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-py310-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          mamba-version: "*"
-          activate-environment: pytensor-test
-          channel-priority: strict
+          micromamba-version: "latest" # any version from https://github.com/mamba-org/micromamba-releases
           environment-file: environment.yml
-          python-version: "3.10"
-          use-mamba: true
-          use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
-      - name: Install-pytensor and mypy dependencies
+          init-shell: bash
+          cache-environment: true
+          post-cleanup: "all"
+      - name: Install pytensor and mypy dependencies
         run: |
-          conda activate pytensor-test
           pip install -e .
           python --version
+        shell: micromamba-shell {0}
       - name: Run mypy
         run: |
-          conda activate pytensor-test
-          python ./scripts/run_mypy.py --verbose
+          python ./scripts/run_mypy.py --verbose
+        shell: micromamba-shell {0}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -55,11 +55,11 @@ jobs:
       matrix:
         python-version: ["3.10", "3.12"]
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - uses: pre-commit/[email protected]
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: pre-commit/[email protected]
 
   test_ubuntu:
     name: "Test py${{ matrix.python-version }} : fast-compile ${{ matrix.fast-compile }} : float32 ${{ matrix.float32 }} : ${{ matrix.part }}"
@@ -72,8 +72,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.12"]
-        fast-compile: [0,1]
-        float32: [0,1]
+        fast-compile: [0, 1]
+        float32: [0, 1]
         install-numba: [0]
         install-jax: [0]
         part:
@@ -84,7 +84,7 @@ jobs:
           - "tests/tensor/conv"
           - "tests/tensor/rewriting"
           - "tests/tensor/test_math.py"
-          - "tests/tensor/test_basic.py tests/tensor/test_inplace.py"          
+          - "tests/tensor/test_basic.py tests/tensor/test_inplace.py"
           - "tests/tensor/test_blas.py tests/tensor/test_elemwise.py tests/tensor/test_math_scipy.py"
         exclude:
           - python-version: "3.10"
@@ -121,11 +121,13 @@ jobs:
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v3
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          python-version: ${{ matrix.python-version }}
+          environment-name: pytensor-test
+          micromamba-version: "latest"
+          init-shell: bash
+          post-cleanup: "all"
+          create-args: python=${{ matrix.python-version }}
 
       - name: Create matrix id
         id: matrix-id
@@ -138,13 +140,13 @@ jobs:
           echo "id=$MATRIX_ID" >> $GITHUB_OUTPUT
 
       - name: Install dependencies
-        shell: bash -l {0}
+        shell: micromamba-shell {0}
         run: |
-          mamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock sympy
-          if [[ $INSTALL_NUMBA == "1" ]]; then mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" "numba>=0.57"; fi
-          if [[ $INSTALL_JAX == "1" ]]; then mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" jax jaxlib numpyro && pip install tensorflow-probability; fi
+          micromamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock sympy
+          if [[ $INSTALL_NUMBA == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" "numba>=0.57"; fi
+          if [[ $INSTALL_JAX == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" jax jaxlib numpyro && pip install tensorflow-probability; fi
           pip install -e ./
-          mamba list && pip freeze
+          micromamba list && pip freeze
           python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))'
           python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"'
         env:
@@ -153,7 +155,7 @@ jobs:
           INSTALL_JAX: ${{ matrix.install-jax }}
 
       - name: Run tests
-        shell: bash -l {0}
+        shell: micromamba-shell {0}
         run: |
           if [[ $FAST_COMPILE == "1" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,mode=FAST_COMPILE; fi
           if [[ $FLOAT32 == "1" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,floatX=float32; fi
@@ -175,55 +177,57 @@ jobs:
           path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml
 
   benchmarks:
-      name: "Benchmarks"
-      needs:
-        - changes
-        - style
-      runs-on: ubuntu-latest
-      if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }}
-      strategy:
-        fail-fast: false
-      steps:
-        - uses: actions/checkout@v4
-          with:
-            fetch-depth: 0
-        - name: Set up Python 3.10
-          uses: conda-incubator/setup-miniconda@v3
-          with:
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
-        - name: Install dependencies
-          shell: bash -l {0}
-          run: |
-            mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark
-            pip install -e ./
-            mamba list && pip freeze
-            python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))'
-            python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"'
-          env:
-            PYTHON_VERSION: 3.10
-        - name: Download previous benchmark data
-          uses: actions/cache@v4
-          with:
-            path: ./cache
-            key: ${{ runner.os }}-benchmark
-        - name: Run benchmarks
-          shell: bash -l {0}
-          run: |
-            export PYTENSOR_FLAGS=mode=FAST_COMPILE,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe
-            python -m pytest --runslow --benchmark-only --benchmark-json output.json
-        - name: Store benchmark result
-          uses: benchmark-action/github-action-benchmark@v1
-          with:
-            name: Python Benchmark with pytest-benchmark
-            tool: 'pytest'
-            output-file-path: output.json
-            external-data-json-path: ./cache/benchmark-data.json
-            alert-threshold: '200%'
-            github-token: ${{ secrets.GITHUB_TOKEN }}
-            comment-on-alert: false
-            fail-on-alert: false
-            auto-push: false
+    name: "Benchmarks"
+    needs:
+      - changes
+      - style
+    runs-on: ubuntu-latest
+    if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }}
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.10
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: pytensor-test
+          micromamba-version: "latest"
+          init-shell: bash
+          post-cleanup: "all"
+      - name: Install dependencies
+        shell: micromamba-shell {0}
+        run: |
+          micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark
+          pip install -e ./
+          micromamba list && pip freeze
+          python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))'
+          python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"'
+        env:
+          PYTHON_VERSION: 3.10
+      - name: Download previous benchmark data
+        uses: actions/cache@v4
+        with:
+          path: ./cache
+          key: ${{ runner.os }}-benchmark
+      - name: Run benchmarks
+        shell: micromamba-shell {0}
+        run: |
+          export PYTENSOR_FLAGS=mode=FAST_COMPILE,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe
+          python -m pytest --runslow --benchmark-only --benchmark-json output.json
+      - name: Store benchmark result
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: Python Benchmark with pytest-benchmark
+          tool: "pytest"
+          output-file-path: output.json
+          external-data-json-path: ./cache/benchmark-data.json
+          alert-threshold: "200%"
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          comment-on-alert: false
+          fail-on-alert: false
+          auto-push: false
 
   all-checks:
     if: ${{ always() }}