Merge remote-tracking branch 'MAINREPO/master'

.circleci/checkout.sh

@@ -2,5 +2,4 @@
 
 # Replace all ssh URLs to submodules with HTTP URLs
 sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
-sed -i 's/git@github.com:/https:\/\/github.com\//' cime/.gitmodules
 git submodule update --init --recursive

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 jobs:
   build:
     machine:
-      image: ubuntu-2004:202010-01
+      image: ubuntu-2004:2024.01.1
     steps:
       - checkout
       - run: bash .circleci/setup.sh

.circleci/container.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
 
-wget -t 3 -O e3sm.sif http://portal.nersc.gov/project/e3sm/lukasz/e3sm.sif || \
-    wget -t 3 -O e3sm.sif https://dabdceba-6d04-11e5-ba46-22000b92c6ec.e.globus.org/containers/public/e3sm.sif
+singularity pull e3sm.sif \
+    docker://ghcr.io/mahf708/e3sm-imgs@sha256:d1030a6f4e3a53f682859436a26b30a9477d69423829ae1d9c1b5ab4e255430d
+
 if [ $? -ne 0 ]; then
     exit -1
 fi

.circleci/run.sh

@@ -57,7 +57,7 @@ rc=$?
 if [ $rc -ne 0 ]; then
     print_bldlog "e3sm"
     print_bldlog "csm_share"
-    print_bldlog "pio"
+    print_bldlog "spio"
     print_bldlog "mct"
     print_bldlog "gptl"
     exit $rc

.circleci/setup.sh

@@ -11,6 +11,10 @@ function download
     return $?
 }
 
+# Install Singularity deps:
+
+sudo apt-get update && sudo apt-get -y install uuid-dev
+
 # Install Singularity
 download && \
     tar -xzf singularity-${VERSION}.tar.gz && \

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    assignees:
+      - "rljacob"
+    reviewers:
+      - "mahf708"
+      - "bartgol"
+    labels:
+      - "AT: Integrate Without Testing"

.github/workflows/e3sm-gh-ci-cime-tests.yml

@@ -0,0 +1,67 @@
+name: gh
+
+on:
+  pull_request:
+    branches: [ master ]
+    paths:
+      # first, yes to these
+      - 'cime_config/**'
+      - 'components/eam/**'
+      - 'components/elm/**'
+      - 'driver-moab/**'
+      - 'driver-mct/**'
+      # second, no to these
+      - '!components/eam/docs/**'
+      - '!components/eam/mkdocs.yml'
+      - '!components/elm/docs/**'
+      - '!components/elm/mkdocs.yml'
+
+  workflow_dispatch:
+
+jobs:
+
+  ci:
+    if: ${{ github.event.repository.name == 'e3sm' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        test: 
+          - SMS_D_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - SMS_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - REP_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - ERS_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - ERS_P4.ne4pg2_oQU480.F2010.singularity_gnu.eam-wcprod_F2010
+          - ERP_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - PET_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - PEM_P4.ne4pg2_oQU480.F2010.singularity_gnu
+    container: 
+      image: ghcr.io/mahf708/e3sm-imgs:v0.0.6
+
+    steps:
+      - 
+        name: Checkout
+        uses: actions/checkout@v4
+        with:
+          show-progress: false
+          submodules: recursive
+      - 
+        name: CIME
+        working-directory: cime/scripts
+        run: |
+          mkdir -p $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
+          wget https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/p3_lookup_table_1.dat-v4.1.2
+          mv p3_lookup_table_1.dat-v4.1.2 $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
+          export USER=test
+          ./create_test ${{ matrix.test }} --wait --debug
+      - 
+        name: Artifacts
+        uses: actions/upload-artifact@v4
+        if: ${{ always() }}
+        with:
+          name: ${{ matrix.test }}
+          path: |
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/TestStatus.log
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/bld/*.bldlog.*
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.log.*
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.cprnc.out

.github/workflows/e3sm-gh-ci-w-cime-tests.yml

@@ -0,0 +1,59 @@
+name: gh
+
+on:
+  pull_request:
+    branches: [ master ]
+    paths-ignore:
+      - 'mkdocs.yaml'
+      - 'docs/**'
+      - 'components/*/docs/**'
+      - 'components/*/mkdocs.yml'
+
+  workflow_dispatch:
+
+jobs:
+
+  ci-w:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        test: 
+          - SMS_D_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - SMS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - REP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu.allactive-wcprod_1850
+          - ERP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - PET_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - PEM_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+    container: 
+      image: ghcr.io/mahf708/e3sm-imgs:v0.0.6
+
+    steps:
+      - 
+        name: Checkout
+        uses: actions/checkout@v4
+        with:
+          show-progress: false
+          submodules: recursive
+      - 
+        name: CIME
+        working-directory: cime/scripts
+        run: |
+          mkdir -p $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
+          wget https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/p3_lookup_table_1.dat-v4.1.2
+          mv p3_lookup_table_1.dat-v4.1.2 $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
+          export USER=test
+          ./create_test ${{ matrix.test }} --wait --debug
+      - 
+        name: Artifacts
+        uses: actions/upload-artifact@v4
+        if: ${{ always() }}
+        with:
+          name: ${{ matrix.test }}
+          path: |
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/TestStatus.log
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/bld/*.bldlog.*
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.log.*
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.cprnc.out

