Merge branch 'main' into doc/dtypes

GenericMappingTools · Feb 7, 2025 · 431d515 · 431d515
2 parents 52e9c3d + e9792fe
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diff --git a/.github/ISSUE_TEMPLATE/1-bug_report.yaml b/.github/ISSUE_TEMPLATE/1-bug_report.yaml
@@ -1,28 +1,30 @@
 name: Bug report
-description: Report a problem/bug to help us improve
+description: Report a problem/bug to help us improve.
 labels: bug
 body:
   - type: markdown
     attributes:
-      value: |
+      value: >
         Thanks for taking the time to fill out this bug report!
   - type: textarea
     attributes:
       label: "Description of the problem"
-      description: |
+      description: >
         Please be as detailed as you can when describing an issue.
         The more information we have, the easier it will be for us to track this down.
     validations:
       required: true
   - type: textarea
     attributes:
       label: "Minimal Complete Verifiable Example"
-      description: |
+      description: >
         So that we can understand and fix the issue quickly and efficiently, please provide
         a minimal, self-contained copy-pastable example that demonstrates the issue.
+
         For more details, check out:
 
         - [Minimal Complete Verifiable Examples](https://stackoverflow.com/help/mcve)
+
         - [Craft Minimal Bug Reports](https://matthewrocklin.com/minimal-bug-reports)
 
       placeholder: "PASTE CODE HERE"
@@ -40,9 +42,11 @@ body:
   - type: textarea
     attributes:
       label: "System information"
-      description: |
-        Please paste the output of `python -c "import pygmt; pygmt.show_versions()"`
-        If this command is not successful, please describe your operating system, how you installed PyGMT, how you installed GMT, and paste the full error message.
+      description: >
+        Please paste the output of `python -c "import pygmt; pygmt.show_versions()"`.
+
+        If this command is not successful, please describe your operating system,
+        how you installed PyGMT, how you installed GMT, and paste the full error message.
       placeholder: "PASTE THE OUTPUT HERE"
       render: bash
     validations:

diff --git a/.github/ISSUE_TEMPLATE/2-feature_request.yaml b/.github/ISSUE_TEMPLATE/2-feature_request.yaml
@@ -5,16 +5,17 @@ body:
   - type: textarea
     attributes:
       label: "Description of the desired feature"
-      description: |
-        Please be as detailed as you can in your description.
-        If possible, include an example of how you would like to use this feature (even better if it's a code example).
+      description: >
+        Please be as detailed as you can in your description. If possible, include
+        an example of how you would like to use this feature (even better if it's a code example).
   - type: dropdown
     id: help
     attributes:
       label: Are you willing to help implement and maintain this feature?
-      description: |
-        Every feature we add is code that we will have to maintain and keep updated. This takes a lot of effort.
-        If you are willing to be involved in the project and help maintain your feature, it will make it easier for us to accept it.
+      description: >
+        Every feature we add is code that we will have to maintain and keep updated.
+        This takes a lot of effort. If you are willing to be involved in the project and
+        help maintain your feature, it will make it easier for us to accept it.
       options:
         - "No"
         - "Yes"

