Merge master into whannah/mmf/pam-updates

E3SM-Project · Jul 8, 2024 · 9e3f3e6 · 9e3f3e6
2 parents 2590f22 + b166730
commit 9e3f3e6
Show file tree

Hide file tree

Showing 967 changed files with 50,916 additions and 29,803 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -11,3 +11,5 @@ updates:
     reviewers:
       - "mahf708"
       - "bartgol"
+    labels:
+      - "AT: Integrate Without Testing"
diff --git a/.github/workflows/e3sm-gh-ci-cime-tests.yml b/.github/workflows/e3sm-gh-ci-cime-tests.yml
@@ -3,12 +3,25 @@ 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

diff --git a/.github/workflows/e3sm-gh-ci-w-cime-tests.yml b/.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
diff --git a/.github/workflows/e3sm-gh-md-linter.yml b/.github/workflows/e3sm-gh-md-linter.yml
@@ -0,0 +1,30 @@
+name: markdown
+
+# if .md files are touched in a PR, lint them!
+
+on:
+  pull_request:
+    branches: ["master"]
+    paths:
+        - '**/*.md'
+        # for now let's not lint files in eamxx
+        - '!components/eamxx/**/*.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: ","
diff --git a/.github/workflows/e3sm-gh-pages.yml b/.github/workflows/e3sm-gh-pages.yml
@@ -15,7 +15,7 @@ concurrency:
 
 jobs:
   Build-and-Deploy-docs:
-    if: ${{ github.event.repository.name != 'scream' }}
+    if: ${{ github.event.repository.name == 'e3sm' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/eamxx-gh-pages.yml b/.github/workflows/eamxx-gh-pages.yml
@@ -53,14 +53,14 @@ jobs:
         run: |
           echo "= The job was automatically triggered by a ${{github.event_name}} event."
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/[email protected]
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install Python deps
         run: |
-          pip install mkdocs pymdown-extensions mkdocs-material mdutils
+          pip install mkdocs pymdown-extensions mkdocs-material mdutils mkdocs-bibtex
   
       - name: Generate EAMxx params docs
         working-directory: components/eamxx/scripts

diff --git a/.github/workflows/eamxx_default_files.yml b/.github/workflows/eamxx_default_files.yml
@@ -0,0 +1,62 @@
+name: inputdata
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '00 00 * * *'
+  workflow_dispatch:
+
+jobs:
+  scream-defaults:
+    runs-on: ubuntu-latest
+    outputs:
+      event_name: ${{ github.event_name }}
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          show-progress: false
+          submodules: false
+      - name: Set up Python 3.11
+        uses: actions/[email protected]
+        with:
+          python-version: "3.11"
+      - name: Run unit tests
+        working-directory: components/eamxx/cime_config/
+        run: |
+          python -m unittest tests/eamxx_default_files.py -v
+
+  notify-scream-defaults:
+    needs: scream-defaults
+    if: ${{ failure() && needs.scream-defaults.outputs.event_name != 'pull_request' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Create issue
+        run: |
+          previous_issue_number=$(gh issue list \
+          --label "$LABELS" \
+          --json number \
+          --jq '.[0].number')
+          if [[ -n $previous_issue_number ]]; then
+            gh issue comment "$previous_issue_number" \
+              --body "$BODY"
+          else
+            gh issue create \
+              --title "$TITLE" \
+              --assignee "$ASSIGNEES" \
+              --label "$LABELS" \
+              --body "$BODY"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          TITLE: Inputdata server file missing
+          ASSIGNEES: mahf708,bartgol
+          LABELS: bug,input file,notify-file-gh-action
+          BODY: |
+            Workflow failed! There's likely a missing file specified in the configs! For more information, please see:
+              - Workflow URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} (number ${{ github.run_number }}, attempt ${{ github.run_attempt }})
+              - Workflow SHA: ${{ github.sha }}
diff --git a/.gitignore b/.gitignore
@@ -9,6 +9,10 @@
 *.la
 *.a
 
+# Shared libraries
+*.so
+*.so.*
+
 # Executables
 *.exe
 
@@ -30,7 +34,20 @@ site
 # Ignore emacs backup files
 *~
 
+#Ignore Mac folder files
+.DS_Store
+
+#Ignore vscode dir
+.vscode
+
+
 # Ignore mkdocs site-generated files in eamxx
 components/eamxx/site/*
 # Ignore auto-generated eamxx_params.md file
 components/eamxx/docs/common/eamxx_params.md
+
+# Python packaging
+*.egg-info
+components/eamxx/src/python/build
+components/eamxx/src/python/build_src
+components/eamxx/src/python/dist
diff --git a/cime b/cime
diff --git a/cime_config/allactive/config_compsets.xml b/cime_config/allactive/config_compsets.xml
@@ -70,6 +70,12 @@
   <lname>1850_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
+<!-- Same as WCYCL1850NS but for 2010 (to avoid needing transient files). Mainly for testing. -->
+<compset>
+  <alias>WCYCL2010NS</alias>
+  <lname>2010_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
 <compset>
   <alias>WCYCL1950</alias>
   <lname>1950SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
@@ -113,12 +119,17 @@
 
