Merge branch 'main' into alias-system

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

@@ -23,7 +23,7 @@ body:
         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

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -19,7 +19,8 @@ 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)
 - [ ] 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

.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.

.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
@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
@@ -87,8 +87,8 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.0.0
+        uses: CodSpeedHQ/action@v3.1.0
         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

@@ -36,14 +36,14 @@ 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@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
@@ -76,7 +76,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: gmt-cache
           include-hidden-files: true

.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@v2.1.0
       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"

.github/workflows/ci_docs.yml

@@ -69,7 +69,7 @@ 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
@@ -80,7 +80,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.9.0
+        uses: mamba-org/setup-micromamba@v2.0.1
         with:
           environment-name: pygmt
           condarc: |
@@ -103,6 +103,7 @@ jobs:
             contextily
             geopandas<1.0
             ipython
+            pyarrow
             rioxarray
             make
             pip
@@ -114,7 +115,7 @@ jobs:
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
-            sphinx_rtd_theme
+            sphinx_rtd_theme<3.0
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -138,7 +139,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.2
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_doctests.yaml

@@ -35,14 +35,14 @@ 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@v2.0.1
         with:
           environment-name: pygmt
           condarc: |