Merge branch 'main' into alexolinhager/hiRes_ocean_GIS_mesh

Author: alexolinhager

.github/dependabot.yml

@@ -10,3 +10,4 @@ updates:
       - "xylar"
     reviewers:
       - "xylar"
+      - "andrewdnolan"

.github/workflows/build_workflow.yml

@@ -28,11 +28,11 @@ jobs:
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Checkout Code Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
@@ -60,7 +60,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
     steps:
       - id: skip_check
@@ -70,19 +70,21 @@ jobs:
           paths_ignore: ${{ env.PATHS_IGNORE }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: mamba-org/setup-micromamba@v2
         with:
-          activate-environment: "compass_ci"
-          miniforge-version: latest
-          channels: conda-forge,e3sm/label/compass
-          channel-priority: strict
-          use-mamba: false
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
+          environment-name: compass_test
+          init-shell: bash
+          condarc: |
+            channel_priority: strict
+            channels:
+                - conda-forge
+                - e3sm/label/compass
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install compass

.github/workflows/docs_workflow.yml

@@ -20,22 +20,24 @@ jobs:
       docs_version: "latest"
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
           fetch-depth: 0
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Set up Conda Environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: mamba-org/setup-micromamba@v2
         with:
-          activate-environment: "compass_ci"
-          miniforge-version: latest
-          channels: conda-forge,e3sm/label/compass
-          channel-priority: strict
-          use-mamba: false
-          auto-update-conda: true
-          python-version: ${{ env.PYTHON_VERSION }}
+          environment-name: compass_test
+          init-shell: bash
+          condarc: |
+            channel_priority: strict
+            channels:
+                - conda-forge
+                - e3sm/label/compass
+          create-args: >-
+            python=${{ env.PYTHON_VERSION }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install compass

.github/workflows/gis_coarse_meshgen.yml

@@ -0,0 +1,68 @@
+name: CI/CD Build Workflow
+
+on:
+  pull_request:
+    branches: [main]
+    paths:
+    - compass/landice/mesh.py
+    - compass/landice/tests/greenland/mesh.py
+
+jobs:
+  gis-coarse-meshgen:
+    name: GIS Coarse Mesh Generation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: recursive
+          path: compass
+      - name: setup_and_run_step
+        run: |
+          # create top level working directory
+          root=$PWD
+          pushd compass
+
+          # create the compass environment
+          ./conda/configure_compass_env.py --conda $root/mambaForge --env_name compass_test --mpi mpich
+
+          # enable the compass environment
+          source load_compass_test_mpich.sh
+
+          popd
+
+          # download the input GIS coarse mesh
+          wget https://rpi.app.box.com/public/static/qytr3c49h1xbucxz594df327qatiu8ds.tgz
+          tar xf qytr3c49h1xbucxz594df327qatiu8ds.tgz
+
+          # create the config file describing the system
+          cat << EOF > system.cfg
+          # This file contains some common config options you might want to set
+          # The paths section describes paths to databases and shared compass environments
+          [paths]
+          database_root =
+          # The parallel section describes options related to running tests in parallel
+          [parallel]
+          # parallel system of execution: slurm or single_node
+          system = single_node
+          # whether to use mpirun or srun to run the model
+          parallel_executable = mpirun
+          # cores per node on the machine, detected automatically by default
+          cores_per_node = 4
+          [mesh]
+          #run quicker - gis takes 20mins on 128 perlmutter cores
+          min_spac = 10.e3
+          [greenland]
+          nprocs = 4
+          data_path = $root/gis4kmSubSampled_01302025
+          measures_filename = greenland_vel_mosaic500_extrap_stride8.nc
+          bedmachine_filename = BedMachineGreenland-v5_edits_floodFill_extrap_stride25.nc
+          EOF
+
+          # setup the greenland mesh generation test case
+          testDir=$root/gis_mesh_gen
+          compass setup -w $testDir -t landice/greenland/mesh_gen -f system.cfg
+
+          # run the test case
+          cd $testDir
+          compass run
+