 <compset>
   <alias>WCYCLSSP585</alias>
-  <lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>SSP585SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCLSSP370</alias>
-  <lname>SSP370SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>SSP370SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>WCYCLSSP245</alias>
+  <lname>SSP245SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <!-- E3SM v1 science compsets -->
@@ -393,7 +404,7 @@
 
 <compset>
   <alias>BGWCYCL1850</alias>
-  <lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_MALI%STATIC_SWAV</lname>
+  <lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_MALI_SWAV</lname>
 </compset>
 
 <!-- EAMXX fully coupled compset -->
@@ -406,8 +417,8 @@
 
 <!-- OCN + CICE + GLC Only Compsets -->
 <compset>
-  <alias>MPAS_LISIO_TEST</alias>
-  <lname>2000_DATM%NYF_SLND_MPASSI_MPASO_DROF%NYF_MALI%SIA_SWAV</lname>
+  <alias>MPAS_LISIO_JRA1p5</alias>
+  <lname>2000_DATM%JRA-1p5_SLND_MPASSI_MPASO%DATMFORCED_DROF%JRA-1p5_MALI%SIA_SWAV</lname>
 </compset>
 
 <!-- Slab ocean cases -->
@@ -443,6 +454,7 @@
       <value  compset="20TR_EAM">1850-01-01</value>
       <value  compset="SSP585.*_EAM">2015-01-01</value>
       <value  compset="SSP370.*_EAM">2015-01-01</value>
+      <value  compset="SSP245.*_EAM">2015-01-01</value>
     </values>
   </entry>
+86 −22		.github/scripts/ghcr-prune.py
+20 −12		.github/workflows/docs.yml
+3 −7		.github/workflows/ghcr-prune.yml
+2 −1		.github/workflows/testing.yml
+1 −0		.gitignore
+2 −0		.pre-commit-config.yaml
+1 −1		CIME/ParamGen/xml_schema/entry_id_pg.xsd
+6 −2		CIME/SystemTests/eri.py
+2 −2		CIME/SystemTests/system_tests_common.py
+4 −1		CIME/Tools/check_case
+2 −1		CIME/Tools/check_lockedfiles
+28 −26		CIME/Tools/xmlchange
+1 −8		CIME/XML/archive_base.py
+8 −3		CIME/XML/env_batch.py
+30 −15		CIME/XML/grids.py
+1 −1		CIME/XML/test_reporter.py
+8 −6		CIME/build.py
+0 −5		CIME/case/case.py
+12 −2		CIME/case/case_run.py
+18 −9		CIME/case/case_setup.py
+0 −4		CIME/case/case_st_archive.py
+19 −10		CIME/case/case_submit.py
+0 −151		CIME/case/check_lockedfiles.py
+4 −1		CIME/config.py
+56 −77		CIME/data/config/cesm/config_files.xml
+0 −6		CIME/hist_utils.py
+185 −8		CIME/locked_files.py
+1 −1		CIME/non_py/cprnc
+1 −1		CIME/tests/base.py
+6 −4		CIME/tests/test_sys_cime_case.py
+4 −1		CIME/tests/test_sys_create_newcase.py
+3 −1		CIME/tests/test_sys_full_system.py
+1 −1		CIME/tests/test_unit_case.py
+55 −0		CIME/tests/test_unit_config.py
+344 −0		CIME/tests/test_unit_locked_files.py
+3 −1		CIME/utils.py
+4 −2		CIME/wait_for_tests.py
+0 −1		doc/requirements.txt
+0 −15		doc/source/_static/custom.css
+0 −23		doc/source/_static/pop_ver.js
+0 −3		doc/source/_templates/layout.html
+64 −0		doc/source/_templates/versions.html
+27 −13		doc/source/conf.py
+10 −13		doc/source/users_guide/cime-dir.rst
+62 −0		doc/source/users_guide/components.rst
+31 −25		doc/source/users_guide/create-a-case.rst
+4 −4		doc/source/users_guide/index.rst
+53 −21		doc/source/users_guide/introduction-and-overview.rst
+29 −7		doc/source/users_guide/setting-up-a-case.rst
+245 −170		doc/source/users_guide/testing.rst
+7 −4		doc/source/what_cime/index.rst
+3 −0		docker/Dockerfile