diff --git a/.github/ISSUE_TEMPLATE/3-module_request.yaml b/.github/ISSUE_TEMPLATE/3-module_request.yaml
@@ -5,23 +5,29 @@ labels: ["feature request"]
 body:
   - type: markdown
     attributes:
-      value: |
-        Please replace `<module-name>` in the issue title and the description with the name of the requested module and add the description of the module.
+      value: >
+        Please replace `<module-name>` in the issue title and the description with the
+        name of the requested module and add the description of the module.
   - type: textarea
     id: which-module
     attributes:
       label: Description of the desired module
-      description: Please be as detailed as you can in your description. If possible, include an example of how you would like to use this feature (even better if it's a code example).
-      placeholder: Implement [`<module-name>`](https://docs.generic-mapping-tools.org/latest/<module-name>.html) which `<insert description of the GMT module>`.
+      description: >
+        Please be as detailed as you can in your description. If possible, include
+        an example of how you would like to use this feature (even better if it's a code example).
+      placeholder: >
+        Implement [`<module-name>`](https://docs.generic-mapping-tools.org/latest/<module-name>.html)
+        which `<insert description of the GMT module>`.
     validations:
       required: true
   - type: dropdown
     id: help
     attributes:
       label: Are you willing to help implement and maintain this feature?
-      description: |
-        Every feature we add is code that we will have to maintain and keep updated. This takes a lot of effort.
-        If you are willing to be involved in the project and help maintain your feature, it will make it easier for us to accept it.
+      description: >
+        Every feature we add is code that we will have to maintain and keep updated.
+        This takes a lot of effort. If you are willing to be involved in the project and
+        help maintain your feature, it will make it easier for us to accept it.
       options:
         - "No"
         - "Yes"
@@ -30,5 +36,6 @@ body:
       required: true
   - type: markdown
     attributes:
-      value: |
-        Progress on wrapping the module will be tracked in the [project board](https://github.com/GenericMappingTools/pygmt/projects/9).
+      value: >
+        Progress on wrapping the module will be tracked in the
+        [project board](https://github.com/orgs/GenericMappingTools/projects/3).
diff --git a/.github/ISSUE_TEMPLATE/4-release_checklist.md b/.github/ISSUE_TEMPLATE/4-release_checklist.md
@@ -1,6 +1,6 @@
 ---
 name: PyGMT release checklist
-about: Checklist for a new PyGMT release.
+about: Checklist for a new PyGMT release. [For project maintainers only!]
 title: Release PyGMT vX.Y.Z
 labels: maintenance
 assignees: ''
@@ -19,17 +19,15 @@ assignees: ''
 
 **Before release**:
 
-- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of GMT, Python and
-      core package dependencies (NumPy, pandas, Xarray)
+- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of GMT, Python and core package dependencies (NumPy, pandas, Xarray)
 - [ ] Review the ["PyGMT Team" page](https://www.pygmt.org/dev/team.html)
+- [ ] README looks good on TestPyPI. Visit [TestPyPI](https://test.pypi.org/project/pygmt/#history), click the latest pre-release, and check the homepage.
 - [ ] Check to ensure that:
-  - [ ] Deprecations and related tests are removed for this version by running `grep --include="*.py" -r vX.Y.Z` from the base of the repository
+  - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs.
   - [ ] All tests pass in the ["GMT Legacy Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_legacy.yaml)
   - [ ] All tests pass in the ["GMT Dev Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml)
   - [ ] All tests pass in the ["Doctests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
-- [ ] Update warnings in `pygmt/_show_versions.py` as well as notes in
-      [Not working transparency](https://www.pygmt.org/dev/install.html#not-working-transparency)
-      regarding GMT-Ghostscript incompatibility
+- [ ] Update warnings in `pygmt/_show_versions.py` as well as notes in [Not working transparency](https://www.pygmt.org/dev/install.html#not-working-transparency) regarding GMT-Ghostscript incompatibility
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
 - [ ] Finish up the "Changelog entry for v0.x.x" Pull Request (Use the previous changelog PR as a reference)
 - [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
@@ -41,18 +39,16 @@ assignees: ''
   - [ ] Edit the draft release notes with the finalized changelog
   - [ ] Set the tag version and release title to vX.Y.Z
   - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
-- [ ] 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
+- [ ] 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
 
 **After release**:
 
-- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock)
-      [Done automatically by conda-forge's bot. Remember to pin Python and SPEC0 versions]
+- [ ] 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]
 - [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt (after conda-forge update)
 - [ ] Announce the release on:
   - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! Requires moderator status)
-  - [ ] [ResearchGate](https://www.researchgate.net) (after forum announcement, add new version as research item via the **code** category, be sure to include the corresponding new Zenodo DOI)
+  - [ ] [ResearchGate](https://www.researchgate.net) (after forum announcement; download the ZIP file of the new release from the release page and add it as research item via the **code** category, be sure to include the corresponding new Zenodo DOI)
+- [ ] Update release checklist template with any additional bullet points that may have arisen during the release
 
 ---
 

diff --git a/.github/ISSUE_TEMPLATE/5-bump_gmt_checklist.md b/.github/ISSUE_TEMPLATE/5-bump_gmt_checklist.md
@@ -1,6 +1,6 @@
 ---
 name: Bump GMT version checklist
-about: Checklist for bumping the minimum required GMT version.
+about: Checklist for bumping the minimum required GMT version. [For project maintainers only!]
 title: Bump to GMT X.Y.Z
 labels: maintenance
 assignees: ''

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -20,7 +20,6 @@ Fixes #
 - [ ] Write detailed docstrings for all functions/methods.
 - [ ] If wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
 - [ ] If adding new functionality, add an example to docstrings or tutorials.
-- [ ] Use underscores (not hyphens) in names of Python files and directories.
 