.github/workflows/e3sm-gh-md-linter.yml

@@ -0,0 +1,28 @@
+name: markdown
+
+# if .md files are touched in a PR, lint them!
+
+on:
+  pull_request:
+    branches: ["master"]
+    paths:
+        - '**/*.md'
+
+jobs:
+  linter:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - uses: tj-actions/changed-files@v44
+      id: changed-files
+      with:
+        files: '**/*.md'
+        separator: ","
+    - uses: DavidAnson/markdownlint-cli2-action@v16
+      if: steps.changed-files.outputs.any_changed == 'true'
+      with:
+        config: 'docs/.markdownlint.json'
+        globs: ${{ steps.changed-files.outputs.all_changed_files }}
+        separator: ","

.github/workflows/e3sm-gh-pages.yml

@@ -0,0 +1,60 @@
+name: Build and deploy gh-pages branch with Mkdocs
+
+on:
+  # Runs every time master branch is updated
+  push:
+    branches: ["master"]
+  # Runs every time a PR is open against master
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+concurrency:
+  # Prevent 2+ copies of this workflow from running concurrently
+  group: e3sm-docs-action
+
+jobs:
+  Build-and-Deploy-docs:
+    if: ${{ github.event.repository.name == 'e3sm' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+          show-progress: false
+          fetch-depth: 0 # Needed, or else gh-pages won't be fetched, and push rejected
+          # TODO: git rid of dependency on CIME
+          # TODO: another option to investigate is a sparse checkout. 
+          # In the scream repo, all other components do not need to be checked out. 
+          # And even in the upstream, we mainly need only components/xyz/docs (and a few more places).
+          submodules: true
+      - name: Show action trigger
+        run: echo "= The job was automatically triggered by a ${{github.event_name}} event on repo ${{github.event.repository.name}}."
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5.1.0
+        with:
+          python-version: "3.10"
+      - name: Install python deps
+        run: python3 -m pip install mkdocs-material pymdown-extensions mkdocs-monorepo-plugin mdutils mkdocs-bibtex
+      # build every time (PR or push to master)
+      - name: Generate EAMxx params docs
+        working-directory: components/eamxx/scripts
+        run: |
+          ./eamxx-params-docs-autogen
+      - name: Build
+        run: mkdocs build --strict --verbose
+      # Only deploy to the main github page when there is a push to master
+      - if: ${{ github.event_name == 'push' }}
+        name: GitHub Pages action
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          # Do not remove existing pr-preview pages
+          clean-exclude: pr-preview
+          folder: ./site/
+      # If it's a PR from within the same repo, deploy to a preview page
+      # For security reasons, PRs from forks cannot write into gh-pages for now
+      - if: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository && github.actor != 'dependabot[bot]' }}
+        name: Preview docs
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: ./site/

.github/workflows/eamxx-gh-pages.yml

@@ -0,0 +1,89 @@
+# This workflow aims to automatically rebuild eamxx documentation
+# every time the master branch is updated on github and within every PR
+
+name: EAMxx Docs
+
+on:
+  # Runs every time master branch is updated
+  push:
+    branches: [ master ]
+    # Only if docs-related files are touched
+    paths:
+      - components/eamxx/mkdocs.yml
+      - components/eamxx/docs/**
+      - components/eamxx/cime_config/namelist_defaults_scream.xml
+  # Runs every time a PR is open against master
+  pull_request:
+    branches: [ master ]
+    # Only if docs-related files are touched
+    paths:
+      - components/eamxx/mkdocs.yml
+      - components/eamxx/docs/**
+      - components/eamxx/cime_config/namelist_defaults_scream.xml
+
+  label:
+    types:
+      - created
+
+  workflow_dispatch:
+
+concurrency:
+  # Prevent 2+ copies of this workflow from running concurrently
+  group: eamxx-docs-action
+
+jobs:
+
+  eamxx-docs:
+    if: ${{ github.event.repository.name == 'scream' }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+          show-progress: false
+          # TODO: git rid of dependency on CIME
+          # TODO: another option to investigate is a sparse checkout. 
+          # In the scream repo, all other components do not need to be checked out. 
+          # And even in the upstream, we mainly need only components/xyz/docs (and a few more places).
+          submodules: true
+
+      - name: Show action trigger
+        run: |
+          echo "= The job was automatically triggered by a ${{github.event_name}} event."
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5.1.0
+        with:
+          python-version: "3.10"
+
+      - name: Install Python deps
+        run: |
+          pip install mkdocs pymdown-extensions mkdocs-material mdutils
+  
+      - name: Generate EAMxx params docs
+        working-directory: components/eamxx/scripts
+        run: |
+          ./eamxx-params-docs-autogen
+
+      - name: Build docs
+        working-directory: components/eamxx
+        run: |
+          mkdocs build --strict --verbose
+
+      # only deploy to the main github page when there is a push to master
+      - if: ${{ github.event_name == 'push' }}
+        name: GitHub Pages action
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          # Do not remove existing pr-preview pages
+          clean-exclude: pr-preview
+          folder: ./components/eamxx/site
+
+      # If it's a PR from within the same repo, deploy to a preview page
+      - if: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository }}
+        name: Preview docs
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: components/eamxx/site/