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Merge branch 'develop' into omega/design-doc-v1-eqns
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‎.github/workflows/e3sm-gh-md-linter.yml‎

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@@ -25,7 +25,7 @@ jobs:
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with:
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files: '**/*.md'
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separator: ","
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- uses: DavidAnson/markdownlint-cli2-action@v19
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- uses: DavidAnson/markdownlint-cli2-action@v20
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if: steps.changed-files.outputs.any_changed == 'true'
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with:
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config: 'docs/.markdownlint.json'

‎.github/workflows/eamxx-gh-clang-format.yml‎

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name: "eamxx-format"
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# if .{cpp,hpp} files are touched in a PR, lint them!
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on:
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pull_request:
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branches: ["master"]
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paths:
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- 'components/eamxx/**/*.cpp'
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- 'components/eamxx/**/*.hpp'
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concurrency:
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group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
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cancel-in-progress: true
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jobs:
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clang-format-linter:
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if: ${{ github.repository == 'E3SM-Project/E3SM' }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: tj-actions/changed-files@v46
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id: changed-files
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with:
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files: 'components/eamxx/**/*.{cpp,hpp}'
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separator: " "
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# 1. runs clang-format on the files changed by this PR, and returns pass/fail
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# error code.
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# 2. prints the diff to screen (action log), comparing to the changes
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# that *would* be made
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# 3. the E3SM-Project fork of DoozyX/[email protected]
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# adds a Step summary to the workflow page, and, on failure, lists the
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# files that fail the clang-format test
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- uses: E3SM-Project/[email protected]
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with:
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source: ${{ steps.changed-files.outputs.all_changed_files }}
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exclude: ''
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extensions: 'hpp,cpp'
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clangFormatVersion: 14
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style: 'file:components/eamxx/.clang-format'

‎.github/workflows/eamxx-v1-testing.yml‎

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short_name: ERS_P16_Ln22.ne30pg2_ne30pg2.FIOP-SCREAMv1-DP.eamxx-dpxx-arm97
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- full_name: ERS_Ln22.ne4pg2_ne4pg2.F2010-SCREAMv1.ghci-snl-cpu_gnu.eamxx-small_kernels--eamxx-output-preset-5
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short_name: ERS_Ln22.ne4pg2_ne4pg2.F2010-SCREAMv1.eamxx-small_kernels--eamxx-output-preset-5
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- full_name: SMS_D_Ln5.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.ghci-snl-cpu_gnu.eamxx-mam4xx-all_mam4xx_procs
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short_name: SMS_D_Ln5.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.eamxx-mam4xx-all_mam4xx_procs
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- full_name: REP_D_Ln5.ne4pg2_oQU480.F2010-EAMxx-MAM4xx.ghci-snl-cpu_gnu
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short_name: REP_D_Ln5.ne4pg2_oQU480.F2010-EAMxx-MAM4xx
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- full_name: "ERS.ne4pg2_ne4pg2.F2010-SCREAMv1.ghci-snl-cpu_gnu.eamxx-prod"
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short_name: ERS.ne4pg2_ne4pg2.F2010-SCREAMv1.eamxx-prod
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fail-fast: false
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name: cpu-gcc / ${{ matrix.test.short_name }}
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steps:

‎.github/workflows/omega-build-workflow.yml‎

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name: CI/CD Build Workflow
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name: omega-pr
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on:
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push:
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branches: [develop]
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paths:
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- 'components/omega/**'
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pull_request:
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branches: [develop]
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paths:
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- 'components/omega/**'
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workflow_dispatch:
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env:
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CANCEL_OTHERS: false
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PATHS_IGNORE: '["**/README.md", "**/doc/**"]'
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PYTHON_VERSION: "3.13"
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jobs:
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build:
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name: lint with pre-commit and build docs
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if: ${{ github.repository == 'E3SM-Project/E3SM' }} or \
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${{ github.repository == 'E3SM-Project/Omega' }}
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name: lint and test docs
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runs-on: ubuntu-latest
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timeout-minutes: 20
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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matrix:
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python-version: ["3.10",]
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steps:
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- id: skip_check
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uses: fkirc/skip-duplicate-actions@master
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with:
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cancel_others: ${{ env.CANCEL_OTHERS }}
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paths_ignore: ${{ env.PATHS_IGNORE }}
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Checkout Code Repository
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- name: Checkout Code Repository
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uses: actions/checkout@v3
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Cache Conda
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uses: actions/cache@v3
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env:
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# Increase this value to reset cache if conda-dev-spec.template has not changed in the workflow
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key:
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${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('components/omega/dev-conda.txt') }}
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Set up Conda Environment
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uses: conda-incubator/setup-miniconda@v2
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- name: Set up Conda Environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: "omega_ci"
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miniforge-version: latest
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channels: conda-forge,defaults
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channels: conda-forge
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channel-priority: strict
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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python-version: ${{ env.PYTHON_VERSION }}
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Install dependencies
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- name: Install dependencies
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run: |
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conda create -n omega_dev --file components/omega/dev-conda.txt \
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python=${{ matrix.python-version }}
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python=${{ env.PYTHON_VERSION }}
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conda activate omega_dev
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conda list
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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id: file_changes
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- id: file_changes
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uses: trilom/[email protected]
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with:
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output: ' '
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Cache pre-commit
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uses: actions/cache@v4
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with:
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path: ~/.cache/pre-commit/
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key: ${{ runner.os }}-${{ matrix.python-version }}-pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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# Run all pre-commit hooks on all the files.
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# Getting only staged files can be tricky in case a new PR is opened
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# since the action is run on a branch in detached head state
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name: Run pre-commit
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- name: Run pre-commit
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run: |
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conda activate omega_dev
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pre-commit run --show-diff-on-failure --files ${{ steps.file_changes.outputs.files}}
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Build Sphinx Docs
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- name: Build Sphinx Docs
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run: |
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conda activate omega_dev
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cd components/omega/doc
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make html
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make html-strict

