Add GitHub workflows to check black, pylint, git-fleximod

.github/workflows/black.yml

@@ -2,11 +2,29 @@ name: black check on push and PR
 #
 # Run the python formatting in check mode
 #
-on: [push, pull_request]
+on:
+  push:
+    paths:
+      - 'python/**'
+      - 'cime_config/SystemTests/**'
+      - 'cime_config/buildlib/**'
+      - 'cime_config/buildnml/**'
+      - '.github/workflows/black.yml'
+  pull_request:
+    paths:
+      - 'python/**'
+      - 'cime_config/SystemTests/**'
+      - 'cime_config/buildlib/**'
+      - 'cime_config/buildnml/**'
+      - '.github/workflows/black.yml'
 
 jobs:
   black-check:
      runs-on: ubuntu-latest
+     strategy:
+       fail-fast: false
+       matrix:
+         python-version: ["3.7.9", "3.8", "3.9", "3.10", "3.11", "3.12"]
      steps:
         # Checkout the code
         - uses: actions/checkout@v2
@@ -15,23 +33,23 @@ jobs:
           with:
              # Use options and version identical to the conda environment
              # Using pyproject.toml makes sure this testing is consistent with our python directory testing
-             options: "--check --config python/pyproject.toml"
+             options: "--check --diff --config python/pyproject.toml"
              src: "./python"
              # Version should be coordinated with the ctsm_pylib conda environment under the python directory
              version: "22.3.0"
           # Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field)
         - uses: psf/black@stable
           with:
-             options: "--check --config python/pyproject.toml"
+             options: "--check --diff --config python/pyproject.toml"
              src: "./cime_config/SystemTests"
              version: "22.3.0"
         - uses: psf/black@stable
           with:
-             options: "--check --config python/pyproject.toml"
+             options: "--check --diff --config python/pyproject.toml"
              src: "./cime_config/buildlib"
              version: "22.3.0"
         - uses: psf/black@stable
           with:
-             options: "--check --config python/pyproject.toml"
+             options: "--check --diff --config python/pyproject.toml"
              src: "./cime_config/buildnml"
              version: "22.3.0"

.github/workflows/fleximod_test.yaml

@@ -0,0 +1,31 @@
+name: git-fleximod test
+#
+# Test git-fleximod update and cleanliness
+# Based closely on workflow from CESM repo
+#
+on: [push, pull_request]
+
+jobs:
+  fleximod-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # oldest supported and latest supported
+        python-version: ["3.7", "3.x"]
+    steps:
+      - id: checkout-CTSM
+        uses: actions/checkout@v4
+      - id: run-fleximod
+        run: |
+          $GITHUB_WORKSPACE/bin/git-fleximod update
+          echo
+          echo "Update complete, checking status"
+          echo
+          $GITHUB_WORKSPACE/bin/git-fleximod test
+      - id: check-cleanliness
+        run: |
+          echo
+          echo "Checking if git fleximod matches expected externals"
+          echo
+          git diff --exit-code

.github/workflows/pylint.yml

@@ -0,0 +1,61 @@
+name: pylint check on push and PR
+#
+# Run the pylint formatting
+#
+on:
+   push:
+     paths:
+       - 'python/ctsm/**'
+       - 'python/requirements.txt'
+       - '.github/workflows/pylint.yml'
+   pull_request:
+     paths:
+      - 'python/ctsm/**'
+      - 'python/requirements.txt'
+      - '.github/workflows/pylint.yml'
+
+jobs:
+   # Disabled pylint-check-old because 3.7.9 requires netCDF to be manually installed first
+#   pylint-check-old:
+#     runs-on: ubuntu-20.04
+#     strategy:
+#       fail-fast: false
+#       matrix:
+#         python-version: ["3.7.9"]
+#     steps:
+#     - uses: actions/checkout@v4
+#     - name: Set up Python ${{ matrix.python-version }}
+#       uses: actions/setup-python@v5
+#       with:
+#         python-version: ${{ matrix.python-version }}
+#     - name: Install dependencies
+#       run: |
+#         python -m pip install --upgrade pip
+#         pip install -r python/requirements.txt
+#     - name: Analysing the code with pylint
+#       run: |
+#         cd python
+#         pylint --rcfile=ctsm/.pylintrc ctsm
+  pylint-check:
+     runs-on: ubuntu-latest
+     strategy:
+       fail-fast: false
+       matrix:
+         # Python 3.8 fails because GEOS C headers aren't installed
+         # Our pylint (2.8.3) is incompatible with Python > 3.10
+         # python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+         python-version: ["3.9", "3.10"]
+     steps:
+     - uses: actions/checkout@v4
+     - name: Set up Python ${{ matrix.python-version }}
+       uses: actions/setup-python@v5
+       with:
+         python-version: ${{ matrix.python-version }}
+     - name: Install dependencies
+       run: |
+         python -m pip install --upgrade pip
+         pip install -r python/requirements.txt
+     - name: Analysing the code with pylint
+       run: |
+         cd python
+         pylint --disable=R0022 --rcfile=ctsm/.pylintrc ctsm

.gitmodules

@@ -31,7 +31,7 @@ url = https://github.com/NGEET/fates
 fxtag = sci.1.80.11_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
-fxDONOTUSEurl = https://github.com/NCAR/fates-release
+fxDONOTUSEurl = https://github.com/NGEET/fates
 
 [submodule "cism"]
 path = components/cism

python/requirements.txt

@@ -1,4 +1,14 @@
-Requirements for testing:
-
-- If using python < 3.3, requires the mock library (this is available in
-  the standard library in python 3.3+)
+pandas
+tqdm
+scipy
+netcdf4
+requests
+packaging
+numpy
+xarray
+xesmf
+numba
+pylint==2.8.3
+black
+cartopy
+matplotlib