Merge branch 'main' into alias/function

Author: seisman

.github/PULL_REQUEST_TEMPLATE.md

@@ -21,7 +21,6 @@ Fixes #
 **Slash Commands**
 
 You can write slash commands (`/command`) in the first line of a comment to perform
-specific operations. Supported slash commands are:
+specific operations. Supported slash command is:
 
 - `/format`: automatically format and lint the code
-- `/test-gmt-dev`: run full tests on the latest GMT development version

.github/workflows/benchmarks.yml

@@ -11,13 +11,10 @@ on:
     branches: [ main ]
     paths:
       - 'pygmt/**/*.py'
-      - '!pygmt/tests/**'
       - '.github/workflows/benchmarks.yml'
+  # Run in PRs but only if the PR has the 'run/benchmark' label
   pull_request:
-    paths:
-      - 'pygmt/**/*.py'
-      - '!pygmt/tests/**'
-      - '.github/workflows/benchmarks.yml'
+    types: [ opened, reopened, labeled, synchronize ]
   # `workflow_dispatch` allows CodSpeed to trigger backtest
   # performance analysis in order to generate initial data.
   workflow_dispatch:
@@ -32,6 +29,7 @@ concurrency:
 jobs:
   benchmarks:
     runs-on: ubuntu-22.04
+    if: github.repository == 'GenericMappingTools/pygmt' && (github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/benchmark'))
     defaults:
       run:
         shell: bash -l {0}
@@ -59,9 +57,9 @@ jobs:
           # $CONDA is an environment variable pointing to the root of the miniconda directory
           # Preprend $CONDA/bin to $PATH so that conda's python is used over system python
           echo $CONDA/bin >> $GITHUB_PATH
-          conda install --solver=libmamba gmt=6.4.0 python=3.12 \
+          conda install --solver=libmamba gmt=6.5.0 python=3.12 \
                         numpy pandas xarray netCDF4 packaging \
-                        geopandas pytest pytest-mpl
+                        geopandas pyarrow pytest pytest-mpl
           python -m pip install -U pytest-codspeed setuptools
 
       # Download cached remote files (artifacts) from GitHub
@@ -88,7 +86,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/[email protected].2
+        uses: CodSpeedHQ/[email protected].3
         with:
           run: |
             python -c "import pygmt; pygmt.show_versions()"

.github/workflows/cache_data.yaml

@@ -5,14 +5,14 @@
 # by other GitHub Actions workflows.
 #
 # It is scheduled to run every Sunday at 12:00 (UTC). If new remote files are
-# needed urgently, maintainers can update the workflow file or
+# needed urgently, maintainers can update the workflow file or the
 # 'pygmt/helpers/caching.py' file to refresh the cache.
 #
 name: Cache data
 
 on:
   pull_request:
-    # Make any changes to the following files to refresh the cache
+    # Make any changes to the following files to refresh the cache in PRs
     paths:
       - 'pygmt/helpers/caching.py'
       - '.github/workflows/cache_data.yaml'
@@ -47,7 +47,7 @@ jobs:
               - nodefaults
           create-args: >-
             python=3.12
-            gmt=6.4.0
+            gmt=6.5.0
             numpy
             pandas
             xarray

.github/workflows/check-links.yml

@@ -18,6 +18,7 @@ jobs:
   check_links:
     name: Check Links
     runs-on: ubuntu-latest
+    if: github.repository == 'GenericMappingTools/pygmt'
 
     steps:
     - name: Checkout the repository
@@ -33,7 +34,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.8.0
+      uses: lycheeverse/lychee-action@v1.9.0
       with:
         # 429: Too many requests
         args: >
@@ -47,8 +48,8 @@ jobs:
           --exclude "^https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z$"
           --exclude "^git"
           --exclude "^file://"
-          --exclude "^https://docs.generic-mapping-tools.org/6.4/%s$"
-          --exclude "^https://docs.generic-mapping-tools.org/6.4/%3Cmodule-name%3E.html$"
+          --exclude "^https://docs.generic-mapping-tools.org/6.5/%s$"
+          --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"
@@ -60,8 +61,6 @@ jobs:
           "repository/**/*.md"
           "repository/**/*.py"
           "documentation/dev/**/*.html"
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Get current date
       id: date