.github/workflows/pre_commit_update_workflow.yml

@@ -9,19 +9,22 @@ on:
     # 4. Entry: Month of the year when the process will be started [1-12]
     # 5. Entry: Weekday when the process will be started [0-6] [0 is Sunday]
     - cron: '0 8 * * 3'
+  # Allow manual triggering of the workflow
+  workflow_dispatch:
 
 env:
   UP_TO_DATE: false
   PYTHON_VERSION: "3.13"
+  REVIEWERS: "xylar,andrewdnolan"
 
 jobs:
   auto-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
@@ -38,10 +41,12 @@ jobs:
           git checkout -b update-pre-commit-deps
           pre-commit autoupdate
           git add .
-          # The second command will fail if no changes were present, so we ignore it
-          git commit -m "Update pre-commit dependencies" || ( echo "UP_TO_DATE=true" >> "$GITHUB_ENV")
+          # Either there are changes, in which case we commit them, or there are no changes,
+          # in which case we can skip the push & pr-create jobs
+          git commit -m "Update pre-commit dependencies" \
+          || ( echo "UP_TO_DATE=true" >> "$GITHUB_ENV")
 
-      - name: Push Changes
+      - name: Push Changes with github-actions bot
         if: ${{ env.UP_TO_DATE == 'false' }}
         uses: ad-m/github-push-action@master
         with:
@@ -52,16 +57,30 @@ jobs:
         env:
           GH_TOKEN: ${{ github.token }}
 
-      - name: Make PR and add reviewers and labels
+      - name: Create PR with github-actions bot
         if: ${{ env.UP_TO_DATE == 'false' }}
         run: |
           cd update-pre-commit-deps
           gh pr create \
-          --title "Update pre-commit and its dependencies" \
-          --body "This PR was auto-generated to update pre-commit and its dependencies." \
-          --head update-pre-commit-deps \
-          --reviewer altheaden,xylar \
-          --label ci
+            --title "Update pre-commit and its dependencies" \
+            --body "This PR was auto-generated to update pre-commit and its dependencies." \
+            --head update-pre-commit-deps
         env:
           GH_TOKEN: ${{ github.token }}
 
+      - name: Add reviewers and labels with PAT
+        if: ${{ env.UP_TO_DATE == 'false' }}
+        run: |
+          cd update-pre-commit-deps
+
+          gh pr edit --add-label ci
+
+          IFS=',' read -ra reviewers <<< "${REVIEWERS}"
+          for reviewer in "${reviewers[@]}"; do
+            echo "Adding reviewer: $reviewer"
+            gh pr edit --add-reviewer "$reviewer"
+          done
+
+        env:
+          REVIEWERS: ${{ env.REVIEWERS }}
+          GH_TOKEN: ${{ secrets.GH_CLI_TOKEN }}

.pre-commit-config.yaml

@@ -4,22 +4,22 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
 
   # Can run individually with `pre-commit run isort --all-files`
   - repo: https://github.com/PyCQA/isort
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: isort
 
   # Can run individually with `pre-commit run flake8 --all-files`
   # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
   # https://github.com/pre-commit/pre-commit/issues/1206
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.2
+    rev: 7.3.0
     hooks:
       - id: flake8
         args: ["--config=setup.cfg"]

E3SM-Project

@@ -697,22 +697,22 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     logger.info('writing grid_converted.nc')
     write_netcdf(dsMesh, 'grid_converted.nc')
     levels = section.get('levels')
-    args = ['create_landice_grid_from_generic_MPAS_grid.py',
+    args = ['create_landice_grid_from_generic_mpas_grid',
             '-i', 'grid_converted.nc',
             '-o', 'grid_preCull.nc',
             '-l', levels, '-v', 'glimmer']
 
     check_call(args, logger=logger)
 
-    args = ['interpolate_to_mpasli_grid.py', '-s',
+    args = ['interpolate_to_mpasli_grid', '-s',
             gridded_dataset, '-d',
             'grid_preCull.nc', '-m', 'b', '-t']
 
     check_call(args, logger=logger)
 
     cullDistance = section.get('cull_distance')
     if float(cullDistance) > 0.:
-        args = ['define_cullMask.py', '-f',
+        args = ['define_landice_cull_mask', '-f',
                 'grid_preCull.nc', '-m',
                 'distance', '-d', cullDistance]
 
