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

.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/formatting_python.yml

@@ -0,0 +1,44 @@
+name: Check Python formatting
+
+on:
+  push:
+    paths:
+      - 'python/**'
+      - 'cime_config/SystemTests/**'
+      - 'cime_config/buildlib/**'
+      - 'cime_config/buildnml/**'
+  pull_request:
+    paths:
+      - 'python/**'
+      - 'cime_config/SystemTests/**'
+      - 'cime_config/buildlib/**'
+      - 'cime_config/buildnml/**'
+
+jobs:
+  lint-and-format-check:
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the code
+      - uses: actions/checkout@v4
+
+      # Set up the conda environment
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ctsm_pylib
+          environment-file: python/conda_env_ctsm_py.yml
+          channels: conda-forge
+          auto-activate-base: false
+
+      # Run pylint check
+      - name: Run pylint
+        run: |
+          cd python
+          conda run -n ctsm_pylib make lint
+
+      # Run black check
+      - name: Run black
+        # Run this step even if previous step(s) failed
+        if: success() || failure()
+        run: |
+          cd python
+          conda run -n ctsm_pylib make black

.gitmodules

@@ -31,7 +31,7 @@ url = https://github.com/NGEET/fates
 fxtag = sci.1.82.3_api.39.0.0
 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

py_env_create

@@ -18,8 +18,8 @@ cd "${SCRIPT_DIR}"
 condadir="${SCRIPT_DIR}/python"
 default_new_env_name=ctsm_pylib
 default_old_env_name=ctsm_pylib_3_7_9
-default_condafile="${condadir}/conda_env_ctsm_py.txt"
-default_condafile_old="${condadir}/conda_env_ctsm_py_old_3.7.9.txt"
+default_condafile="${condadir}/conda_env_ctsm_py.yml"
+default_condafile_old="${condadir}/conda_env_ctsm_py_old_3.7.9.yml"
 
 condafile="${default_condafile}"
 quiet=""
@@ -228,26 +228,15 @@ if [[ ${conda_env_does_exist} -gt 0 ]]; then
 fi
 
 #
-# Create the environment
-#
-echo "Create $new_env_name"
-if [[ "${quiet}" == "--quiet" ]]; then
-   (set -x; ${condamamba} create ${yes} --name $new_env_name ${quiet} 1>/dev/null)
-else
-   (set -x; ${condamamba} create ${yes} --name $new_env_name ${verbose})
-fi
-
-#
-# Install the environment
+# Create and install the environment
 #
 echo "Installing $new_env_name; this can take a few minutes."
-cmd=""
 if [[ "${quiet}" == "--quiet" ]]; then
-   # -q/--quiet option not available on Derecho
-   (set -x; ${condamamba} install ${yes} --channel conda-forge --name $new_env_name --file $condafile $option ${quiet} 1>/dev/null)
+   (set -x; ${condamamba} env create ${yes} --file "${condafile}" --name $new_env_name ${quiet} $option 1>/dev/null)
 else
-   (set -x; ${condamamba} install ${yes} --channel conda-forge --name $new_env_name --file $condafile $option ${verbose})
+   (set -x; ${condamamba} env create ${yes} --file "${condafile}" --name $new_env_name $option ${verbose})
 fi
+
 #
 # Report on success
 #

python/conda_env_ctsm_py.yml

@@ -0,0 +1,22 @@
+# This file is used by py_env_create to install the latest version of the ctsm_pylib conda environment.
+name: ctsm_pylib
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.13.2
+  - xarray=2025.1.2
+  - tqdm=4.67.1
+  - scipy=1.15.2
+  - netcdf4=1.7.2
+  - requests=2.32.3
+  - xesmf=0.8.8
+  - numba=0.61.0
+  - pylint=3.3.4
+  - black=25.1.0
+  - cartopy=0.24.0
+  - matplotlib=3.10.1
+
+  # Used in ctsm_postprocessing repo
+  - pytest=8.3.5
+  - coverage=7.8.0

python/conda_env_ctsm_py_old_3.7.9.yml

@@ -0,0 +1,24 @@
+# This file is used by py_env_create to install the previous version of the ctsm_pylib environment,
+# which used Python 3.7.9. Doing so is only useful for running CTSM python tools in repos from
+# before the new ctsm_pylib version (with Python 3.13.2) was introduced.
+#
+name: ctsm_pylib_3_7_9
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.7.9
+  - pandas=1.3.5
+  - tqdm=4.67.1
+  - scipy=1.7.3
+  - netcdf4=1.6.0
+  - requests=2.32.2
+  - packaging=21.3
+  - numpy=1.19.5
+  - xarray=0.17.0
+  - xesmf=0.7.0
+  - numba=0.55.2
+  - pylint=2.8.3
+  - black=22.3.0
+  - cartopy=0.20.2
+  - matplotlib=3.3.2