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Merge branch 'main' into sphinx-gallery-optional
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‎.github/ISSUE_TEMPLATE/bump_gmt_checklist.md

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**To-Do for bumping the GMT version in CI**:
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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/cache_data.yaml`
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- [ ] Update `.github/workflows/ci_doctests.yaml`
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- [ ] Update `.github/workflows/ci_docs.yml`
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- [ ] Update `.github/workflows/ci_tests.yaml`
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- [ ] Update `ci/requirements/docs.yml`
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- [ ] Update `environment.yml`
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- [ ] Add the legacy GMT version to `.github/workflows/ci_tests_legacy.yaml`
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- [ ] Fix failing tests (1 or more PRs)
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- [ ] Fix [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
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**To-Do for bumping the minimum required GMT version**:
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- [ ] Bump the minimum required GMT version (1 PR)
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- [ ] Update `doc/install.rst`
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- [ ] Update `required_version` in `pygmt/clib/session.py`
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- [ ] Update `test_get_default` in `pygmt/tests/test_clib.py`
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- [ ] Update compatibility table in `README.rst`
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- [ ] Remove unsupported GMT version from `.github/workflows/ci_tests_legacy.yaml`
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- [ ] Remove [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
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- [ ] Update deprecated syntax in source code and examples based on the [GMT Changelog](https://docs.generic-mapping-tools.org/latest/changes.html)

‎.github/ISSUE_TEMPLATE/release_checklist.md

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- [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt (after conda-forge update)
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- [ ] Announce the release on:
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- [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! draft on https://hackmd.io/@pygmt. requires moderator status)
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- [ ] [ResearchGate](https://www.researchgate.net/project/PyGMT-A-Python-interface-for-the-Generic-Mapping-Tools) (after forum announcement)
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- [ ] [Twitter](https://twitter.com/gmt_dev) (after forum announcement)
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---
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‎.github/release-drafter.yml

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label: 'maintenance'
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exclude-labels:
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- 'skip-changelog'
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exclude-contributors:
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- 'actions-bot'
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- 'dependabot'
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- 'dependabot[bot]'
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category-template: '### $TITLE'
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change-template: '* $TITLE ([#$NUMBER]($URL))'
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sort-by: 'title'

‎.github/workflows/cache_data.yaml

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# This workflow gets and uploads the GMT data artifacts used in the PyGMT CI tests
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# Cache GMT remote data files and uploads 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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#
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name: Cache data
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on:
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jobs:
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gmt_cache:
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name: Cache GMT artifacts
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runs-on: macOS-latest
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runs-on: macos-latest
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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/[email protected].0
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uses: actions/[email protected].2
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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 Mambaforge with conda-forge dependencies
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- name: Setup Mambaforge
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uses: conda-incubator/[email protected]
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- name: Setup Micromamba
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uses: mamba-org/provision-with-micromamba@v15
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with:
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environment-name: pygmt
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environment-file: false
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channels: conda-forge,nodefaults
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channel-priority: strict
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miniforge-version: latest
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miniforge-variant: Mambaforge
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mamba-version: "*"
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run-post: false
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use-mamba: true
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# Install GMT and other required dependencies from conda-forge
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- name: Install dependencies
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run: |
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mamba install gmt=6.4.0 numpy pandas xarray netCDF4 packaging \
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build
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extra-specs: |
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python=3.11
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gmt=6.4.0
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numpy
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pandas
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xarray
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netCDF4
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packaging
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build
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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: |
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python -m build --sdist
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pip install dist/*
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python -m pip install dist/*
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# Download remote files
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- name: Download remote data

‎.github/workflows/check-links.yml

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# This workflow checks the links in plaintext and HTML files
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# Check links in the repository and documentation
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#
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# This workflow runs the lychee tool to check all external links in plaintext
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# and HTML files. It will create an issue if broken links are found.
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#
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# It is scheduled to run weekly at 12 noon every Sunday.
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#
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name: Check Links
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on:
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steps:
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- name: Checkout the repository
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uses: actions/[email protected].0
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uses: actions/[email protected].2
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with:
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path: repository
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- name: Checkout the documentation
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uses: actions/[email protected].0
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uses: actions/[email protected].2
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with:
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ref: gh-pages
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path: documentation
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- name: Link Checker
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id: lychee
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uses: lycheeverse/lychee-action@v1.6.1
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uses: lycheeverse/lychee-action@v1.7.0
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with:
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# 429: Too many requests
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args: >

