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Merge branch 'main' into refactor/virtualfile_in_extra_arrays
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.github/workflows/benchmarks.yml

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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
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permissions: {}
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jobs:
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benchmarks:
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runs-on: ubuntu-latest
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with:
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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- name: Get current week number of year
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id: date
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# Run the benchmark tests
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- name: Run benchmarks
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uses: CodSpeedHQ/action@v3.4.0
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uses: CodSpeedHQ/action@v3.5.0
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with:
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# 'bash -el -c' is needed to use the custom shell.
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# See https://github.com/CodSpeedHQ/action/issues/65.

.github/workflows/cache_data.yaml

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schedule:
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- cron: '0 12 * * 0'
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permissions: {}
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jobs:
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gmt_cache:
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name: Cache GMT artifacts
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with:
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba

.github/workflows/check-links.yml

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schedule:
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- cron: '0 12 * * 0'
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permissions: {}
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jobs:
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check_links:
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name: Check Links
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uses: actions/checkout@v4.2.2
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with:
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path: repository
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persist-credentials: false
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- name: Checkout the documentation
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uses: actions/checkout@v4.2.2
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with:
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ref: gh-pages
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path: documentation
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persist-credentials: false
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- name: Link Checker
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id: lychee
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if: env.lychee_exit_code != 0
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run: |
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cd repository/
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title="Link Checker Report on ${{ steps.date.outputs.date }}"
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title="Link Checker Report on ${CURRENT_DATE}"
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gh issue create --title "$title" --body-file /tmp/lychee-out.md
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env:
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GH_TOKEN: ${{ github.token }}
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CURRENT_DATE: ${{ steps.date.outputs.date }}

.github/workflows/ci_docs.yml

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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
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permissions: {}
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jobs:
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docs:
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name: ${{ matrix.os }}
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with:
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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- name: Get current week number of year
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id: date
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if: github.event_name == 'push' && matrix.os == 'ubuntu-latest'
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- name: Upload the HTML ZIP archive and PDF as release assets
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run: gh release upload ${{ github.ref_name }} doc/_build/pygmt-docs.zip doc/_build/pygmt-docs.pdf
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run: gh release upload ${REF_NAME} doc/_build/pygmt-docs.zip doc/_build/pygmt-docs.pdf
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if: github.event_name == 'release' && matrix.os == 'ubuntu-latest'
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env:
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GH_TOKEN: ${{ github.token }}
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REF_NAME: ${{ github.ref_name }}
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- name: Checkout the gh-pages branch
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uses: actions/checkout@v4.2.2
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path: deploy
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# Download the entire history
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fetch-depth: 0
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persist-credentials: false
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if: (github.event_name == 'release' || github.event_name == 'push') && (matrix.os == 'ubuntu-latest')
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- name: Push the built HTML to gh-pages

.github/workflows/ci_doctests.yaml

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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
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permissions: {}
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jobs:
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test:
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name: ${{ matrix.os }}
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with:
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba

.github/workflows/ci_tests.yaml

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with:
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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- name: Get current week number of year
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id: date
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GH_TOKEN: ${{ github.token }}
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- name: Install uv
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uses: astral-sh/setup-uv@v5.2.2
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uses: astral-sh/setup-uv@v5.3.1
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with:
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python-version: ${{ matrix.python-version }}
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# Upload coverage to Codecov
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v5.3.1
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uses: codecov/codecov-action@v5.4.0
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if: success() || failure()
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with:
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use_oidc: true

.github/workflows/ci_tests_dev.yaml

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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
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permissions: {}
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jobs:
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test_gmt_dev:
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name: ${{ matrix.os }} - GMT ${{ matrix.gmt_git_ref }}
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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- name: Get current week number of year
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id: date
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repository: 'GenericMappingTools/gmt'
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ref: ${{ matrix.gmt_git_ref }}
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path: 'gmt'
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persist-credentials: false
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# Build GMT from source on Linux/macOS, script is adapted from
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# https://github.com/GenericMappingTools/gmt/blob/6.5.0/ci/build-gmt.sh
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mkdir build
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cd build
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cmake -G Ninja .. \
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-DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} \
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-DCMAKE_INSTALL_PREFIX=${GMT_INSTALL_DIR} \
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-DCMAKE_BUILD_TYPE=Release \
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-DGMT_ENABLE_OPENMP=TRUE \
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-DGMT_USE_THREADS=TRUE
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cd build
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call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
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cmake -G Ninja .. ^
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-DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} ^
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-DCMAKE_INSTALL_PREFIX=%GMT_INSTALL_DIR% ^
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-DCMAKE_BUILD_TYPE=Release ^
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-DCMAKE_PREFIX_PATH=${{ env.MAMBA_ROOT_PREFIX }}\envs\pygmt\Library ^
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-DGMT_ENABLE_OPENMP=TRUE ^

.github/workflows/ci_tests_legacy.yaml

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group: ${{ github.workflow }}-${{ github.ref }}
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permissions: {}
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jobs:
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test:
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name: ${{ matrix.os }} - GMT ${{ matrix.gmt_version }}
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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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persist-credentials: false
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba

.github/workflows/dvc-diff.yml

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- 'pygmt/tests/baseline/*.png.dvc'
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permissions: {}
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dvc-diff:
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name: DVC image diff
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with:
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# fetch all history so that dvc diff works
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fetch-depth: 0
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persist-credentials: false
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- name: Setup data version control (DVC)
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uses: iterative/setup-dvc@v1.1.2
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- name: Generate the image diff report
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env:
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repo_token: ${{ github.token }}
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PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
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run: |
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echo -e "## Summary of changed images\n" > report.md
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echo -e "This is an auto-generated report of images that have changed on the DVC remote\n" >> report.md
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echo -e "</details>\n" >> report.md
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# Mention git commit SHA in the report
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echo -e "Report last updated at commit ${{ github.event.pull_request.head.sha }}" >> report.md
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echo -e "Report last updated at commit ${PR_HEAD_SHA}" >> report.md
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# create/update PR comment
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cml comment update report.md

.github/workflows/format-command.yml

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# This workflow is triggered in a PR if the slash command `/format` is used.
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#
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name: format-command
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on:
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repository_dispatch:
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types: [format-command]
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permissions: {}
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format:
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runs-on: ubuntu-latest
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token: ${{ steps.generate-token.outputs.token }}
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repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
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ref: ${{ github.event.client_payload.pull_request.head.ref }}
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persist-credentials: false
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# Setup Python environment
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- uses: actions/setup-python@v5.4.0

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