Merge pull request #50 from mvertens/feature/update_to_esmci

update NorESMhub CIME to and ESMCI cime6.0.173

The only difference between NorESMhub CIME in this PR and and ESMCI cime6.0.173 is the addition of blom in
CIME/data/config/cesm/config_files.xml

Test suite: Ran SMS_D_Ld1.T62_tn14.NOINYOC.betzy_intel and verified that it was bfb.
Test baseline:
Test namelist changes:
Test status: bfb

User interface changes?: None

Update gh-pages html (Y/N)?: No

.github/workflows/container.yml

@@ -0,0 +1,60 @@
+name: container build/publish
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'docker/**'
+
+  pull_request:
+    branches:
+      - master
+    paths:
+      - 'docker/**'
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Only build container if there has been a change.
+  build-containers:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/ESMCI/cime
+          flavor: |
+            latest=auto
+          tags: |
+            type=sha
+      - name: Build and push
+        uses: docker/build-push-action@v3
+        with:
+          target: base
+          context: docker/
+          push: ${{ github.event_name == 'push' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/docs.yml

@@ -4,36 +4,55 @@ on:
   push:
     branches:
       - master
+    paths:
+      - 'doc/**'
 
   pull_request:
     branches:
       - master
+    paths:
+      - 'doc/**'
+
+  workflow_dispatch:
 
 permissions:
   contents: read
 jobs:
-  check-changes:
-    name: Check for changes to documentation
+  cleanup:
+    permissions:
+      contents: write  #  for git push
+    name: Cleanup branch previews
     runs-on: ubuntu-latest
-    outputs:
-      any_changed: ${{ steps.changed-check.outputs.any_changed }}
+    if: ${{ github.event_name == 'push' }}
     steps:
       - uses: actions/checkout@v3
         with:
+          ref: 'gh-pages'
           fetch-depth: 0
           lfs: true
-      - uses: tj-actions/changed-files@v32
-        id: changed-check
-        with:
-          files: doc
+          path: gh-pages
+      - name: Remove branch previews
+        run: |
+          pushd $GITHUB_WORKSPACE/gh-pages
+
+          for name in `ls branch/`
+          do
+            if [[ -z "$(git show-ref --quiet ${name})" ]]
+            then
+              git rm -rf branch/${name}
+            fi
+          done
+
+          git config user.name github-actions[bot]
+          git config user.email github-actions[bot]@users.noreply.github.com
+          git commit -m "Clean up branch previews"
+          git push
   build-and-deploy:
     permissions:
       contents: write  #  for peaceiris/actions-gh-pages to push
       pull-requests: write  #  to comment on pull requests
-    needs: check-changes
-    if: |
-      needs.check-changes.outputs.any_changed == 'true' &&
-      github.event.pull_request.head.repo.full_name == github.repository
+    needs: cleanup
+    if: ${{ always() }}
     name: Build and deploy documentation
     runs-on: ubuntu-latest
     steps:
@@ -61,7 +80,9 @@ jobs:
         run: |
           make BUILDDIR=${PWD}/_build -C doc/ html
       - name: Push PR preview
-        if: ${{ github.event_name == 'pull_request' }}
+        if: |
+          github.event_name == 'pull_request' &&
+          github.event.pull_request.head.repo.full_name == github.repository
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{secrets.GITHUB_TOKEN}}
@@ -99,31 +120,3 @@ jobs:
           destination_dir: './versions/master/html'
           user_name: 'github-actions[bot]'
           user_email: 'github-actions[bot]@users.noreply.github.com'
-  cleanup:
-    permissions:
-      contents: write  #  for git push
-    needs: build-and-deploy
-    name: Cleanup branch previews
-    runs-on: ubuntu-latest
-    if: ${{ github.event_name == 'push' }}
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          ref: 'gh-pages'
-          fetch-depth: 0
-          lfs: true
-      - name: Remove branch previews
-        run: |
-          for name in `ls branch/`
-          do
-            if [[ -z "$(git show-ref --quiet ${name})" ]]
-            then
-              git rm -rf branch/${name}
-            fi
-          done
-      - name: Commit and push local changes to gh-pages
-        run: |
-          git config user.name github-actions[bot]
-          git config user.email github-actions[bot]@users.noreply.github.com
-          git commit -m "Clean up branch previews"
-          git push

.github/workflows/stale.yml

@@ -0,0 +1,24 @@
+name: 'Close stale issues and PRs'
+on:
+  schedule:
+    # Run every day at 1:30AM
+    - cron: '30 1 * * *'
+jobs:
+  stale:
+    permissions:
+      issues: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v8
+        with:
+          stale-issue-message: 'This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 5 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 5 days with no activity.'
+          days-before-stale: 90
+          days-before-close: 5
+          days-before-pr-close: -1
+          # Issues with this label are exempt from being checked if they are stale...
+          exempt-issue-labels: Low Priority
+          # Below are currently defaults, but given in case we decide to change
+          operations-per-run: 30
+          stale-issue-label: Stale
+          close-issue-reason: not_planned

