Combine test workflows into one

.github/workflows/pytest.yml → .github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: pytest
+name: tests
 
 on:
   pull_request:
@@ -19,7 +19,6 @@ on:
       - "codecov.yml"
       - "scripts/*.sh"
 
-
 # Tests are split into multiple jobs to accelerate the CI.
 # Different jobs should be organized to take approximately the same
 # time to complete (and not be prohibitely slow).
@@ -249,3 +248,148 @@ jobs:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
+  jax:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        floatx: [float64]
+        test-subset:
+          - pymc/tests/test_sampling_jax.py
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    env:
+      TEST_SUBSET: ${{ matrix.test-subset }}
+      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+          # Increase this value to reset cache if environment-test-py39.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-envs/environment-test-py39.yml') }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if requirements.txt has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/pip
+            $RUNNER_TOOL_CACHE/Python/*
+            ~\AppData\Local\pip\Cache
+          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
+            hashFiles('requirements.txt') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          mamba-version: "*"
+          activate-environment: pymc-test-py39
+          channel-priority: strict
+          environment-file: conda-envs/environment-test-py39.yml
+          use-mamba: true
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Install pymc
+        run: |
+          conda activate pymc-test-py39
+          pip install -e .
+          python --version
+      - name: Install jax specific dependencies
+        run: |
+          conda activate pymc-test-py39
+          pip install "numpyro>=0.8.0"
+          pip install git+https://github.com/blackjax-devs/blackjax.git@main
+      - name: Run tests
+        run: |
+          python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          env_vars: TEST_SUBSET
+          name: JAX tests - ${{ matrix.os }} ${{ matrix.floatx }}
+          fail_ci_if_error: false
+  arviz:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        floatx: [float64]
+        test-subset:
+          - |
+            pymc/tests/test_parallel_sampling.py
+            pymc/tests/test_posteriors.py
+            pymc/tests/test_sampling.py
+
+          - |
+            pymc/tests/test_data_container.py
+            pymc/tests/test_idata_conversion.py
+            pymc/tests/test_missing.py
+            pymc/tests/test_model.py
+            pymc/tests/test_shape_handling.py
+            pymc/tests/test_shared.py
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    env:
+      TEST_SUBSET: ${{ matrix.test-subset }}
+      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+          # Increase this value to reset cache if environment-test-py39.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-envs/environment-test-py39.yml') }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if requirements.txt has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/pip
+            $RUNNER_TOOL_CACHE/Python/*
+            ~\AppData\Local\pip\Cache
+          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
+            hashFiles('requirements.txt') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          mamba-version: "*"
+          activate-environment: pymc-test-py39
+          channel-priority: strict
+          environment-file: conda-envs/environment-test-py39.yml
+          use-mamba: true
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Install pymc
+        run: |
+          conda activate pymc-test-py39
+          pip install -e .
+          python --version
+      - name: Install latest arviz
+        run: |
+          conda activate pymc-test-py39
+          pip uninstall arviz -y
+          pip install git+https://github.com/arviz-devs/arviz
+      - name: Run tests
+        run: |
+          python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          env_vars: TEST_SUBSET
+          name: ArviZ compat - ${{ matrix.os }} ${{ matrix.floatx }}
+          fail_ci_if_error: false

scripts/check_all_tests_are_covered.py

@@ -36,7 +36,7 @@ def from_yaml():
     """
     # First collect the matrix definitions from testing workflows
     matrices = {}
-    for wf in ["pytest.yml", "arviz_compat.yml", "jaxtests.yml"]:
+    for wf in ["tests.yml"]:
         wfname = wf.strip(".yml")
         wfdef = yaml.safe_load(open(Path(".github", "workflows", wf)))
         for jobname, jobdef in wfdef["jobs"].items():