 **Slash Commands**
 

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
           condarc: |
@@ -58,14 +58,14 @@ jobs:
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
             gmt=6.5.0
-            python=3.12
+            python=3.13
             numpy
             pandas
             xarray
             netCDF4
             packaging
             geopandas
-            pyarrow
+            pyarrow-core
             pytest
             pytest-codspeed
             pytest-mpl
@@ -87,8 +87,8 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.1.0
+        uses: CodSpeedHQ/action@v3.2.0
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.
-          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed"
+          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed --override-ini addopts='--verbose'"
diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -43,15 +43,15 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
           condarc: |
             channels:
               - conda-forge
               - nodefaults
           create-args: >-
-            python=3.12
+            python=3.13
             gmt=6.5.0
             numpy
             pandas
@@ -76,7 +76,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v4.4.3
+        uses: actions/upload-artifact@v4.6.0
         with:
           name: gmt-cache
           include-hidden-files: true

diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -35,7 +35,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v2.0.2
+      uses: lycheeverse/lychee-action@v2.2.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md

diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -55,7 +55,7 @@ jobs:
         # Is it a draft Pull Request (true or false)?
         isDraft:
           - ${{ github.event.pull_request.draft }}
-        # Only run one job (Ubuntu + Python 3.12) for draft PRs
+        # Only run jobs on Ubuntu for draft PRs
         exclude:
           - os: macos-latest
             isDraft: true
@@ -80,7 +80,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
           condarc: |
@@ -92,7 +92,7 @@ jobs:
           # environment cache is persistent for one week.
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
-            python=3.12
+            python=3.13
             gmt=6.5.0
             ghostscript=10.04.0
             numpy
@@ -101,21 +101,25 @@ jobs:
             netCDF4
             packaging
             contextily
-            geopandas<1.0
+            geopandas
             ipython
-            pyarrow
+            pyarrow-core
             rioxarray
             make
             pip
             python-build
+            geodatasets
             myst-nb
             panel
-            sphinx
+            sphinx>=6.2
             sphinx-autodoc-typehints
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
             sphinx_rtd_theme<3.0
+            cairosvg
+            sphinxcontrib-svg2pdfconverter
+            tectonic
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -134,9 +138,11 @@ jobs:
           python -m build --sdist
           python -m pip install dist/*
 
-      # Build the documentation
-      - name: Build the documentation
-        run: make -C doc clean all
+      - name: Build the HTML documentation
+        run: make -C doc clean html
+
+      - name: Build the PDF documentation
+        run:  make -C doc pdf
 
       - name: Checkout the gh-pages branch
         uses: actions/[email protected]
@@ -162,9 +168,14 @@ jobs:
           # to get the right commit hash.
           message="Deploy $version from $(git rev-parse --short HEAD)"
           cd deploy
-          # Need to have this file so that GitHub doesn't try to run Jekyll
+          # Create some files in the root directory.
+          # .nojekyll: Need to have this file so that GitHub doesn't try to run Jekyll
           touch .nojekyll
-          # Delete all the files and replace with our new  set
+          # CNAME: Set the custom domain name
+          echo "www.pygmt.org" > CNAME
+          # index.html: Redirect to the latest version
+          echo '<meta http-equiv="Refresh" content="0;url=latest/"/>' > index.html
+          # Delete all the files and replace with our new set
           echo -e "\nRemoving old files from previous builds of ${version}:"
           rm -rvf ${version}
           echo -e "\nCopying HTML files to ${version}:"

diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -42,15 +42,15 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].1
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
           condarc: |
             channels:
               - conda-forge
               - nodefaults
           create-args: >-
-            python=3.12
+            python=3.13
             gmt=6.5.0
             numpy
             pandas
@@ -60,7 +60,7 @@ jobs:
             contextily
             geopandas
             ipython
-            pyarrow
+            pyarrow-core
             rioxarray
             make
             pip