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Merge branch 'feature/read' into dep/netcdf
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‎.github/ISSUE_TEMPLATE/4-release_checklist.md

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@@ -11,6 +11,7 @@ assignees: ''
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**Scheduled Date**: 20YY/MM/DD
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**Pull request due date**: 20YY/MM/DD
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**DOI**: `10.5281/zenodo.XXXXXXX`
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**Announcement draft**: https://hackmd.io/@pygmt/xxxxxxxx
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**Priority PRs/issues to complete prior to release**
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@@ -39,11 +40,15 @@ assignees: ''
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- [ ] Edit the draft release notes with the finalized changelog
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- [ ] Set the tag version and release title to vX.Y.Z
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- [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
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- [ ] Verify that [all workflows triggered by the release](https://github.com/GenericMappingTools/pygmt/actions?query=event%3Arelease) pass
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- [ ] The latest version is correct on [PyPI](https://pypi.org/project/pygmt/)
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- [ ] The latest version is correct on https://www.pygmt.org/latest/
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- [ ] The [release page](https://github.com/GenericMappingTools/pygmt/releases) has five assets, including `baseline-images.zip`, `pygmt-docs.zip` and `pygmt-docs.pdf`
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- [ ] Download pygmt-X.Y.Z.zip (rename to pygmt-vX.Y.Z.zip) and baseline-images.zip from the release page, and upload the two zip files to https://zenodo.org/deposit, ensure that they are filed under the correct reserved DOI
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**After release**:
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- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Done automatically by conda-forge's bot. Remember to pin GMT, Python and SPEC0 versions]
51+
- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) (Done automatically by conda-forge's bot. If you don't want to wait, open a new issue in the `conda-forge/pygmt-feedstock` repository with the title `@conda-forge-admin, please update version`. This will trigger the bot immediately. Remember to pin GMT, Python and SPEC0 versions)
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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! Requires moderator status)

‎.github/workflows/benchmarks.yml

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@@ -23,6 +23,8 @@ 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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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
@@ -81,7 +84,7 @@ jobs:
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# Run the benchmark tests
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- name: Run benchmarks
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uses: CodSpeedHQ/action@v3.2.0
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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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@@ -25,6 +25,8 @@ on:
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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
@@ -40,6 +42,7 @@ jobs:
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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
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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/[email protected].0
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uses: actions/[email protected].2
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with:
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name: gmt-cache
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include-hidden-files: true

