Merge pull request #2 from jeremy-lilly/mpaso/fb-lts

Update to E3SM master

.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

.github/dependabot.yml

@@ -0,0 +1,13 @@
+version: 2
+
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    assignees:
+      - "rljacob"
+    reviewers:
+      - "mahf708"
+      - "bartgol"

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

@@ -15,22 +15,32 @@ concurrency:
 
 jobs:
   Build-and-Deploy-docs:
+    if: ${{ github.event.repository.name != 'scream' }}
     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
-          submodules: false # speeds up clone and not building anything in submodules
+          # 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."
+        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@v4.7.0
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.10"
       - name: Install python deps
-        run: python3 -m pip install mkdocs-material pymdown-extensions mkdocs-monorepo-plugin mdutils
+        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

.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/[email protected]
+        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/

.gitignore

@@ -29,3 +29,8 @@ site
 
 # Ignore emacs backup files
 *~
+
+# Ignore mkdocs site-generated files in eamxx
+components/eamxx/site/*
+# Ignore auto-generated eamxx_params.md file
+components/eamxx/docs/common/eamxx_params.md

.gitmodules

@@ -73,9 +73,13 @@
 [submodule "components/eam/src/physics/crm/pam/external"]
 	path = components/eam/src/physics/crm/pam/external
 	url = [email protected]:E3SM-Project/PAM.git
+[submodule "components/mpas-seaice/src/icepack"]
+	path = components/mpas-seaice/src/icepack
+	url = [email protected]:E3SM-Project/Icepack.git
 [submodule "externals/haero"]
 	path = externals/haero
 	url = [email protected]:eagles-project/haero.git
 [submodule "externals/mam4xx"]
 	path = externals/mam4xx
 	url = [email protected]:eagles-project/mam4xx.git
+

cime_config/allactive/config_compsets.xml

@@ -14,7 +14,7 @@
     TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys][_ESP%phys][_BGC%phys]
     Where for the EAM specific compsets below the following is supported
     TIME = Time period (e.g. 2000, HIST, RCP8...)
-    ATM  = [EAM, SATM, SCREAM]
+    ATM  = [EAM, EAMXX, SATM, SCREAM]
     LND  = [ELM,  SLND]
     ICE  = [MPASSI, CICE, DICE, SICE]
     OCN  = [MPASO, DOCN, SOCN]
@@ -41,33 +41,33 @@
 
 <compset>
   <alias>WCYCL1850</alias>
-  <lname>1850SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850_chemUCI-Linozv3</alias>
-  <lname>1850SOI_EAM%CHEMUCI-LINOZV3_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CHEMUCI-LINOZV3_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850_chemUCI-Linozv3-mam5</alias>
-  <lname>1850SOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850-1pctCO2</alias>
-  <lname>1850SOI_EAM%CMIP6-1pctCO2_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6-1pctCO2_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850-4xCO2</alias>
-  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <!-- WCYCL1850NS uses no spun-up ICs for mpaso and mpassi. It is only being used for nigthly tests on small grids such as ne11_oQU480-->
 <compset>
   <alias>WCYCL1850NS</alias>
-  <lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
@@ -77,7 +77,7 @@
 
 <compset>
   <alias>WCYCL20TR</alias>
-  <lname>20TRSOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>20TRSOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <!-- ************************************************ -->
@@ -108,7 +108,7 @@
 
 <compset>
   <alias>WCYCL20TR_chemUCI-Linozv3-mam5</alias>
-  <lname>20TRSOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>20TRSOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
@@ -396,6 +396,14 @@
   <lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_MALI%STATIC_SWAV</lname>
 </compset>
 
+<!-- EAMXX fully coupled compset -->
+
+<compset>
+  <alias>WCYCLXX2010</alias>
+  <lname>2010_EAMXX_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
+
 <!-- OCN + CICE + GLC Only Compsets -->
 <compset>
   <alias>MPAS_LISIO_TEST</alias>