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Merge branch 'main' into test/timestamp
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‎.github/ISSUE_TEMPLATE/bump_gmt_checklist.md‎

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- [ ] Bump the GMT version in CI (1 PR)
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- [ ] Update `environment.yml`
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- [ ] Update `ci/requirements/docs.yml`
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- [ ] Update `.github/workflows/benchmarks.yml`
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- [ ] Update `.github/workflows/cache_data.yaml`
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- [ ] Update `.github/workflows/ci_doctests.yaml`
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- [ ] Update `.github/workflows/ci_docs.yml`

‎.github/workflows/benchmarks.yml‎

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# Run performance benchmarks
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#
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# Continuous benchmarking using pytest-codspeed. Measures the execution speed
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# of tests marked with @pytest.mark.benchmark decorator.
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name: Benchmarks
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on:
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# Run on pushes to the main branch
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push:
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branches: [ main ]
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paths:
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- 'pygmt/**/*.py'
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- '!pygmt/tests/**'
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- '.github/workflows/benchmarks.yml'
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pull_request:
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paths:
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- 'pygmt/**/*.py'
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- '!pygmt/tests/**'
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- '.github/workflows/benchmarks.yml'
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# `workflow_dispatch` allows CodSpeed to trigger backtest
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# performance analysis in order to generate initial data.
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workflow_dispatch:
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release:
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types:
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- published
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concurrency:
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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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jobs:
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benchmarks:
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runs-on: ubuntu-22.04
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if: github.repository == 'GenericMappingTools/pygmt'
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defaults:
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run:
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shell: bash -l {0}
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steps:
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# Checkout current git repository
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- name: Checkout
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uses: actions/checkout@v4.1.1
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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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# Install Miniconda with conda-forge dependencies
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v3.0.1
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with:
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auto-activate-base: true
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activate-environment: "" # base environment
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channels: conda-forge,nodefaults
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channel-priority: strict
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# Install GMT and dependencies from conda-forge
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- name: Install dependencies
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run: |
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# $CONDA is an environment variable pointing to the root of the miniconda directory
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# Preprend $CONDA/bin to $PATH so that conda's python is used over system python
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echo $CONDA/bin >> $GITHUB_PATH
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conda install --solver=libmamba gmt=6.4.0 python=3.12 \
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numpy pandas xarray netCDF4 packaging \
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geopandas pytest pytest-mpl
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python -m pip install -U pytest-codspeed setuptools
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# Download cached remote files (artifacts) from GitHub
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- name: Download remote data from GitHub
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uses: dawidd6/action-download-artifact@v3.0.0
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with:
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workflow: cache_data.yaml
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workflow_conclusion: success
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name: gmt-cache
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path: .gmt
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# Move downloaded files to ~/.gmt directory and list them
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- name: Move and list downloaded remote files
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run: |
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mkdir -p ~/.gmt
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mv .gmt/* ~/.gmt
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# Change modification times of the two files, so GMT won't refresh it
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touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
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ls -lhR ~/.gmt
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# Install the package that we want to test
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- name: Install the package
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run: make install
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# Run the benchmark tests
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- name: Run benchmarks
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uses: CodSpeedHQ/action@v2.0.2
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with:
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run: |
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python -c "import pygmt; pygmt.show_versions()"
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PYGMT_USE_EXTERNAL_DISPLAY="false" python -m pytest -r P --pyargs pygmt --codspeed
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env:
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GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

‎.github/workflows/cache_data.yaml‎

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# Cache GMT remote data files and uploads as artifacts
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# Cache GMT remote data files and upload as artifacts
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#
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# This workflow downloads data files needed by PyGMT tests/documentation from
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# the GMT data server and uploads as workflow artifacts which can be accessed
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# by other GitHub Actions workflows.
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#
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# It is scheduled to run every Sunday at 12:00 (UTC). If new remote files are
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# needed urgently, maintainers can manually uncomment the 'pull_request:' line
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# below to refresh the cache.
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# needed urgently, maintainers can update the workflow file or
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# 'pygmt/helpers/caching.py' file to refresh the cache.
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#
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name: Cache data
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on:
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# Uncomment the 'pull_request' line below to manually re-cache data artifacts
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# pull_request:
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pull_request:
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# Make any changes to the following files to refresh the cache
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paths:
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- 'pygmt/helpers/caching.py'
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- '.github/workflows/cache_data.yaml'
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# Schedule runs on 12 noon every Sunday
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schedule:
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- cron: '0 12 * * 0'
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1.7.0
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uses: mamba-org/setup-micromamba@v1.7.3
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with:
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environment-name: pygmt
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condarc: |
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# Download remote files
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- name: Download remote data
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run: |
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python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
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python -c "from pygmt.helpers.caching import cache_data; cache_data()"
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# Upload the downloaded files as artifacts to GitHub
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- name: Upload artifacts to GitHub
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: gmt-cache
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path: |

‎.github/workflows/check-links.yml‎

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check_links:
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name: Check Links
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runs-on: ubuntu-latest
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if: github.repository == 'GenericMappingTools/pygmt'
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steps:
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- name: Checkout the repository

‎.github/workflows/ci_docs.yml‎

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docs:
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name: ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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if: github.repository == 'GenericMappingTools/pygmt'
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strategy:
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fail-fast: false
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matrix:
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1.7.0
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uses: mamba-org/setup-micromamba@v1.7.3
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with:
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environment-name: pygmt
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condarc: |
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channels:
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- conda-forge
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- nodefaults
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cache-downloads: true
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cache-downloads: false
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cache-environment: true
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create-args: >-
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python=3.12
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# Download cached remote files (artifacts) from GitHub
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- name: Download remote data from GitHub
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uses: dawidd6/action-download-artifact@v2.28.0
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uses: dawidd6/action-download-artifact@v3.0.0
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with:
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workflow: cache_data.yaml
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workflow_conclusion: success

‎.github/workflows/ci_doctests.yaml‎

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test:
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name: ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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if: github.repository == 'GenericMappingTools/pygmt'
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strategy:
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fail-fast: false
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matrix:
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1.7.0
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uses: mamba-org/setup-micromamba@v1.7.3
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with:
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environment-name: pygmt
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condarc: |
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# Download cached remote files (artifacts) from GitHub
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- name: Download remote data from GitHub
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uses: dawidd6/action-download-artifact@v2.28.0
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uses: dawidd6/action-download-artifact@v3.0.0
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with:
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workflow: cache_data.yaml
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workflow_conclusion: success

‎.github/workflows/ci_tests.yaml‎

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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1.7.0
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uses: mamba-org/setup-micromamba@v1.7.3
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with:
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environment-name: pygmt
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condarc: |
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channels:
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- conda-forge
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- nodefaults
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cache-downloads: true
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cache-downloads: false
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cache-environment: true
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create-args: >-
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python=${{ matrix.python-version }}${{ matrix.optional-packages }}
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# Download cached remote files (artifacts) from GitHub
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- name: Download remote data from GitHub
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uses: dawidd6/action-download-artifact@v2.28.0
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uses: dawidd6/action-download-artifact@v3.0.0
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with:
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workflow: cache_data.yaml
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workflow_conclusion: success
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# Pull baseline image data from dvc remote (DAGsHub)
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- name: Pull baseline image data from dvc remote
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run: |
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dvc pull --verbose
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ls -lhR pygmt/tests/baseline/
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run: dvc pull --verbose && ls -lhR pygmt/tests/baseline/
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# Install the package that we want to test
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- name: Install the package
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# Upload diff images on test failure
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- name: Upload diff images if any test fails
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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if: ${{ failure() }}
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with:
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name: artifact-${{ runner.os }}-${{ matrix.python-version }}

‎.github/workflows/ci_tests_dev.yaml‎

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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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# Generate token from GenericMappingTools bot
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- name: Generate token from GenericMappingTools bot
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uses: tibdex/github-app-token@v2
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if: github.event_name == 'repository_dispatch'
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id: generate-token
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with:
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app_id: ${{ secrets.APP_ID }}
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private_key: ${{ secrets.APP_PRIVATE_KEY }}
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# Checkout the pull request branch
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- name: Checkout
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uses: actions/checkout@v4.1.1
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if: github.event_name == 'repository_dispatch'
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with:
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token: ${{ steps.generate-token.outputs.token }}
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token: ${{ secrets.GITHUB_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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# fetch all history so that setuptools-scm works
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fetch-depth: 0
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- name: Show job URL
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uses: peter-evans/create-or-update-comment@v3.1.0
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if: github.event_name == 'repository_dispatch' && (matrix.os == 'ubuntu-latest')
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if: github.event_name == 'repository_dispatch' && runner.os == 'Linux'
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with:
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token: ${{ steps.generate-token.outputs.token }}
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token: ${{ secrets.GITHUB_TOKEN }}
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repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
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comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
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body: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
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# Install Micromamba with conda-forge dependencies
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1.7.0
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uses: mamba-org/setup-micromamba@v1.7.3
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with:
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environment-name: pygmt
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condarc: |
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channels:
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- conda-forge
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- nodefaults
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cache-downloads: true
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cache-downloads: false
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cache-environment: true
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create-args: >-
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run: curl https://raw.githubusercontent.com/GenericMappingTools/gmt/master/ci/build-gmt.sh | bash
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env:
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GMT_GIT_REF: ${{ matrix.gmt_git_ref }}
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GMT_INSTALL_DIR: ${{ github.workspace }}/gmt-install-dir
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GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
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if: runner.os != 'Windows'
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- name: Install GMT ${{ matrix.gmt_git_ref }} branch (Windows)
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-DGMT_USE_THREADS=TRUE
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cmake --build .
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cmake --build . --target install
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cd ..
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rm -rf gmt/
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env:
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GMT_GIT_REF: ${{ matrix.gmt_git_ref }}
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GMT_INSTALL_DIR: ${{ github.workspace }}/gmt-install-dir
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GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
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if: runner.os == 'Windows'
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- name: Add GMT's bin to PATH
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run: echo '${{ github.workspace }}/gmt-install-dir/bin' >> $GITHUB_PATH
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run: echo '${{ runner.temp }}/gmt-install-dir/bin' >> $GITHUB_PATH
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# Install dependencies from PyPI
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- name: Install dependencies
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# Pull baseline image data from dvc remote (DAGsHub)
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- name: Pull baseline image data from dvc remote
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run: |
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dvc pull
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ls -lhR pygmt/tests/baseline/
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run: dvc pull --verbose && ls -lhR pygmt/tests/baseline/
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# Download cached remote files (artifacts) from GitHub
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- name: Download remote data from GitHub
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uses: dawidd6/action-download-artifact@v2.28.0
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uses: dawidd6/action-download-artifact@v3.0.0
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with:
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workflow: cache_data.yaml
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workflow_conclusion: success
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- name: Test with pytest
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run: make test PYTEST_EXTRA="-r P"
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env:
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GMT_LIBRARY_PATH: ${{ github.workspace }}/gmt-install-dir/lib
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GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib
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# Upload diff images on test failure
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- name: Upload diff images if any test fails
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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if: ${{ failure() }}
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with:
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name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}

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