‎.github/workflows/ci_docs.yml

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# This workflow installs PyGMT, builds and deploys documentation
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# Build and deploy documentation
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#
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# This workflow builds the documentation on Linux/macOS/Windows.
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#
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# It is run on every commit to the main and pull request branches, and also
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# when a new release is published.
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# In draft pull requests, only the job on Linux is triggered to save on
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# Continuous Integration resources.
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#
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# On the main branch, the workflow also handles the documentation deployment:
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#
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# * Updating the development documentation by pushing the built HTML pages
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# from the main branch onto the dev folder of the gh-pages branch.
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# * Updating the latest documentation link to the new release.
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#
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name: Docs
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on:
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jobs:
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docs:
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name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
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name: ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.11']
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os: [ubuntu-latest, macOS-latest, windows-latest]
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os: [ubuntu-latest, macos-latest, windows-latest]
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# Is it a draft Pull Request (true or false)?
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isDraft:
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- ${{ github.event.pull_request.draft }}
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# Only run one job (Ubuntu + Python 3.11) for draft PRs
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exclude:
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- os: macOS-latest
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- os: macos-latest
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isDraft: true
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- os: windows-latest
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isDraft: true
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# Checkout current git repository
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- name: Checkout
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uses: actions/[email protected].0
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uses: actions/[email protected].2
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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 Mambaforge with conda-forge dependencies
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- name: Setup Mambaforge
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uses: conda-incubator/[email protected]
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- name: Setup Micromamba
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uses: mamba-org/provision-with-micromamba@v15
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with:
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activate-environment: pygmt
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python-version: ${{ matrix.python-version }}
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environment-name: pygmt
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environment-file: false
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channels: conda-forge,nodefaults
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channel-priority: strict
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miniforge-version: latest
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miniforge-variant: Mambaforge
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mamba-version: "*"
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run-post: false
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use-mamba: true
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# Install GMT and other required dependencies from conda-forge
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- name: Install dependencies
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run: |
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mamba install gmt=6.4.0 numpy pandas xarray netCDF4 packaging \
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build ipython make myst-parser contextily geopandas rioxarray \
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sphinx sphinx-copybutton sphinx-design sphinx-gallery sphinx_rtd_theme
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# Show installed pkg information for postmortem diagnostic
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- name: List installed packages
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run: mamba list
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cache-downloads: true
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cache-env: true
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extra-specs: |
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python=3.11
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gmt=6.4.0
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numpy
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pandas
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xarray
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netCDF4
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packaging
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contextily
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geopandas
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ipython
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rioxarray
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build
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make
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pip
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myst-parser
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sphinx
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sphinx-copybutton
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sphinx-design
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sphinx-gallery
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sphinx_rtd_theme
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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@v2.26.1
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uses: dawidd6/action-download-artifact@v2.27.0
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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: Install the package
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run: |
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python -m build --sdist
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pip install dist/*
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python -m pip install dist/*
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# Build the documentation
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- name: Build the documentation
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run: make -C doc clean all
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- name: Checkout the gh-pages branch
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uses: actions/[email protected].0
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uses: actions/[email protected].2
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with:
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ref: gh-pages
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# Checkout to this folder instead of the current one

‎.github/workflows/ci_doctests.yaml

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# Run all doctests on Linux/macOS/Windows
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#
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# This workflow runs all PyGMT doctests. It is scheduled to run weekly every
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# Sunday.
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#
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name: Doctests
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on:
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# push:
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# branches: [ main ]
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# pull_request:
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# Schedule weekly tests on Sunday
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schedule:
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- cron: '0 0 * * 0'
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jobs:
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test:
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name: ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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timeout-minutes: 30
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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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# Cancel previous runs that are not completed
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- name: Cancel Previous Runs
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uses: styfle/[email protected]
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with:
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access_token: ${{ github.token }}
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# Checkout current git repository
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- name: Checkout
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uses: actions/[email protected]
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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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- name: Setup Micromamba
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uses: mamba-org/provision-with-micromamba@v15
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with:
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environment-name: pygmt
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environment-file: false
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channels: conda-forge,nodefaults
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extra-specs: |
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python=3.11
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gmt=6.4.0
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numpy
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pandas
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xarray
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netCDF4
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packaging
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contextily
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geopandas
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ipython
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rioxarray
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build
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make
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pip
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pytest
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pytest-doctestplus
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pytest-mpl
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sphinx-gallery
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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/[email protected]
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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 doctests
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- name: Run doctests
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run: make doctest PYTEST_EXTRA="-r P"

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