Add xarray upstream CI workflow with cron job (#1327)

### What kind of change does this PR introduce? * Splits the existing upstream testing stage into its own workflow * This workflow uses xarray-developed actions for opening issues when this workflow fails * Is triggered when a PR is merged to master or every day at midnight. * Can be triggered via cron job or manually (using `workflow_dispatch`) * Unites the CI workflows for PyPI/`tox`-based jobs into one action with a strategy matrix ### Does this PR introduce a breaking change? No. ### Other information: See: corteva/rioxarray#654
Ouranosinc · Mar 23, 2023 · 1c9fcfb · 1c9fcfb
2 parents 63b05be + 5cdb18f
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,4 +1,4 @@
-name: "xclim Testing Suite"
+name: xclim Testing Suite
 
 on:
   push:
@@ -24,78 +24,109 @@ env:
 
 jobs:
   black:
+    name: Black (Python${{ matrix.python-version }})
     runs-on: ubuntu-latest
     if: |
       ((github.event_name == 'pull_request') && (github.event.action != 'labeled')) ||
       (github.event.review.state == 'approved') ||
       (github.event_name == 'push')
+    strategy:
+      matrix:
+        python-version:
+          - "3.8"
     steps:
       - name: Cancel previous runs
         uses: styfle/[email protected]
         with:
           access_token: ${{ github.token }}
       - uses: actions/checkout@v3
-      - name: Set up Python3.8
+      - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
-      - name: Install tox
-        run: pip install tox~=4.0
+          python-version: ${{ matrix.python-version }}
+      - name: Install pylint and tox
+        run: pip install pylint tox~=4.0
+      - name: Run pylint
+        run: pylint --rcfile=pylintrc --disable=import-error --exit-zero xclim
       - name: Run linting suite
         run: tox -e black
 
   test-py38:
+    name: test-${{ matrix.tox-env }} (Python${{ matrix.python-version }})
     needs: black
     if: |
       (github.event_name == 'pull_request') && !contains(github.event.pull_request.labels.*.name, 'approved')
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        tox-env:
+          - "py38"
+        python-version:
+          - "3.8"
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python3.8
+      - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: ${{ matrix.python-version }}
       - name: Install tox
         run: pip install tox~=4.0
       - name: Test with tox
-        run: tox -e py38
+        run: tox -e ${{ matrix.tox-env }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  test-py39-upstream-sbck-eofs-coverage:
+  test-pypi:
     needs: black
+    name: test-${{ matrix.tox-env }} (Python${{ matrix.python-version }})
     if: |
       contains(github.event.pull_request.labels.*.name, 'approved') ||
       (github.event.review.state == 'approved') ||
       (github.event_name == 'push')
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - tox-env: py38-coverage
+            python-version: "3.8"
+          - tox-env: py39-coverage-sbck-eofs
+            python-version: "3.9"
+          - tox-env: notebooks_doctests
+            python-version: "3.10"
     steps:
       - uses: actions/checkout@v3
       - name: Install Eigen3
+        if: ${{ matrix.tox-env == 'py39-coverage-sbck-eofs' }}
         run: |
           sudo apt-get update
           sudo apt-get install libeigen3-dev
-      - name: Set up Python3.9
+      - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: ${{ matrix.python-version }}
       - name: Install tox
         run: pip install tox~=4.0
       - name: Test with tox
-        run: tox -e py39-upstream-sbck-eofs-coverage
+        run: tox -e ${{ matrix.tox-env }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-py39-upstream-sbck-eofs
+          COVERALLS_FLAG_NAME: run-{{ matrix.tox-env }}
           COVERALLS_PARALLEL: true
           COVERALLS_SERVICE_NAME: github
 
