Merge pull request #1025 from ioos/develop

Merge in develop branch in preparation for Compliance Checker v5.1.0
ioos · May 17, 2023 · cb451c5 · cb451c5
2 parents a745fc7 + 07a7874
commit cb451c5
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diff --git a/.github/workflows/cc-checker-ugrid-test.yml b/.github/workflows/cc-checker-ugrid-test.yml
@@ -3,7 +3,6 @@ name: UGRID Plugin Tests
 on:
   pull_request:
   push:
-    branches: [master]
 
 jobs:
   run:
@@ -12,32 +11,24 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Setup Conda
-      uses: s-weigand/setup-conda@v1
+    - name: Setup Micromamba
+      uses: mamba-org/provision-with-micromamba@v15
       with:
-        activate-conda: false
-        conda-channels: conda-forge
+        environment-file: false
 
-    - name: Python ${{ matrix.python-version }}
+    - name: Setup Env
       shell: bash -l {0}
-      run: |
-        conda create --name TEST python=${{ matrix.python-version }} python=3 pip --file requirements.txt --file test_requirements.txt --strict-channel-priority
-        source activate TEST
-        pip install -e . --no-deps --force-reinstall
-
-    - name: Conda Info
-      shell: bash -l {0}
-      run: |
-        source activate TEST
-        conda info --all
-        conda list
+      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
 
     - name: cc-plugin-glider tests
       shell: bash -l {0}
-      run: |
-        source activate TEST
-        git clone https://github.com/ioos/cc-checker-ugrid.git
-        cd cc-checker-ugrid
-        pip install -e . --no-deps --force-reinstall
-        conda install --file requirements.txt --file requirements-dev.txt ;
-        pytest -s -rxs -v cc_plugin_ugrid
+      run: >
+        micromamba activate TEST
+        && 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
diff --git a/.github/workflows/cc-plugin-glider-test.yml b/.github/workflows/cc-plugin-glider-test.yml
@@ -12,11 +12,11 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v14
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: false
 
-    - name: Python
+    - name: Setup Env
       shell: bash -l {0}
       run: >
         micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge

diff --git a/.github/workflows/cc-plugin-sgrid-test.yml b/.github/workflows/cc-plugin-sgrid-test.yml
@@ -12,11 +12,11 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: false
 
-    - name: Python
+    - name: Setup Env
       shell: bash -l {0}
       run: >
         micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge

diff --git a/.github/workflows/cc-plugin-ugrid-test.yml b/.github/workflows/cc-plugin-ugrid-test.yml
@@ -12,11 +12,11 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v14
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: false
 
-    - name: Python
+    - name: Setup Env
       shell: bash -l {0}
       run: >
         micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -12,11 +12,11 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v14
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: false
 
-    - name: Python
+    - name: Setup Env
       shell: bash -l {0}
       run: >
         micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge

diff --git a/.github/workflows/default-tests.yml b/.github/workflows/default-tests.yml
@@ -17,11 +17,11 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v14
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: false
 
-    - name: Python ${{ matrix.python-version }}
+    - name: Setup Env ${{ matrix.python-version }}
       shell: bash -l {0}
       run: >
         micromamba create --name TEST python=${{ matrix.python-version }} pip --file requirements.txt --file test_requirements.txt --channel conda-forge

diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -0,0 +1,48 @@
+
+name: Documentation
+
+on:
+  pull_request:
+  push:
+  release:
+    types:
+      - published
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Setup Mamba
+      uses: mamba-org/provision-with-micromamba@v15
+      with:
+        environment-file: false
+
+    - name: Build environment
+      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
+      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
@@ -3,7 +3,6 @@ name: Integration Tests
 on:
   pull_request:
   push:
-    branches: [master,develop]
 
 jobs:
   run:
@@ -13,11 +12,11 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v14
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: false
 
-    - name: Create Environment
+    - name: Setup Env
       shell: bash -l {0}
       run: >
         micromamba create --name TEST python=3 pip --file requirements.txt --file test_requirements.txt --channel conda-forge

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -3,8 +3,6 @@ name: Publish to PyPI
 on:
   pull_request:
   push:
-    branches:
-      - master
   release:
     types:
       - published
@@ -29,7 +27,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
     - name: Install build tools
       run: |
@@ -49,7 +47,7 @@ jobs:
 
     - name: Publish a Python distribution to PyPI
       if: success() && github.event_name == 'release'
-      uses: pypa/gh-action-pypi-publish@v1.8.5
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_ACCESS_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -110,3 +110,7 @@ activate
 # coverage output
 coverage/
 coverage.xml
+
+# shpinx docs
+docs/source/generated/
+docs/source/quickintro.md
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,42 +10,49 @@ repos:
       exclude: compliance_checker/tests/data
     - id: check-docstring-first
     - id: check-added-large-files
+    - id: check-json
+    - id: check-merge-conflict
+    - id: check-yaml
     - id: requirements-txt-fixer
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
-  hooks:
-    - id: flake8
-      exclude: docs/source/conf.py
-      args: [--max-line-length=200, "--ignore=E203,E501,W503", "--select=select=C,E,F,W,B,B950"]
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    additional_dependencies: [toml]
-    args: ["--profile", "black", "--filter-files"]
+      args:
+        - requirements.txt
+        - test_requirements.txt
 
 - repo: https://github.com/psf/black
   rev: 23.3.0
   hooks:
   - id: black
     language_version: python3
 
+- repo: https://github.com/asottile/add-trailing-comma
+  rev: v2.4.0
+  hooks:
+    - id: add-trailing-comma
+
+
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.267
+  hooks:
+    - id: ruff
+
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: 0.11.2
+  hooks:
+    - id: pyproject-fmt
+
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.4
   hooks:
     - id: codespell
       args:
-        - --ignore-words-list=degreee,varn,poit,uint,sur,herat,claus,dedent,dedenting,dedents,dedented
+        - --ignore-words-list=degreeE,degreee,varn,poit,uint,sur,herat,claus,tung,messsages
       exclude: >
           (?x)^(
               .*\.xml|
               .*\.cdl|
-              .*_version\.py|
-              .*versioneer\.py|
-              compliance_checker/tests/cassettes/test_netcdf_content_type\.yaml|
-              compliance_checker/data/seanames\.csv
+              .*\.yaml|
+              .*_version.py|
+              .*versioneer.py
           )$
 
 ci: