Merge branch 'main' into states/figure

Author: seisman

.dvcignore

@@ -1,3 +1,2 @@
-# Add patterns of files dvc should ignore, which could improve
-# the performance. Learn more at
-# https://dvc.org/doc/user-guide/dvcignore
+# Add patterns of files dvc should ignore, which could improve the performance.
+# Learn more at https://dvc.org/doc/user-guide/project-structure/dvcignore-files

.github/ISSUE_TEMPLATE/1-bug_report.yaml

@@ -1,29 +1,31 @@
 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](http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+
+        - [Craft Minimal Bug Reports](https://matthewrocklin.com/minimal-bug-reports)
 
       placeholder: "PASTE CODE HERE"
       render: python
@@ -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:

.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"

.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).

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -1,56 +1,55 @@
 ---
 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: ''
 
 ---
 
 **Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
-**Scheduled Date**: YYYY/MM/DD
-**Pull request due date**: YYYY/MM/DD
+**Scheduled Date**: 20YY/MM/DD
+**Pull request due date**: 20YY/MM/DD
+**DOI**: `10.5281/zenodo.XXXXXXX`
 
 **Priority PRs/issues to complete prior to release**
+
 - [ ] Wrap X ()
 - [ ] Wrap Y ()
 
 **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)
-- [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
+
+- [ ] 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:
+  - [ ] 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)
-  - [ ] Deprecations and related tests are removed for this version by running `grep --include="*.py" -r 'remove_version="vX.Y.Z"' pygmt` from the base of the repository
-- [ ] Update warnings in `pygmt.show_versions()` as well as notes in [Common installation issues](https://www.pygmt.org/dev/install.html#not-working-transparency)
-      and [Testing your install]((https://www.pygmt.org/dev/install.html#testing-your-install) 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"
-- [ ] Review the ["PyGMT Team" page](https://www.pygmt.org/dev/team.html)
-- [ ] Finish up 'Changelog entry for v0.x.x' Pull Request:
-  - [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
-  - [ ] Update `CITATION.cff` and BibTeX at https://github.com/GenericMappingTools/pygmt#citing-pygmt
-    - [ ] Update authorship list
-    - [ ] Update DOI (and url for BibTeX)
-    - [ ] Update version
-    - [ ] Update date released
-  - [ ] Add the documentation link `doc/minversions.md`
-  - [ ] Add minimum required version information `doc/minversions.md`
-  - [ ] Copy draft changelog from Release Drafter and edit it to look nice ([see maintainers guide for details](https://www.pygmt.org/dev/maintenance.html#updating-the-changelog))
+- [ ] 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`
+- [ ] Draft the announcement on https://hackmd.io/@pygmt
 
 **Release**:
+
 - [ ] At the [PyGMT release page on GitHub](https://github.com/GenericMappingTools/pygmt/releases):
   - [ ] 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
-- [ ] Manually upload the pygmt-vX.Y.Z.zip and baseline-images.zip files to https://zenodo.org/deposit, ensure that it is 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, but remember to pin 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! draft on https://hackmd.io/@pygmt. 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)
+  - [ ] 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; 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
+
 ---
 
 - [ ] Party :tada: (don't tick before all other checkboxes are ticked!)

.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: ''

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,6 +8,10 @@
 Fixes #
 
 
+<!-- If significant changes to the documentation are made, please insert the link to the documentation page after it has been built. -->
+**Preview**:
+
+
 **Reminders**
 
 - [ ] Run `make format` and `make check` to make sure the code follows the style guide.
@@ -16,7 +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**
 

.github/release-drafter.yml

@@ -24,6 +24,8 @@ exclude-contributors:
   - 'actions-bot'
   - 'dependabot'
   - 'dependabot[bot]'
+  - 'pre-commit-ci'
+  - 'pre-commit-ci[bot]'
 category-template: '### $TITLE'
 change-template: '* $TITLE ([#$NUMBER]($URL))'
 sort-by: 'title'

.github/workflows/benchmarks.yml

@@ -25,7 +25,7 @@ concurrency:
 
 jobs:
   benchmarks:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     if: github.repository == 'GenericMappingTools/pygmt' && (github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/benchmark'))
     defaults:
       run:
@@ -34,7 +34,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -45,27 +45,22 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
-          cache-downloads: false
           cache-environment: true
           # environment cache is persistent for one week.
           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 +82,8 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.0.0
+        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'"

.github/workflows/cache_data.yaml

@@ -36,22 +36,18 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
           create-args: >-
-            python=3.12
+            python=3.13
             gmt=6.5.0
             numpy
             pandas
@@ -76,9 +72,10 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.6.0
         with:
           name: gmt-cache
+          include-hidden-files: true
           path: |
             ~/.gmt/cache
             ~/.gmt/server

.github/workflows/check-links.yml

@@ -23,44 +23,41 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.2
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.2
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.10.0
+      uses: lycheeverse/lychee-action@v2.3.0
       with:
+        fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md
         # 429: Too many requests
         args: >
           --accept 429
-          --exclude "^https://doi.org/10.5281/zenodo$"
-          --exclude "^https://zenodo.org/badge/DOI/$"
-          --exclude "^https://zenodo.org/badge/DOI/10.5281/zenodo$"
-          --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
-          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
+          --exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%s$"
+          --exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%3Cmodule-name%3E.html$"
+          --exclude "^https://doi.org"
           --exclude "^https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/edit"
           --exclude "^https://github.com/GenericMappingTools/pygmt/issues/new"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/releases/tag/%7B%7Bpath%7D%7D"
-          --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
-          --exclude "^git"
-          --exclude "^file://"
-          --exclude "https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
-          --exclude "^https://docs.generic-mapping-tools.org/6.5/%s$"
-          --exclude "^https://docs.generic-mapping-tools.org/6.5/%3Cmodule-name%3E.html$"
-          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
           --exclude "^https://hackmd.io/@pygmt"
-          --exclude "^https://doi.org"
-          --exclude "^https://www.researchgate.net/"
           --exclude "^https://test.pypi.org/simple/"
+          --exclude "^https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
+          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
+          --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
+          --exclude "^https://www.researchgate.net/"
+          --exclude "^https://zenodo.org/badge/DOI/"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"