-  test-py310-opt-slow:
+  test-conda:
     needs: black
+    name: test-conda-${{ matrix.tox-env }} (Python${{ matrix.python-version }})
     if: |
       contains(github.event.pull_request.labels.*.name, 'approved') ||
       (github.event.review.state == 'approved') ||
       (github.event_name == 'push')
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - tox-env: py310
+            python-version: "3.10"
     defaults:
       run:
         shell: bash -l {0}
@@ -108,22 +139,22 @@ jobs:
           micromamba-version: 'latest'
           environment-file: environment.yml
           extra-specs: |
-            python="3.10"
+            python=${{ matrix.python-version }}
       - name: Conda and Mamba versions
         run: |
           conda --version
           echo "micromamba: $(micromamba --version)"
       - name: Install xclim
         run: |
           python -m pip install --no-user .
-      - name: Test
+      - name: Check versions
         run: |
-          pip list
+          conda list
+          xclim show_version_info
           pip check
+      - name: Test with pytest
+        run: |
           pytest xclim --numprocesses=logical --durations=10 --cov=xclim --cov-report=term-missing
-        env:
-          CONDA_EXE: mamba
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 #      - name: Install tox
 #        shell: bash -l {0}
 #        run: |
@@ -142,63 +173,14 @@ jobs:
           coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-py310-opt-slow
-          COVERALLS_PARALLEL: true
-          COVERALLS_SERVICE_NAME: github
-
-  test-py38-coverage:
-    needs: black
-    if: |
-      contains(github.event.pull_request.labels.*.name, 'approved') ||
-      (github.event.review.state == 'approved') ||
-      (github.event_name == 'push')
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python3.8
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-      - name: Install tox
-        run: pip install tox~=4.0
-      - name: Test with tox
-        run: tox -e py38-coverage
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-py38-coverage
-          COVERALLS_PARALLEL: true
-          COVERALLS_SERVICE_NAME: github
-
-  py38-notebooks_doctests:
-    needs: black
-    if: |
-      contains(github.event.pull_request.labels.*.name, 'approved') ||
-      (github.event.review.state == 'approved') ||
-      (github.event_name == 'push')
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python3.8
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-      - name: Install pylint and tox
-        run: pip install pylint tox~=4.0
-      - name: Run pylint
-        run: pylint --rcfile=pylintrc --disable=import-error --exit-zero xclim
-      - name: Test with tox
-        run: tox -e notebooks_doctests
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-py38-notebooks_doctests
+          COVERALLS_FLAG_NAME: run-{{ matrix.tox-env }}-opt-slow
           COVERALLS_PARALLEL: true
           COVERALLS_SERVICE_NAME: github
 
   finish:
     needs:
-      - py38-notebooks_doctests
-      - test-py38-coverage
-      - test-py310-opt-slow
+      - test-pypi
+      - test-conda
     runs-on: ubuntu-latest
     container: python:3-slim
     steps:

diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml
@@ -0,0 +1,77 @@
+name: xclim Upstream dependencies
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - CHANGES.rst
+      - README.rst
+      - pyproject.toml
+      - setup.cfg
+      - xclim/__init__.py
+  schedule:
+    - cron: "0 0 * * *" # Daily “At 00:00” UTC
+  workflow_dispatch: # allows you to trigger the workflow run manually
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  upstream-dev:
+    name: test-upstream-dev (Python${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    if: |
+      (github.event_name == 'schedule') ||
+      (github.event_name == 'workflow_dispatch') ||
+      (github.event_name == 'push')
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.10"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+      - name: Set up conda environment
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          cache-downloads: true
+          micromamba-version: 'latest'
+          environment-file: environment.yml
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            pytest-reportlog
+      - name: Conda and Mamba versions
+        run: |
+          conda --version
+          echo "micromamba: $(micromamba --version)"
+      - name: Install upstream versions
+        run: |
+          python -m pip install -r requirements_upstream.txt
+      - name: Install xclim
+        run: |
+          python -m pip install --no-user --no-deps .
+      - name: Check versions
+        run: |
+          conda list
+          xclim show_version_info
+          pip check
+      - name: Run Tests
+        if: success()
+        id: status
+        run: |
+          pytest xclim --numprocesses=logical --durations=10 --cov=xclim --cov-report=term-missing --report-log output-${{ matrix.python-version }}-log.jsonl
+      - name: Generate and publish the report
+        if: |
+          failure()
+          && steps.status.outcome == 'failure'
+          && github.event_name == 'schedule'
+          && github.repository_owner == 'Ouranosinc'
+        uses: xarray-contrib/issue-from-pytest-log@v1
+        with:
+          log-path: output-${{ matrix.python-version }}-log.jsonl
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -38,6 +38,7 @@ Internal changes
 * Changes in testing setup now prevent ``test_mean_radiant_temperature`` from sometimes causing a segmentation fault. (:issue:`1303`, :pull:`1315`).
 * Addressed a formatting bug that caused `Indicators` with multiple variables returned to not be properly formatted in the documentation. (:issue:`1305`, :pull:`1317`).
 * `tox` now include `sbck` and `eofs` flags for easier testing of dependencies. CI builds now test against `sbck-python` @ master.  (:pull:`1328`).
+* `upstream` CI tests are now run on push to master, at midnight, and can also be triggered via `workflow_dispatch`. Failures from upstream build will open issues using `xarray-contrib/issue-from-pytest-log`. (:pull:`1327`).
 
 0.41.0 (2023-02-28)
 -------------------

diff --git a/xclim/testing/utils.py b/xclim/testing/utils.py
@@ -31,15 +31,20 @@
 _xclim_deps = [
     "xclim",
     "xarray",
+    "statsmodels",
     "sklearn",
     "scipy",
     "pint",
     "pandas",
     "numba",
+    "lmoments3",
+    "jsonpickle",
+    "flox",
     "dask",
     "cf_xarray",
     "cftime",
     "clisops",
+    "click",
     "bottleneck",
     "boltons",
 ]