Merge branch 'main' into replace-A-period

Ouranosinc · Sep 19, 2024 · 5646b1e · 5646b1e
2 parents adea760 + f7a76f0
commit 5646b1e
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diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -1,21 +1,25 @@
-* xclim version:
-* Python version:
-* Operating System:
+- xclim version:
+- Python version:
+- Operating System:
 
 ### Description
+
 <!--Describe what you were trying to get done.
 Tell us what happened, what went wrong, and what you expected to happen.-->
 
-
 ### What I Did
+
 <!--Paste the command(s) you ran and the output.
 If there was a crash, please include the traceback below.-->
+
 ```
 $ pip install foo --bar
 ```
 
 ### What I Received
+
 <!--Paste the output or the stack trace of the problem you experienced here.-->
+
 ```
 Traceback (most recent call last):
   File "/path/to/file/script.py", line 3326, in run_code

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -3,13 +3,19 @@ updates:
   - package-ecosystem: github-actions
     directory: /
     schedule:
-      interval: daily
+      interval: weekly
       time: '12:00'
-    open-pull-requests-limit: 5
+    groups:
+      actions:
+        patterns:
+          - "*"
 
   - package-ecosystem: pip
     directory: /
     schedule:
-      interval: daily
+      interval: weekly
       time: '12:00'
-    open-pull-requests-limit: 5
+    groups:
+      python:
+        patterns:
+          - "*"
diff --git a/.github/publish-mastodon.template.md → .github/publish-mastodon-template.md b/.github/publish-mastodon.template.md → .github/publish-mastodon-template.md
diff --git a/.github/workflows/add-to-project.yml b/.github/workflows/add-to-project.yml
@@ -16,7 +16,7 @@ jobs:
       repository-projects: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block
@@ -25,7 +25,7 @@ jobs:
 
       - name: Generate App Token
         id: token_generator
-        uses: actions/create-github-app-token@3378cda945da322a8db4b193e19d46352ebe2de5 # v1.10.4
+        uses: actions/create-github-app-token@5d869da34e18e7287c1daad50e0b8ea0f506ce69 # v1.11.0
         with:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}

diff --git a/.github/workflows/bump-version.yml b/.github/workflows/bump-version.yml
@@ -35,7 +35,7 @@ jobs:
       actions: read
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block
@@ -46,7 +46,7 @@ jobs:
             pypi.org:443
       - name: Generate App Token
         id: token_generator
-        uses: actions/create-github-app-token@3378cda945da322a8db4b193e19d46352ebe2de5 # v1.10.4
+        uses: actions/create-github-app-token@5d869da34e18e7287c1daad50e0b8ea0f506ce69 # v1.11.0
         with:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}

diff --git a/.github/workflows/cache-cleaner.yml b/.github/workflows/cache-cleaner.yml
@@ -15,7 +15,7 @@ jobs:
       actions: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -40,7 +40,7 @@ jobs:
           - 'python'
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/first-pull-request.yml b/.github/workflows/first-pull-request.yml
@@ -16,7 +16,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/label-on-approval.yml b/.github/workflows/label-on-approval.yml
@@ -24,7 +24,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block
@@ -51,7 +51,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/label.yml b/.github/workflows/label.yml
@@ -27,7 +27,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -32,19 +32,15 @@ permissions:
 
 jobs:
   lint:
-    name: Lint (Python${{ matrix.python-version }})
+    name: Lint
     runs-on: ubuntu-latest
     if: |
       (github.event.action != 'labeled') ||
       (github.event.review.state == 'approved') ||
       (github.event_name == 'push')
-    strategy:
-      matrix:
-        python-version:
-          - "3.9"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block
@@ -54,13 +50,21 @@ jobs:
             pypi.org:443
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
-      - name: Set up Python${{ matrix.python-version }}
+      - name: Set up Python3
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.x"
+          cache: 'pip'
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+      - name: Environment Caching
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+        with:
+          path: |
+            ${{ matrix.testdata-cache }}
+            .tox
+          key: ${{ runner.os }}-xclim-testdata-${{ env.XCLIM_TESTDATA_BRANCH }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-lint
       - name: Run pylint
         run: |
           python -m pylint --rcfile=.pylintrc.toml --disable=import-error --exit-zero xclim
@@ -69,16 +73,17 @@ jobs:
           python -m tox -e lint
 
   test-preliminary:
-    name: Python${{ matrix.python-version }} (ubuntu-latest)
+    name: Python${{ matrix.python-version }} (${{ matrix.os }})
     needs: lint
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version:
-          - "3.9"
+        os: [ 'ubuntu-latest' ]
+        python-version: [ "3.10" ]
+        testdata-cache: [ '~/.cache/xclim-testdata' ]
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block
@@ -95,9 +100,17 @@ jobs:
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+      - name: Environment Caching
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+        with:
+          path: |
+            ${{ matrix.testdata-cache }}
+            .tox
