Merge pull request #1061 from ioos/develop

Merge in develop changes for 5.1.1 release preparation
ioos · Apr 12, 2024 · 03e279b · 03e279b
2 parents cb451c5 + 7c7fa9d
commit 03e279b
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diff --git a/.github/workflows/cc-checker-ugrid-test.yml b/.github/workflows/cc-checker-ugrid-test.yml
diff --git a/.github/workflows/cc-plugin-glider-test.yml b/.github/workflows/cc-plugin-glider-test.yml
@@ -9,26 +9,29 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v15
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
 
-    - name: Setup Env
+    - name: Install compliance-checker
       shell: bash -l {0}
-      run: >
-        micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge
-        && micromamba activate TEST
-        && pip install -e . --no-deps --force-reinstall
+      run: |
+        python -m pip install -v -e . --no-deps --force-reinstall
 
     - name: cc-plugin-glider tests
       shell: bash -l {0}
       run: >
-        micromamba activate TEST
-        && git clone https://github.com/ioos/cc-plugin-glider.git
+        git clone https://github.com/ioos/cc-plugin-glider.git
         && cd cc-plugin-glider
         && micromamba install --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        && pip install -e . --no-deps --force-reinstall
-        && pytest -s -rxs -v cc_plugin_glider
+        && python -m pip install -e . --no-deps --force-reinstall
+        && python -m pytest -s -rxs -v cc_plugin_glider
diff --git a/.github/workflows/cc-plugin-sgrid-test.yml b/.github/workflows/cc-plugin-sgrid-test.yml
@@ -9,25 +9,28 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v15
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
 
-    - name: Setup Env
+    - name: Install compliance-checker
       shell: bash -l {0}
-      run: >
-        micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge
-        && micromamba activate TEST
-        && pip install -e . --no-deps --force-reinstall
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
 
-    - name: cc-plugin-glider tests
+    - name: cc-plugin-sgrid tests
       shell: bash -l {0}
       run: >
-        micromamba activate TEST
-        && git clone https://github.com/ioos/cc-plugin-sgrid.git
+        git clone https://github.com/ioos/cc-plugin-sgrid.git
         && cd cc-plugin-sgrid
-        && pip install -e . --no-deps --force-reinstall
-        && pytest -s -rxs -v cc_plugin_sgrid
+        && python -m pip install -e . --no-deps --force-reinstall
+        && python -m pytest -s -rxs -v cc_plugin_sgrid
diff --git a/.github/workflows/cc-plugin-ugrid-test.yml b/.github/workflows/cc-plugin-ugrid-test.yml
@@ -9,26 +9,29 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v15
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
 
-    - name: Setup Env
+    - name: Install compliance-checker
       shell: bash -l {0}
-      run: >
-        micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge
-        && micromamba activate TEST
-        && pip install -e . --no-deps --force-reinstall
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
 
-    - name: cc-plugin-glider tests
+    - name: cc-plugin-ugrid tests
       shell: bash -l {0}
       run: >
-        micromamba activate TEST
-        && git clone https://github.com/ioos/cc-checker-ugrid.git
+        git clone https://github.com/ioos/cc-checker-ugrid.git
         && cd cc-checker-ugrid
         && micromamba install --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        && pip install -e . --no-deps --force-reinstall
-        && pytest -s -rxs -v cc_plugin_ugrid
+        && python -m pip install -e . --no-deps --force-reinstall
+        && python -m pytest -s -rxs -v cc_plugin_ugrid
diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -9,31 +9,34 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v15
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
 
-    - name: Setup Env
+    - name: Install compliance-checker
       shell: bash -l {0}
-      run: >
-        micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge
-        && micromamba activate TEST
-        && pip install -e . --no-deps --force-reinstall
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
 
     - name: Run tests with coverage
       shell: bash -l {0}
       run: |
-        micromamba activate TEST
-        pytest --cov=compliance_checker --cov-report=xml compliance_checker/tests
+        python -m pytest --cov=compliance_checker --cov-report=xml compliance_checker/tests
       # pass this step even if there are individual test failures, we are
       # interested in the overall level of coverage and other checks can
       # report on test failures.
       continue-on-error: true
 
     - name: Upload to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         files: coverage.xml
diff --git a/.github/workflows/default-tests.yml b/.github/workflows/default-tests.yml
@@ -9,27 +9,29 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         os: [windows-latest, ubuntu-latest, macos-latest]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v15
+    - name: Setup Micromamba ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
 
-    - name: Setup Env ${{ matrix.python-version }}
+    - name: Install compliance-checker
       shell: bash -l {0}
-      run: >
-        micromamba create --name TEST python=${{ matrix.python-version }} pip --file requirements.txt --file test_requirements.txt --channel conda-forge
-        && micromamba activate TEST
-        && pip install -e . --no-deps --force-reinstall
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
 
     - name: Default Tests
       shell: bash -l {0}
-      run: |
-        micromamba activate TEST
-        pytest -s -rxs -v -k "not integration" compliance_checker
+      run: python -m pytest -s -rxs -v -k "not integration" compliance_checker
diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -14,35 +14,38 @@ jobs:
 
     steps:
     - name: checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
-    - name: Setup Mamba
-      uses: mamba-org/provision-with-micromamba@v15
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
-
-    - name: Build environment
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
+
+    - name: Install compliance-checker
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=3 --file requirements.txt --file test_requirements.txt --channel conda-forge
-        micromamba activate TEST
         python -m pip install -e . --no-deps --force-reinstall
 
     - name: Build documentation
       shell: bash -l {0}
       run: |
         set -e
-        micromamba activate TEST
         pushd docs
         cp  ../README.md source/quickintro.md
         make clean html linkcheck
         popd
 
     - name: Deploy
       if: success() && github.event_name == 'release'
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/build/html
diff --git a/.github/workflows/integration-tests.yml b/.github/workflows/integration-tests.yml
@@ -9,22 +9,24 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v15
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements.txt
+          --file test_requirements.txt
+          --channel conda-forge
 
-    - name: Setup Env
+    - name: Install compliance-checker
       shell: bash -l {0}
-      run: >
-        micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge
-        && micromamba activate TEST
-        && pip install -e . --no-deps --force-reinstall
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
 
     - name: Integration Tests
       shell: bash -l {0}
-      run: |
-        micromamba activate TEST
-        pytest -m "integration" -s -rxs -v --vcr-record=none compliance_checker
+      run: python -m pytest -m "integration" -s -rxs -v --vcr-record=none compliance_checker
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -15,7 +15,7 @@ jobs:
   packages:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         # Should be enough for setuptools-scm
         fetch-depth: 100
@@ -25,7 +25,7 @@ jobs:
       run: git fetch origin 'refs/tags/*:refs/tags/*'
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: "3.11"
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
     - id: trailing-whitespace
       exclude: compliance_checker/tests/data
@@ -19,29 +19,29 @@ repos:
         - test_requirements.txt
 
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 24.3.0
   hooks:
   - id: black
     language_version: python3
 
 - repo: https://github.com/asottile/add-trailing-comma
-  rev: v2.4.0
+  rev: v3.1.0
   hooks:
     - id: add-trailing-comma
 
 
-- repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.267
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.3.5
   hooks:
     - id: ruff
 
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: 0.11.2
+  rev: 1.7.0
   hooks:
     - id: pyproject-fmt
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.4
+  rev: v2.2.6
   hooks:
     - id: codespell
       args: