Update to latest submodule versions and changes to develop branch

.circleci/config.yml

@@ -14,7 +14,6 @@ commands:
               software-properties-common \
               libopenmpi3 \
               libopenmpi-dev \
-              libboost-all-dev \
               python3 \
               python3-pip \
       - run:
@@ -134,7 +133,7 @@ jobs:
 
   lint:
     docker:
-    - image: cimg/python:3.8
+      - image: cimg/python:3.8
     resource_class: small
     steps:
       - checkout
@@ -159,7 +158,7 @@ jobs:
 
   doctest:
     docker:
-    - image: cimg/python:3.8
+      - image: cimg/python:3.8
     steps:
       - checkout
       - run:
@@ -471,7 +470,7 @@ jobs:
 
   push_docs:
     docker:
-    - image: cimg/python:3.8
+      - image: cimg/python:3.8
     steps:
       - checkout
       - run:

.github/dependabot.yml

@@ -1,8 +1,8 @@
 version: 2
 updates:
-- package-ecosystem: gitsubmodule
-  directory: "/"
-  schedule:
-    interval: daily
-    time: "13:00"
-  open-pull-requests-limit: 10
+  - package-ecosystem: gitsubmodule
+    directory: "/"
+    schedule:
+      interval: daily
+      time: "13:00"
+    open-pull-requests-limit: 10

.github/workflows/container_build_test.yaml

@@ -0,0 +1,21 @@
+on:
+  push:
+    branches:
+      - 'develop'
+  schedule:
+    - cron: '0 0 * * 0' # sundays @ midnight
+
+jobs:
+  test-container-builds:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Files
+        uses: actions/checkout@v6
+        with:
+          submodules: recursive
+      - name: Build Dockerfile
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: false
+          file: "Dockerfile"

.github/workflows/create_cache.yml

@@ -0,0 +1,44 @@
+name: "Create GHA cache"
+
+# GitHub puts the following restrictions on cache sharing. PRs can access
+#
+# - caches that were created by the PR / earlier runs of the PR
+# - caches that were created on the target branch
+#
+# To get effective cache sharing between PRs, we create caches on the `develop`
+# branch (which is where almost all PRs merge into).
+
+on:
+  push:
+    branches: [develop]
+
+# Cancel running jobs if there's a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # GitHub Actions cache of the pre-commit environment
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup Python 3.12
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      - uses: actions/cache@v5
+        id: cache
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit_${{ env.pythonLocation }}_${{ hashFiles('.pre-commit-config.yaml') }}
+          lookup-only: true  # don't actually download the cache
+
+      - name: Populate pre-commit environment (if not cached)
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          pip install pre-commit
+          pre-commit install --install-hooks

.github/workflows/lint.yaml

@@ -1,26 +1,36 @@
 name: "Lint"
+
+# Run these these whenever ...
 on:
-  pull_request:
+  pull_request: # ... a PR is opened / updated
+  merge_group: # ... the PR is added to the merge queue
+  push:
+    branches:
+      - main # ... when merging into the main branch
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-        - name: Checkout Pace repository
-          uses: actions/[email protected]
-          with:
-            submodules: 'recursive'
-        - name: Step Python 3.11.7
-          uses: actions/[email protected]
-          with:
-            python-version: '3.11.7'
-        - name: Install OpenMPI for gt4py
-          run: |
-            sudo apt-get install libopenmpi-dev
-        - name: Install Python packages
-          run: |
-            python -m pip install --upgrade pip
-            pip install -r requirements_dev.txt -r requirements_lint.txt
-        - name: Run lint via pre-commit
-          run: |
-            pre-commit run --all-files
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          submodules: 'recursive'
+
+      - name: Step Python 3.12
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      # Only restore (don't save) caches on PRs. New caches created from PRs won't be
+      # accessible from other PRs, see workflows/create-cache.yaml.
+      - uses: actions/cache/restore@v5
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit_${{ env.pythonLocation }}_${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run lint via pre-commit
+        run: pre-commit run --all-files

.github/workflows/main_unit_tests.yaml

@@ -1,6 +1,8 @@
 name: "pace main unit tests"
+
+# Run these these whenever ...
 on:
-  workflow_call:
+  workflow_call: # ... called from a downstream repo
     inputs:
       component_trigger:
         type: boolean
@@ -10,7 +12,15 @@ on:
         type: string
         default: ''
         required: false
-  pull_request:
+      python_version:
+        type: string
+        default: ''
+        required: false
+  pull_request: # ... a PR is opened / updated
+  merge_group:  # ... the PR is added to the merge queue
+  push:
+    branches:
+      - main # ... when merging into the main branch
 
 # cancel running jobs if theres a newer push
 concurrency:
@@ -20,47 +30,63 @@ concurrency:
 jobs:
   pace_main_unit_tests:
     runs-on: ubuntu-latest
-    container:
-      image: ghcr.io/noaa-gfdl/miniforge:mpich
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      python_default: '3.12'
+
     steps:
-        - name: external trigger Checkout pace/develop
-          if:  ${{ inputs.component_trigger }}
-          uses: actions/checkout@v4
-          with:
-            submodules: 'recursive'
-            repository: NOAA-GFDL/pace
-            path: pace
-            ref: develop
+      - name: "External trigger: Checkout pace/develop"
+        if: ${{ inputs.component_name }}
+        uses: actions/checkout@v6
+        with:
+          submodules: 'recursive'
+          repository: NOAA-GFDL/pace
+          path: pace
+
+      - name: 'Setup Python ${{ inputs.python_version && inputs.python_version || env.python_default }}'
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ inputs.python_version && inputs.python_version || env.python_default }}
+
+      - name: Install mpi (MPICH flavor)
+        run: pip install mpich
+
+      - name: Install numpy==1.26.4
+        # Front-load installing numpy to force its usage in the radiation
+        # scheme of pySHiELD.
+        # TODO: This is an ugly hack and it should be cleaned up latest once
+        #       we add support for numpy >= 2.0
+        run: pip install numpy==1.26.4
 
-        - name: external trigger Remove existing component in pace/develop
-          if:  ${{ inputs.component_trigger }}
-          run: rm -rf ${GITHUB_WORKSPACE}/pace/${{inputs.component_name}}
+      - name: "External trigger: Remove existing component in pace/develop"
+        if: ${{ inputs.component_name }}
+        run: rm -rf ${GITHUB_WORKSPACE}/pace/${{inputs.component_name}}
 
-        - name: Checkout out hash that triggered CI
-          uses: actions/checkout@v4
-          with:
-            submodules: 'recursive'
-            path: pace/${{inputs.component_name}}
+      - name: Checkout out hash that triggered CI
+        uses: actions/checkout@v6
+        with:
+          submodules: 'recursive'
+          path: pace/${{inputs.component_name}}
 
-        - name: install packages
-          run: |
-            cd ${GITHUB_WORKSPACE}/pace
-            pip3 install --upgrade pip setuptools wheel
-            pip3 install -r requirements_dev.txt -c constraints.txt
+      - name: Install packages
+        run: |
+          cd ${GITHUB_WORKSPACE}/pace
+          pip install .[test]
 
-        - name: prepare input files
-          run: |
-            cd ${GITHUB_WORKSPACE}/pace
-            mkdir tests/main/input
-            python3 examples/generate_eta_files.py
-            mv *eta*.nc tests/main/input
+      - name: Print versions
+        run: |
+          python --version
+          pip --version
+          pip list
 
-        - name: run tests
-          run: |
-            cd ${GITHUB_WORKSPACE}/pace
-            pytest -x tests/main
+      - name: Run tests
+        run: |
+          cd ${GITHUB_WORKSPACE}/pace
+          python -m pytest -x tests/main
 
-        - name: run baroclinic
-          run: |
-            cd ${GITHUB_WORKSPACE}/pace
-            mpiexec -np 6 --oversubscribe python -m pace.run examples/configs/baroclinic_c12.yaml
+      - name: Run baroclinic test case
+        run: |
+          cd ${GITHUB_WORKSPACE}/pace
+          mpiexec -np 6 python -m pace.run examples/configs/baroclinic_c48_no_out.yaml

.gitmodules

@@ -5,9 +5,9 @@
 	branch = develop
 [submodule "pyFV3"]
 	path = pyFV3
-	url = https://github.com/NOAA-GFDL/PyFV3.git
+	url = https://github.com/NOAA-GFDL/pyFV3.git
 	branch = develop
 [submodule "pySHiELD"]
 	path = pySHiELD
-	url = https://github.com/NOAA-GFDL/PySHiELD.git
+	url = https://github.com/NOAA-GFDL/pySHiELD.git
 	branch = develop

.jenkins/driver_configs/baroclinic_c192_54ranks.yaml

@@ -1,14 +1,14 @@
 stencil_config:
   compilation_config:
-    backend: dace:gpu
+    backend: st:dace:gpu:KJI
     rebuild: false
     validate_args: true
     format_source: false
     device_sync: true
 initialization:
   type: analytic
   config:
-    case: baroclinic
+    case: baroclinic_instability
 diagnostics_config:
   path: "output.zarr"
   names:

.jenkins/driver_configs/baroclinic_c192_6ranks.yaml

@@ -1,14 +1,14 @@
 stencil_config:
   compilation_config:
-    backend: dace:gpu
+    backend: st:dace:gpu:KJI
     rebuild: false
     validate_args: true
     format_source: false
     device_sync: true
 initialization:
   type: analytic
   config:
-    case: baroclinic
+    case: baroclinic_instability
 diagnostics_config:
   path: "output.zarr"
   names:
@@ -18,7 +18,7 @@ diagnostics_config:
 output_initial_state: true
 performance_config:
   collect_performance: true
-  experiment_name: c192_baroclinic
+  experiment_name: c192_baroclinic_instability
 nx_tile: 192
 nz: 79
 dt_atmos: 200

.jenkins/driver_configs/baroclinic_c48_6ranks_dycore_only.yaml

@@ -2,7 +2,7 @@ dycore_only: true
 disable_step_physics: true
 stencil_config:
   compilation_config:
-    backend: gt:gpu
+    backend: st:gt:gpu:KJI
     rebuild: false
     validate_args: true
     format_source: false
@@ -11,7 +11,7 @@ stencil_config:
 initialization:
   type: analytic
   config:
-    case: baroclinicc
+    case: baroclinic_instability
 performance_config:
   collect_performance: false
 nx_tile: 48

.jenkins/driver_configs/baroclinic_c48_6ranks_dycore_only_serialbox.yaml

@@ -2,7 +2,7 @@ dycore_only: true
 disable_step_physics: true
 stencil_config:
   compilation_config:
-    backend: gt:gpu
+    backend: st:gt:gpu:KJI
     rebuild: false
     validate_args: true
     format_source: false