.github/workflows/testing.yml

@@ -4,17 +4,30 @@ on:
   push:
     branches:
       - master
+    paths:
+      - 'CIME/**'
+      - 'scripts/**'
+      - 'tools/**'
+      - 'utils/**'
 
   pull_request:
     branches:
       - master
+    paths:
+      - 'CIME/**'
+      - 'scripts/**'
+      - 'tools/**'
+      - 'utils/**'
+
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
 permissions:
   contents: read # to fetch code (actions/checkout)
+  packages: read
 
 jobs:
   pre-commit:
@@ -39,67 +52,18 @@ jobs:
 
           pre-commit run -a
 
-  # Check if there has been a change to any file under docker/
-  get-docker-changes:
-    runs-on: ubuntu-latest
-    outputs:
-      any_changed: ${{ steps.get-changed-files.outputs.any_changed }}
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 2
-      - name: Get changed files
-        id: get-changed-files
-        uses: tj-actions/changed-files@v29
-        with:
-          files: docker
-
-  # Only build container if there has been a change.
-  build-containers:
-    runs-on: ubuntu-latest
-    needs: get-docker-changes
-    if: ${{ needs.get-docker-changes.outputs.any_changed == 'true' }}
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Login to DockerHub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      - name: Docker meta
-        id: meta
-        uses: docker/metadata-action@v4
-        with:
-          images: jasonb87/cime
-          tags: |
-            type=raw,value=latest
-            type=sha,prefix={{ date 'YYYYMMDD' }}_,format=short
-      - name: Build and push
-        uses: docker/build-push-action@v3
-        with:
-          target: base
-          context: docker/
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=registry,ref=jasonb87/cime:buildcache
-          cache-to: type=registry,ref=jasonb87/cime:buildcache,mode=max
-
   # Runs unit testing under different python versions.
   unit-testing:
     runs-on: ubuntu-latest
-    needs: build-containers
     if: ${{ always() && ! cancelled() }}
-    container: jasonb87/cime:latest
+    container:
+      image: ghcr.io/esmci/cime:latest
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.8', '3.9', '3.10']
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
@@ -130,9 +94,12 @@ jobs:
   # Run system tests
   system-testing:
     runs-on: ubuntu-latest
-    needs: build-containers
     if: ${{ always() && ! cancelled() }}
-    container: jasonb87/cime:latest
+    container:
+      image: ghcr.io/esmci/cime:latest
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
     strategy:
       matrix:
         model: ["e3sm", "cesm"]
@@ -183,6 +150,8 @@ jobs:
         if: ${{ failure() }}
         shell: bash
         run: tar -czvf /testing-logs-${GITHUB_RUN_NUMBER}.tar.gz /storage/cases/
+        # How to download artifacts:
+        # https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts
       - name: Upload testing logs
         if: ${{ failure() }}
         uses: actions/upload-artifact@v3

CIME/SystemTests/README

@@ -47,7 +47,7 @@ ERP    pes counts hybrid (open-MP/MPI) restart bfb test from startup, default 6
        do an 11 day initial test - write a restart at day 6     (suffix base)
        half the number of tasks and threads for each component
        do a  5  day restart test starting from restart at day 6 (suffix rest)
-       this is just like an ERS test but the pe-counts/threading count are modified on retart
+       this is just like an ERS test but the pe-counts/threading count are modified on restart
 
 ERI    hybrid/branch/exact restart test, default (by default STOP_N is 22 days)
        (1) ref1case

CIME/SystemTests/dae.py

@@ -27,7 +27,7 @@ class DAE(SystemTestsCompareTwo):
     """
 
     ###########################################################################
-    def __init__(self, case):
+    def __init__(self, case, **kwargs):
         ###########################################################################
         SystemTestsCompareTwo.__init__(
             self,
@@ -36,6 +36,7 @@ def __init__(self, case):
             run_two_suffix="da",
             run_one_description="no data assimilation",
             run_two_description="data assimilation",
+            **kwargs,
         )
 
     ###########################################################################

CIME/SystemTests/eri.py

@@ -38,11 +38,11 @@ def _helper(dout_sr, refdate, refsec, rundir):
 
 
 class ERI(SystemTestsCommon):
-    def __init__(self, case):
+    def __init__(self, case, **kwargs):
         """
         initialize an object interface to the ERI system test
         """
-        SystemTestsCommon.__init__(self, case)
+        SystemTestsCommon.__init__(self, case, **kwargs)
         self._testname = "ERI"
 
     def run_phase(self):

CIME/SystemTests/erio.py

@@ -10,11 +10,11 @@
 
 
 class ERIO(SystemTestsCommon):
-    def __init__(self, case):
+    def __init__(self, case, **kwargs):
         """
         initialize an object interface to file env_test.xml in the case directory
         """
-        SystemTestsCommon.__init__(self, case, expected=["TEST"])
+        SystemTestsCommon.__init__(self, case, expected=["TEST"], **kwargs)
 
         self._pio_types = self._case.get_env("run").get_valid_values("PIO_TYPENAME")
         self._stop_n = self._case.get_value("STOP_N")

CIME/SystemTests/erp.py

@@ -15,7 +15,7 @@
 
 
 class ERP(RestartTest):
-    def __init__(self, case):
+    def __init__(self, case, **kwargs):
         """
         initialize a test object
         """
@@ -26,6 +26,7 @@ def __init__(self, case):
             run_two_suffix="rest",
             run_one_description="initial",
             run_two_description="restart",
+            **kwargs
         )
 
     def _case_two_setup(self):