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Merge branch 'mom-ocean:main' into dev/gfdl
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‎.codecov.yml‎

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threshold: 100%
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base: parent
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comment:
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# This must be set to the number of test cases (TCs)
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after_n_builds: 8
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# This is set to the number of TCs, plus unit, but can be removed
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# (i.e. set to 1) when reporting is separated from coverage.
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after_n_builds: 9

‎.github/actions/macos-setup/action.yml‎

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name: 'install-macos-prerequisites'
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description: 'Install prerequisites for Mac OS compilation'
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runs:
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using: 'composite'
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steps:
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- name: Install macOS packages
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shell: bash
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run: |
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echo "::group::Install packages"
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brew update
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brew install automake
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brew install netcdf
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brew install mpich
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echo "::endgroup::"

‎.github/actions/testing-setup/action.yml‎

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name: 'Build-.testing-prerequisites'
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description: 'Build pre-requisites for .testing including FMS and a symmetric MOM6 executable'
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inputs:
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build_symmetric:
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description: 'If true, will build the symmetric MOM6 executable'
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required: false
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default: 'true'
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install_python:
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description: 'If true, will install the local python env needed for .testing'
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required: false
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default: 'true'
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runs:
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using: 'composite'
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steps:
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- name: Git info
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shell: bash
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run: |
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echo "::group::Git commit info"
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echo "git log:"
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git log | head -60
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echo "::endgroup::"
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- name: Env
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shell: bash
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run: |
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echo "::group::Environment"
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env
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echo "::endgroup::"
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- name: Compile FMS library
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shell: bash
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run: |
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echo "::group::Compile FMS library"
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cd .testing
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make deps/lib/libFMS.a -s -j
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echo "::endgroup::"
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- name: Store compiler flags used in Makefile
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shell: bash
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run: |
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echo "::group::config.mk"
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cd .testing
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echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
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echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
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echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
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cat config.mk
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echo "::endgroup::"
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- name: Compile MOM6 in symmetric memory mode
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shell: bash
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run: |
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echo "::group::Compile MOM6 in symmetric memory mode"
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cd .testing
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test ${{ inputs.build_symmetric }} == true && make build/symmetric/MOM6 -j
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echo "::endgroup::"
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- name: Install local python venv for generating input data
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shell: bash
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run: |
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echo "::group::Create local python env for input data generation"
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cd .testing
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test ${{ inputs.install_python }} == true && make work/local-env
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echo "::endgroup::"
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- name: Set flags
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shell: bash
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run: |
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echo "TIMEFORMAT=... completed in %lR (user: %lU, sys: %lS)" >> $GITHUB_ENV

‎.github/actions/ubuntu-setup/action.yml‎

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name: 'install-ubuntu-prerequisites'
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description: 'Install prerequisites for Ubuntu Linux compilation'
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runs:
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using: 'composite'
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steps:
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- name: Install Ubuntu Linux packages
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shell: bash
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run: |
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echo "::group::Install linux packages"
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sudo apt-get update
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sudo apt-get install netcdf-bin
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sudo apt-get install libnetcdf-dev
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sudo apt-get install libnetcdff-dev
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sudo apt-get install mpich
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sudo apt-get install libmpich-dev
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sudo apt-get install linux-tools-common
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echo "::endgroup::"

‎.github/workflows/coupled-api.yml‎

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name: API for coupled drivers
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on: [push, pull_request]
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jobs:
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test-top-api:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/ubuntu-setup
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- uses: ./.github/actions/testing-setup
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with:
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build_symmetric: 'false'
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install_python: 'false'
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- name: Compile MOM6 for the GFDL coupled driver
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shell: bash
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run: make check_mom6_api_coupled -j
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- name: Compile MOM6 for the NUOPC driver
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shell: bash
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run: make check_mom6_api_nuopc -j
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- name: Compile MOM6 for the MCT driver
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shell: bash
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run: make check_mom6_api_mct -j

‎.github/workflows/coverage.yml‎

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name: Code coverage
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on: [push, pull_request]
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jobs:
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build-test-nans:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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env:
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REPORT_COVERAGE: true
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/ubuntu-setup
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- uses: ./.github/actions/testing-setup
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- name: Compile unit testing
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run: make -j build/unit/MOM6
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- name: Run unit tests
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run: make unit.cov.upload
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- name: Compile MOM6 with code coverage
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run: make -j build/cov/MOM6
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- name: Run and post coverage
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run: make run.cov -k -s

‎.github/workflows/documentation-and-style.yml‎

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name: Doxygen and style
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on: [push, pull_request]
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jobs:
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doxygen:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- name: Check white space (non-blocking)
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run: |
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./.testing/trailer.py -e TEOS10 -l 120 src config_src 2>&1 | tee style_errors
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continue-on-error: true
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- name: Install packages used when generating documentation
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run: |
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sudo apt-get update
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sudo apt-get install python3-sphinx python3-lxml perl
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sudo apt-get install texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
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sudo apt-get install graphviz
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- name: Build doxygen HTML
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run: |
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cd docs
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perl -e 'print "perl version $^V" . "\n"'
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mkdir _build && make nortd DOXYGEN_RELEASE=Release_1_8_13 UPDATEHTMLEQS=Y
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cat _build/doxygen_warn_nortd_log.txt
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- name: Report doxygen or style errors
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run: |
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grep "warning:" docs/_build/doxygen_warn_nortd_log.txt | grep -v "as part of a" | tee doxy_errors
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cat style_errors doxy_errors > all_errors
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cat all_errors
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test ! -s all_errors

‎.github/workflows/expression.yml‎

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name: Expression verification
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on: [push, pull_request]
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jobs:
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test-repro-and-dims:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/ubuntu-setup
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- uses: ./.github/actions/testing-setup
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- name: Compile MOM6 using repro optimization
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run: make build/repro/MOM6 -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Run tests
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run: make test.repro test.dim -k -s

‎.github/workflows/macos-regression.yml‎

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name: MacOS regression
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on: [pull_request]
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jobs:
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test-macos-regression:
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runs-on: macOS-latest
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env:
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CC: gcc-11
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FC: gfortran-11
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/macos-setup
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- uses: ./.github/actions/testing-setup
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- name: Compile reference model
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run: make build.regressions MOM_TARGET_SLUG=$GITHUB_REPOSITORY MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF DO_REGRESSION_TESTS=true -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Regression test
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run: make test.regression DO_REGRESSION_TESTS=true -k -s

‎.github/workflows/macos-stencil.yml‎

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name: MacOS stencil tests
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on: [push, pull_request]
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jobs:
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test-macos-stencil:
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runs-on: macOS-latest
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env:
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CC: gcc-11
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FC: gfortran-11
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/macos-setup
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- uses: ./.github/actions/testing-setup
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- name: Compile MOM6 in asymmetric memory mode
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run: make build/asymmetric/MOM6 -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Run tests
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run: make test.grid test.layout test.rotate -k -s

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