.github/workflows/ci_docs.yml

@@ -18,13 +18,22 @@ name: Docs
 on:
   push:
     branches: [ main ]
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - 'doc/**'
+      - 'examples/**'
+      - 'README.rst'
+      - '.github/workflows/ci_docs.yml'
   pull_request:
     types: [opened, reopened, synchronize, ready_for_review]
-    paths-ignore:
-      - 'pygmt/tests/**'
-      - '*.md'
-      - 'LICENSE.txt'
-      - '.gitignore'
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - 'doc/**'
+      - 'examples/**'
+      - 'README.rst'
+      - '.github/workflows/ci_docs.yml'
   release:
     types:
       - published
@@ -37,6 +46,7 @@ jobs:
   docs:
     name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
+    if: github.repository == 'GenericMappingTools/pygmt'
     strategy:
       fail-fast: false
       matrix:
@@ -76,8 +86,8 @@ jobs:
           cache-environment: true
           create-args: >-
             python=3.12
-            gmt=6.4.0
-            ghostscript=9.54.0
+            gmt=6.5.0
+            ghostscript=10.02.1
             numpy
             pandas
             xarray

.github/workflows/ci_doctests.yaml

@@ -21,6 +21,7 @@ jobs:
   test:
     name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
+    if: github.repository == 'GenericMappingTools/pygmt'
     strategy:
       fail-fast: false
       matrix:
@@ -49,7 +50,7 @@ jobs:
               - nodefaults
           create-args: >-
             python=3.12
-            gmt=6.4.0
+            gmt=6.5.0
             numpy
             pandas
             xarray

.github/workflows/ci_tests.yaml

@@ -25,15 +25,14 @@ name: Tests
 on:
   push:
     branches: [ main ]
+    paths:
+      - 'pygmt/**'
+      - '.github/workflows/ci_tests.yaml'
   pull_request:
     types: [opened, reopened, synchronize, ready_for_review]
-    paths-ignore:
-      - 'doc/**'
-      - 'examples/**'
-      - '*.md'
-      - 'README.rst'
-      - 'LICENSE.txt'
-      - '.gitignore'
+    paths:
+      - 'pygmt/**'
+      - '.github/workflows/ci_tests.yaml'
   release:
     types:
       - published
@@ -105,8 +104,8 @@ jobs:
           cache-environment: true
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}
-            gmt=6.4.0
-            ghostscript=9.54.0
+            gmt=6.5.0
+            ghostscript=10.02.1
             numpy=${{ matrix.numpy-version }}
             pandas
             xarray

.github/workflows/ci_tests_dev.yaml

@@ -1,31 +1,25 @@
 # Test PyGMT with GMT dev version on Linux/macOS/Windows
 #
-# This workflow runs regular PyGMT tests with the GMT dev version, and also
-# pre-release versions of several dependencies like NumPy, Pandas, Xarray, etc.
-# If any tests fail, it also uploads the diff images as workflow artifacts.
-# The GMT dev version is installed by fetching the latest source codes from
-# the GMT master branch and compiling.
+# This workflow runs regular PyGMT tests with the GMT dev version, and also pre-release
+# versions of several dependencies like NumPy, Pandas, Xarray, etc. If any tests fail,
+# it also uploads the diff images as workflow artifacts. The GMT dev version is
+# installed by fetching the latest source codes from the GMT master branch and
+# compiling.
 #
-# It is triggered when a pull request is marked as "ready as review", or using
-# the slash command `/test-gmt-dev`. It is also scheduled to run on Monday,
-# Wednesday, and Friday on the main branch.
+# It is triggered when a pull request is marked as "ready as review", or labeled with
+# 'run/test-gmt-dev'. It is also scheduled to run on Monday, Wednesday, and Friday on
+# the main branch.
 #
 name: GMT Dev Tests
 