@@ -724,7 +724,7 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     if geojson_file is not None:
         # This step is only necessary because the GeoJSON region
         # is defined by lat-lon.
-        args = ['set_lat_lon_fields_in_planar_grid.py', '-f',
+        args = ['set_lat_lon_fields_in_planar_grid', '-f',
                 'grid_preCull.nc', '-p', projection]
 
         check_call(args, logger=logger)
@@ -751,7 +751,7 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     write_netcdf(dsMesh, 'culled.nc')
 
     logger.info('Marking horns for culling')
-    args = ['mark_horns_for_culling.py', '-f', 'culled.nc']
+    args = ['mark_horns_for_culling', '-f', 'culled.nc']
 
     check_call(args, logger=logger)
 
@@ -762,24 +762,24 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     dsMesh = sort_mesh(dsMesh)
     write_netcdf(dsMesh, 'dehorned.nc')
 
-    args = ['create_landice_grid_from_generic_MPAS_grid.py', '-i',
+    args = ['create_landice_grid_from_generic_mpas_grid', '-i',
             'dehorned.nc', '-o',
             mesh_name, '-l', levels, '-v', 'glimmer',
             '--beta', '--thermal', '--obs', '--diri']
 
     check_call(args, logger=logger)
 
-    args = ['interpolate_to_mpasli_grid.py', '-s',
+    args = ['interpolate_to_mpasli_grid', '-s',
             gridded_dataset, '-d', mesh_name, '-m', 'b']
 
     check_call(args, logger=logger)
 
     logger.info('Marking domain boundaries dirichlet')
-    args = ['mark_domain_boundaries_dirichlet.py',
+    args = ['mark_domain_boundaries_dirichlet',
             '-f', mesh_name]
     check_call(args, logger=logger)
 
-    args = ['set_lat_lon_fields_in_planar_grid.py', '-f',
+    args = ['set_lat_lon_fields_in_planar_grid', '-f',
             mesh_name, '-p', projection]
     check_call(args, logger=logger)
 
@@ -1016,8 +1016,8 @@ def preprocess_ais_data(self, source_gridded_dataset,
     return preprocessed_gridded_dataset
 
 
-def interp_gridded2mali(self, source_file, mali_scrip, nProcs, dest_file, proj,
-                        variables="all"):
+def interp_gridded2mali(self, source_file, mali_scrip, parallel_executable,
+                        nProcs, dest_file, proj, variables="all"):
     """
     Interpolate gridded dataset (e.g. MEASURES, BedMachine) onto a MALI mesh
 
@@ -1029,6 +1029,9 @@ def interp_gridded2mali(self, source_file, mali_scrip, nProcs, dest_file, proj,
     mali_scrip : str
         name of scrip file corresponding to destination MALI mesh
 
+    parallel_executable : str
+        executable needed to launch a parallel job
+
     nProcs : int
         number of processors to use for generating remapping weights
 
@@ -1070,7 +1073,7 @@ def __guess_scrip_name(filename):
 
     logger.info('creating scrip file for source dataset')
     # Note: writing scrip file to workdir
-    args = ['create_SCRIP_file_from_planar_rectangular_grid.py',
+    args = ['create_scrip_file_from_planar_rectangular_grid',
             '-i', source_file,
             '-s', source_scrip,
             '-p', proj,
@@ -1079,7 +1082,7 @@ def __guess_scrip_name(filename):
 
     # Generate remapping weights
     logger.info('generating gridded dataset -> MPAS weights')
-    args = ['srun', '-n', nProcs, 'ESMF_RegridWeightGen',
+    args = [parallel_executable, '-n', nProcs, 'ESMF_RegridWeightGen',
             '--source', source_scrip,
             '--destination', mali_scrip,
             '--weight', weights_filename,
@@ -1089,8 +1092,8 @@ def __guess_scrip_name(filename):
     check_call(args, logger=logger)
 
     # Perform actual interpolation using the weights
-    logger.info('calling interpolate_to_mpasli_grid.py')
-    args = ['interpolate_to_mpasli_grid.py',
+    logger.info('calling interpolate_to_mpasli_grid')
+    args = ['interpolate_to_mpasli_grid',
             '-s', source_file,
             '-d', dest_file,
             '-m', 'e',