Merge branch 'main' into refactor/meca-convention

Author: seisman

.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:

.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/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/[email protected].1
+        uses: actions/[email protected].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/[email protected].0
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |
@@ -87,8 +87,8 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.0.1
+        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

@@ -36,14 +36,14 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].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/[email protected].0
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/check-links.yml

@@ -23,19 +23,19 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v2.0.2
+      uses: lycheeverse/lychee-action@v2.1.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md

.github/workflows/ci_docs.yml

@@ -69,7 +69,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].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/[email protected].0
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |
@@ -101,20 +101,21 @@ jobs:
             netCDF4
             packaging
             contextily
-            geopandas<1.0
+            geopandas
             ipython
+            pyarrow
             rioxarray
             make
             pip
             python-build
             myst-nb
             panel
-            sphinx
+            sphinx>=6.2
             sphinx-autodoc-typehints
             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/[email protected].1
+        uses: actions/[email protected].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/[email protected].1
+        uses: actions/[email protected].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/[email protected].0
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |

.github/workflows/ci_tests.yaml

@@ -1,24 +1,26 @@
 # Test PyGMT on Linux/macOS/Windows
 #
-# This workflow runs regular PyGMT tests and uploads test coverage reports stored
-# in `.coverage.xml` to https://app.codecov.io/gh/GenericMappingTools/pygmt
-# via the [Codecov GitHub Action](https://github.com/codecov/codecov-action).
-# More codecov related configurations are stored in `.github/codecov.yml`.
-# If any tests fail, it also uploads the diff images as workflow artifacts.
+# This workflow runs regular PyGMT tests and uploads test coverage reports stored in
+# `.coverage.xml` to https://app.codecov.io/gh/GenericMappingTools/pygmt via the
+# [Codecov GitHub Action](https://github.com/codecov/codecov-action). More codecov
+# related configurations are stored in `.github/codecov.yml`. If any tests fail, it also
+# uploads the diff images as workflow artifacts.
 #
 # It is run:
 # 1. on every commit to the main branch
-# 2. on every commit to the pull request branches, unless the pull requests only
-#    contain non-code changes.
+# 2. on every commit to the pull request branches, unless the pull requests only contain
+#    non-code changes.
 # 3. when a new release is published
 #
 # It is also scheduled to run daily on the main branch.
 #
-# In draft pull request, only two jobs on Linux are triggered to save on
-# Continuous Integration resources:
+# In draft pull request, only jobs on Linux are triggered to save on Continuous
+# Integration resources:
 #
-# - Minimum supported Python, NumPy, pandas, Xarray versions following [SPEC 0](https://scientific-python.org/specs/spec-0000/)
-# - Latest Python, NumPy versions + optional packages (e.g. GeoPandas)
+# - Minimum supported Python + core packages (minimum supported versions)
+#   + optional packages (minimum supported versions if any)
+# - Latest Python + core packages (latest versions) + optional packages
+# - Last release before the latest Python + core packages
 #
 name: Tests
 
@@ -59,35 +61,32 @@ jobs:
         # Is it a draft Pull Request (true or false)?
         isDraft:
           - ${{ github.event.pull_request.draft }}
-        # Only run two jobs (Ubuntu + Python 3.10/3.12) for draft PRs
+        # Only run three jobs on Ubuntu for draft PRs
         exclude:
           - os: macos-latest
             isDraft: true
           - os: windows-latest
             isDraft: true
-        # Pair Python 3.10 with the minimum supported versions of NumPy, pandas, Xarray
-        # and Python 3.12 with the latest versions of NumPy, pandas, Xarray
-        # Only install optional packages on Python 3.12
         include:
+          # Python 3.10 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
           - python-version: '3.10'
             numpy-version: '1.24'
             pandas-version: '=2.0'
             xarray-version: '=2023.04'
-            optional-packages: ''
+            optional-packages: ' contextily geopandas<1 ipython pyarrow rioxarray sphinx-gallery'
+          # Python 3.12 + core packages (latest versions) + optional packages
           - python-version: '3.12'
             numpy-version: '2.1'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' contextily geopandas ipython pyarrow rioxarray sphinx-gallery'
-          # The job below is for testing GeoPandas v0.x on Ubuntu.
-          # The python-version here can't be the versions in the matrix.python-version
-          # defined above. Otherwise, other jobs will be overridden by this one.
+            optional-packages: ' contextily geopandas>=1.0 ipython pyarrow rioxarray sphinx-gallery'
+          # Python 3.11 + core packages (Linux only)
           - os: 'ubuntu-latest'
-            python-version: '3.11'  # Can't be 3.10 or 3.12.
-            numpy-version: '1.24'
+            python-version: '3.11'
+            numpy-version: ''
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' geopandas<1'
+            optional-packages: ''
 
     timeout-minutes: 30
     defaults:
@@ -103,7 +102,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -114,7 +113,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].0
+        uses: mamba-org/[email protected].2
         with:
           environment-name: pygmt
           condarc: |
@@ -143,7 +142,6 @@ jobs:
             pytest-doctestplus
             pytest-mpl
             pytest-rerunfailures
-            pytest-xdist
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -166,7 +164,7 @@ jobs:
 
       # Run the regular tests
       - name: Run tests
-        run: make test PYTEST_EXTRA="-r P -n auto --reruns 2"
+        run: make test PYTEST_EXTRA="-r P --reruns 2"
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
@@ -178,10 +176,10 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.7
         if: success() || failure()
         with:
           use_oidc: true
-          file: ./coverage.xml # optional
+          files: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY
           fail_ci_if_error: false