 on:
   # push:
   #   branches: [ main ]
   pull_request:
-    types: [ready_for_review]
-    paths-ignore:
-      - 'doc/**'
-      - 'examples/**'
-      - '*.md'
-      - 'README.rst'
-      - 'LICENSE.txt'
-      - '.gitignore'
-  repository_dispatch:
-    types: [test-gmt-dev-command]
+    types: [ opened, reopened, labeled, synchronize ]
+    paths:
+      - 'pygmt/**'
+      - '.github/workflows/ci_tests_dev.yaml'
   # Schedule tests on Monday/Wednesday/Friday
   schedule:
     - cron: '0 0 * * 1,3,5'
@@ -38,6 +32,7 @@ jobs:
   test_gmt_dev:
     name: ${{ matrix.os }} - GMT ${{ matrix.gmt_git_ref }}
     runs-on: ${{ matrix.os }}
+    if: github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/test-gmt-dev')
     strategy:
       fail-fast: false
       matrix:
@@ -52,40 +47,10 @@ jobs:
       # Checkout current git repository
       - name: Checkout
         uses: actions/[email protected]
-        if: github.event_name != 'repository_dispatch'
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Generate token from GenericMappingTools bot
-      - name: Generate token from GenericMappingTools bot
-        uses: tibdex/github-app-token@v2
-        if: github.event_name == 'repository_dispatch'
-        id: generate-token
-        with:
-          app_id: ${{ secrets.APP_ID }}
-          private_key: ${{ secrets.APP_PRIVATE_KEY }}
-
-      # Checkout the pull request branch
-      - name: Checkout
-        uses: actions/[email protected]
-        if: github.event_name == 'repository_dispatch'
-        with:
-          token: ${{ steps.generate-token.outputs.token }}
-          repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.client_payload.pull_request.head.ref }}
-          # fetch all history so that setuptools-scm works
-          fetch-depth: 0
-
-      - name: Show job URL
-        uses: peter-evans/[email protected]
-        if: github.event_name == 'repository_dispatch' && (matrix.os == 'ubuntu-latest')
-        with:
-          token: ${{ steps.generate-token.outputs.token }}
-          repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
-          comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
-          body: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
-
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
         uses: mamba-org/[email protected]
@@ -104,7 +69,7 @@ jobs:
             ninja
             curl
             fftw
-            ghostscript=9.54.0
+            ghostscript=10.02.1
             glib
             hdf5
             libblas

.github/workflows/ci_tests_legacy.yaml

@@ -11,15 +11,12 @@ name: GMT Legacy Tests
 on:
   # push:
   #   branches: [ main ]
+  # Uncomment the 'pull_request' line below to trigger the workflow in PR
   # pull_request:
     # types: [ready_for_review]
-    # paths-ignore:
-    #  - 'doc/**'
-    #  - 'examples/**'
-    #  - '*.md'
-    #  - 'README.rst'
-    #  - 'LICENSE.txt'
-    #  - '.gitignore'
+    # paths:
+    #  - 'pygmt/**'
+    #  - '.github/workflows/ci_tests_legacy.yaml'
   # Schedule tests on Tuesday
   schedule:
     - cron: '0 0 * * 2'
@@ -32,11 +29,12 @@ jobs:
   test:
     name: ${{ matrix.os }} - GMT ${{ matrix.gmt_version }}
     runs-on: ${{ matrix.os }}
+    if: github.repository == 'GenericMappingTools/pygmt'
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, macos-11, windows-2019]
-        gmt_version: ['6.3']
+        gmt_version: ['6.3', '6.4']
     timeout-minutes: 30
     defaults:
       run:

.github/workflows/format-command.yml

@@ -32,7 +32,7 @@ jobs:
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          python -m pip install docformatter ruff
+          python -m pip install ruff
           python -m pip list
           sudo apt-get install dos2unix