+          key: ${{ runner.os }}-xclim-testdata-${{ env.XCLIM_TESTDATA_BRANCH }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-Python${{ matrix.python-version }}
       - name: Test with tox
         run: |
           python -m tox -- -m 'not slow'
@@ -118,44 +131,52 @@ jobs:
       matrix:
         include:
           # Linux builds
-          - os: ubuntu-latest
+          - os: 'ubuntu-latest'
+            testdata-cache: '~/.cache/xclim-testdata'
             markers: -m 'not slow'
             python-version: "3.10"
             tox-env: standard
-          - os: ubuntu-latest
+          - os: 'ubuntu-latest'
+            testdata-cache: '~/.cache/xclim-testdata'
             markers: -m 'not slow'
             python-version: "3.11"
             tox-env: standard
-          - os: ubuntu-latest
+          - os: 'ubuntu-latest'
+            testdata-cache: '~/.cache/xclim-testdata'
             markers: -m 'not slow'
             python-version: "3.12"
             tox-env: standard
           # Windows builds
-          - os: windows-latest
+          - os: 'windows-latest'
+            testdata-cache: 'C:\Users\runneradmin\AppData\Local\xclim-testdata\xclim-testdata\Cache'
             markers: -m 'not slow'
-            python-version: "3.9"
-            tox-env: py39-coverage-prefetch  # Test data prefetch is needed for Windows
-          # macOS builds
-          - os: macos-latest
             python-version: "3.10"
+            tox-env: py310-coverage-prefetch  # Test data prefetch is needed for Windows
+          # macOS builds
+          - os: 'macos-latest'
+            testdata-cache: '~/Library/Caches/xclim-testdata'
             markers: ''  # Slow tests
-            tox-env: py310-coverage-extras
+            python-version: "3.11"
+            tox-env: py311-coverage-extras
           # Specialized tests
-          - os: ubuntu-latest
+          - os: 'ubuntu-latest'
+            testdata-cache: '~/.cache/xclim-testdata'
             markers: -m 'not requires_internet and not slow'
-            python-version: "3.9"
-            tox-env: py39-coverage-offline-prefetch
-          - os: ubuntu-latest
-            markers: ''
+            python-version: "3.11"
+            tox-env: py311-coverage-sbck-offline-prefetch
+          - os: 'ubuntu-latest'
+            testdata-cache: '~/.cache/xclim-testdata'
+            markers: '' # No markers for notebooks
             python-version: "3.10"
             tox-env: notebooks
-          - os: ubuntu-latest
-            markers: ''
+          - os: 'ubuntu-latest'
+            testdata-cache: '~/.cache/xclim-testdata'
+            markers: '' # No markers for doctests
             python-version: "3.12"
             tox-env: doctests
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: block
           allowed-endpoints: >
@@ -174,17 +195,27 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Install Eigen3 (SBCK)
-        if: ${{ matrix.python-version == '3.11' }}
+        if: ${{ matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest' }}
         run: |
           sudo apt-get update
           sudo apt-get install libeigen3-dev
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+      - name: Environment Caching
+        # if prefetch is not in tox-env
+        if: contains(matrix.tox-env, 'prefetch') == false
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+        with:
+          path: |
+            ${{ matrix.testdata-cache }}
+            .tox
+          key: ${{ runner.os }}-xclim-testdata-${{ env.XCLIM_TESTDATA_BRANCH }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-Python${{ matrix.python-version }}
       - name: Test with tox
         if: ${{ matrix.tox-env == 'standard' }}
         run: |
@@ -212,14 +243,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ "3.9", "3.12" ]
+        os: [ 'ubuntu-latest' ]
+        python-version: [ "3.10", "3.12" ]
+        testdata-cache: [ '~/.cache/xclim-testdata' ]
     defaults:
       run:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           disable-sudo: true
           egress-policy: block
@@ -247,6 +279,12 @@ jobs:
       - name: Micromamba version
         run: |
           echo "micromamba: $(micromamba --version)"
+      - name: Test Data Caching
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+        with:
+          path: |
+            ${{ matrix.testdata-cache }}
+          key: ${{ runner.os }}-xclim-testdata-${{ env.XCLIM_TESTDATA_BRANCH }}-conda-${{ hashFiles('pyproject.toml', 'tox.ini') }}-Python${{ matrix.python-version }}
       - name: Install xclim
         run: |
           python -m pip install --no-user --editable .
@@ -284,18 +322,13 @@ jobs:
       - test-pypi
       - test-conda
     runs-on: ubuntu-latest
-    container: python:3-slim
     steps:
-      - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      - name: Harden Runner
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
-          sparse-checkout: |
-            CI/requirements_ci.txt
-      - name: Install CI libraries
-        run: |
-          python -m pip install --require-hashes -r CI/requirements_ci.txt
-      - name: Coveralls finished
-        run: |
-          python -m coveralls --finish
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          disable-sudo: true
+          egress-policy: audit
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@643bc377ffa44ace6394b2b5d0d3950076de9f63 # v2.3.0
+        with:
+          parallel-finished: true