‎.github/workflows/check-links.yml

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@@ -1,7 +1,7 @@
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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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# This workflow runs the lychee tool to check all external links in plaintext and HTML
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# 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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#
@@ -15,6 +15,9 @@ on:
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schedule:
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- cron: '0 12 * * 0'
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permissions:
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issues: write
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jobs:
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check_links:
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name: Check Links
@@ -26,16 +29,18 @@ jobs:
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uses: actions/[email protected]
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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/[email protected]
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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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uses: lycheeverse/lychee-action@v2.3.0
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uses: lycheeverse/lychee-action@v2.4.0
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with:
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fail: false # Don't fail action on broken links
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output: /tmp/lychee-out.md
@@ -45,11 +50,14 @@ jobs:
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--exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%s$"
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--exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%3Cmodule-name%3E.html$"
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--exclude "^https://doi.org"
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--exclude "^https://github.com/%7Brepository%7D"
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--exclude "^https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z$"
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--exclude "^https://github.com/GenericMappingTools/pygmt/edit"
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--exclude "^https://github.com/GenericMappingTools/pygmt/issues/new"
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--exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
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--exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
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--exclude "^https://github.com/GenericMappingTools/pygmt/releases/download/%7B%7Bpath%7D%7D/pygmt-docs.pdf"
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--exclude "^https://github.com/GenericMappingTools/pygmt/releases/download/%7B%7Bpath%7D%7D/pygmt-docs.zip"
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--exclude "^https://github.com/GenericMappingTools/pygmt/releases/tag/%7B%7Bpath%7D%7D"
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--exclude "^https://hackmd.io/@pygmt"
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--exclude "^https://test.pypi.org/simple/"
@@ -59,8 +67,7 @@ jobs:
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--exclude "^https://www.researchgate.net/"
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--exclude "^https://zenodo.org/badge/DOI/"
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--verbose
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"repository/**/*.rst"
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"repository/**/*.md"
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"repository/*.md"
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"repository/**/*.py"
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"documentation/dev/**/*.html"
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run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
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- name: Create Issue From File
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if: env.lychee_exit_code != 0
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if: steps.lychee.outputs.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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#
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# This workflow builds the documentation on Linux/macOS/Windows.
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#
5-
# 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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# It is run on every commit to the main and pull request branches, and also when a new
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# release is published. In draft pull requests, only the job on Linux is triggered to
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# save on 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 development documentation by pushing the built HTML pages from the main
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# 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
@@ -43,6 +42,9 @@ 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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permissions:
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contents: write
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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
@@ -110,7 +113,7 @@ jobs:
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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<3.0
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sphinx_rtd_theme
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cairosvg
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sphinxcontrib-svg2pdfconverter
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tectonic
@@ -146,15 +149,23 @@ jobs:
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mv latex/pygmt.pdf pygmt-docs.pdf
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cd ../..
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- name: Upload PDF as artifact for previewing on pull requests
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uses: actions/[email protected]
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if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
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with:
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name: artifact-pygmt-docs-pdf
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path: doc/_build/pygmt-docs.pdf
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- name: Copy the HTML ZIP archive and PDF to the html folder for dev version
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run: cp -v doc/_build/pygmt-docs.zip doc/_build/pygmt-docs.pdf doc/_build/html/
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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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path: deploy
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# Download the entire history
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fetch-depth: 0
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persist-credentials: true
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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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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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jobs:
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test:
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name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
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name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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permissions:
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id-token: write # This is required for requesting OIDC token for codecov
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include:
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# Python 3.11 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
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- python-version: '3.11'
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numpy-version: '1.25'
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pandas-version: '=2.0'
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xarray-version: '=2023.04'
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optional-packages: ' contextily geopandas<1 ipython pyarrow-core rioxarray sphinx-gallery'
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numpy-version: '1.26'
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pandas-version: '=2.1'
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xarray-version: '=2023.07'
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optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray sphinx-gallery'
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# Python 3.13 + core packages (latest versions) + optional packages
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- python-version: '3.13'
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numpy-version: '2.2'
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pandas-version: ''
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xarray-version: ''
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optional-packages: ' contextily geopandas>=1.0 ipython pyarrow-core rioxarray sphinx-gallery'
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optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray sphinx-gallery'
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# Python 3.12 + core packages (Linux only)
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- os: 'ubuntu-latest'
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python-version: '3.12'
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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@v5.4.1
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with:
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python-version: ${{ matrix.python-version }}
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@@ -173,15 +174,15 @@ jobs:
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# Upload diff images on test failure
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- name: Upload diff images if any test fails
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uses: actions/[email protected].0
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uses: actions/[email protected].2
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if: failure()
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with:
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name: artifact-${{ matrix.os }}-${{ matrix.python-version }}
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path: tmp-test-dir-with-unique-name
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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
@@ -96,6 +99,7 @@ jobs:
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repository: 'GenericMappingTools/gmt'
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ref: ${{ matrix.gmt_git_ref }}
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path: 'gmt'
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persist-credentials: false
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# Build GMT from source on Linux/macOS, script is adapted from
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# https://github.com/GenericMappingTools/gmt/blob/6.5.0/ci/build-gmt.sh
@@ -105,7 +109,7 @@ jobs:
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mkdir build
106110
cd build
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cmake -G Ninja .. \
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-DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} \
112+
-DCMAKE_INSTALL_PREFIX=${GMT_INSTALL_DIR} \
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-DCMAKE_BUILD_TYPE=Release \
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-DGMT_ENABLE_OPENMP=TRUE \
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-DGMT_USE_THREADS=TRUE
@@ -125,7 +129,7 @@ jobs:
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cd build
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call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
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cmake -G Ninja .. ^
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-DCMAKE_INSTALL_PREFIX=${{ 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 ^
@@ -182,7 +186,7 @@ jobs:
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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/[email protected].0
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uses: actions/[email protected].2
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if: ${{ failure() }}
187191
with:
188192
name: artifact-${{ matrix.os }}-GMT-${{ matrix.gmt_git_ref }}

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