‎.github/workflows/omega-docs-workflow.yml‎

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name: CI/CD Release Workflow
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name: omega-release
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on:
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push:
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branches: [develop]
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# But only if Omega docs-related files are touched
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paths:
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- components/omega/doc/**
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env:
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PYTHON_VERSION: "3.13"
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jobs:
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publish-docs:
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if: ${{ github.repository == 'E3SM-Project/E3SM' }} or \
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${{ github.repository == 'E3SM-Project/Omega' }}
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runs-on: ubuntu-latest
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defaults:
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run:
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persist-credentials: false
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fetch-depth: 0
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- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
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name: Cache Conda
22-
uses: actions/cache@v3
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env:
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# Increase this value to reset cache if conda-dev-spec.template has not changed in the workflow
25-
CACHE_NUMBER: 0
26-
with:
27-
path: ~/conda_pkgs_dir
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key:
29-
${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{
30-
hashFiles('components/omega/dev-conda.txt') }}
31-
32-
- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
33-
name: Set up Conda Environment
34-
uses: conda-incubator/setup-miniconda@v2
28+
- name: Set up Conda Environment
29+
uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: "omega_ci"
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miniforge-version: latest
38-
channels: conda-forge,defaults
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channels: conda-forge
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channel-priority: strict
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auto-update-conda: true
41-
python-version: ${{ matrix.python-version }}
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python-version: ${{ env.PYTHON_VERSION }}
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43-
- if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
44-
name: Install dependencies
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- name: Install dependencies
4539
run: |
4640
conda create -n omega_dev --file components/omega/dev-conda.txt \
47-
python=${{ matrix.python-version }}
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python=${{ env.PYTHON_VERSION }}
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conda activate omega_dev
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conda list
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- name: Build Sphinx Docs
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- name: Build Omega Docs with Sphinx
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# Use 'make html' (not html-strict) so docs always update, even if warnings exist.
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run: |
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conda activate omega_dev
5449
cd components/omega/doc
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conda activate omega_dev
5954
cd components/omega/doc
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# gh-pages branch must already exist
61-
git clone https://github.com/E3SM-Project/Omega.git --branch gh-pages --single-branch gh-pages
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git clone https://github.com/${{ github.repository }}.git --branch gh-pages --single-branch gh-pages
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# Make sure we're in the gh-pages directory.
6358
cd gh-pages
64-
# Create `.nojekyll` (if it doesn't already exist) for proper GH Pages configuration.
65-
touch .nojekyll
66-
# Create an omega directory to store the documentation
67-
mkdir -p omega
68-
# Add `index.html` to point to the `main` branch automatically.
69-
printf '<meta http-equiv="refresh" content="0; url=./develop/index.html" />' > omega/index.html
70-
# Replace `develop` docs with latest changes
71-
rm -rf omega/develop
72-
mkdir omega/develop
73-
cp -r ../_build/html/* omega/develop/
59+
# Replace `Omega` docs with latest changes
60+
rm -rf Omega
61+
mkdir Omega
62+
cp -r ../_build/html/* Omega/
7463
# Configure git using GitHub Actions credentials.
7564
git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git config --local user.name "github-actions[bot]"

‎.gitmodules‎

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@@ -22,8 +22,8 @@
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branch = scorpio_classic
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[submodule "cosp2"]
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path = components/eam/src/physics/cosp2/external
25-
url = [email protected]:bartgol/COSPv2.0.git
26-
branch = bartgol/fix-cosp_optical_inputs
25+
url = [email protected]:e3sm-project/COSPv2.0.git
26+
branch = e3sm-master
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[submodule "cime"]
2828
path = cime
2929
url = [email protected]:ESMCI/cime.git
@@ -85,3 +85,12 @@
8585
[submodule "externals/cpptrace"]
8686
path = externals/cpptrace
8787
url = [email protected]:jeremy-rifkin/cpptrace
88+
[submodule "components/omega/external/yaml-cpp"]
89+
path = components/omega/external/yaml-cpp
90+
url = https://github.com/jbeder/yaml-cpp.git
91+
[submodule "components/omega/external/GSW-C"]
92+
path = components/omega/external/GSW-C
93+
url = [email protected]:E3SM-Project/GSW-C.git
94+
[submodule "components/omega/external/yaml-cpp"]
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path = components/omega/external/yaml-cpp
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url = https://github.com/jbeder/yaml-cpp.git

‎README.md‎

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Energy Exascale Earth System Model (E3SM)
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================================================================================
77

8-
E3SM is a state-of-the-art fully coupled model of the Earth's climate including
8+
E3SM is a state-of-the-art fully coupled model of the Earth System including
99
important biogeochemical and cryospheric processes. It is intended to address
10-
the most challenging and demanding climate-change research problems and
10+
the most challenging and demanding earth system research problems and
1111
Department of Energy mission needs while efficiently using DOE Leadership
1212
Computing Facilities.
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‎cime‎

Submodule cime updated 26 files

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