Merge branch 'main' into shift_origin-context-manager

.github/ISSUE_TEMPLATE/release_checklist.md → .github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -23,7 +23,10 @@ assignees: ''
   - [ ] 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
 - [ ] 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
@@ -43,7 +46,7 @@ assignees: ''
 - [ ] 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
 
 **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 NEP29 versions]
+- [ ] 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]
 - [ ] 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)

.github/ISSUE_TEMPLATE/bump_gmt_checklist.md → .github/ISSUE_TEMPLATE/5-bump_gmt_checklist.md

@@ -35,7 +35,7 @@ using the following command:
 **To-Do for bumping the minimum required GMT version**:
 
 - [ ] Bump the minimum required GMT version (1 PR)
-  - [ ] Update `required_version` in `pygmt/clib/session.py`
+  - [ ] Update `required_gmt_version` in `pygmt/clib/__init__.py`
   - [ ] Update `test_get_default` in `pygmt/tests/test_clib.py`
   - [ ] Update minimum required versions in `doc/minversions.md`
   - [ ] Remove unsupported GMT version from `.github/workflows/ci_tests_legacy.yaml`

.github/dependabot.yml

@@ -6,7 +6,7 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      # Check for updates to GitHub Actions every weekday
+      # Check for updates to GitHub Actions on Tuesdays
       interval: "weekly"
       day: "tuesday"
     # Allow up to 2 open pull requests at a time

.github/workflows/benchmarks.yml

@@ -1,7 +1,7 @@
 # Run performance benchmarks
 #
-# Continuous benchmarking using pytest-codspeed. Measures the execution speed
-# of tests marked with @pytest.mark.benchmark decorator.
+# Continuous benchmarking using pytest-codspeed. Measures the execution speed of tests
+# marked with @pytest.mark.benchmark decorator.
 
 name: Benchmarks
 
@@ -15,12 +15,9 @@ on:
   # Run in PRs but only if the PR has the 'run/benchmark' label
   pull_request:
     types: [ opened, reopened, labeled, synchronize ]
-  # `workflow_dispatch` allows CodSpeed to trigger backtest
-  # performance analysis in order to generate initial data.
+  # 'workflow_dispatch' allows CodSpeed to trigger backtest performance analysis
+  # in order to generate initial data.
   workflow_dispatch:
-  release:
-    types:
-      - published
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -37,59 +34,61 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Install Miniconda with conda-forge dependencies
-      - name: Setup Miniconda
-        uses: conda-incubator/[email protected]
-        with:
-          auto-activate-base: true
-          activate-environment: ""  # base environment
-          channels: conda-forge,nodefaults
-          channel-priority: strict
+      - name: Get current week number of year
+        id: date
+        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT  # e.g., 2024-W19
 
-      # Install GMT and dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          # $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 >> $GITHUB_PATH
-          conda install --solver=libmamba gmt=6.5.0 python=3.12 \
-                        numpy pandas xarray netCDF4 packaging \
-                        geopandas pyarrow pytest pytest-mpl
-          python -m pip install -U pytest-codspeed setuptools
+      # Install Micromamba with conda-forge dependencies
+      - name: Setup Micromamba
+        uses: mamba-org/[email protected]
+        with:
+          environment-name: pygmt
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+          cache-downloads: false
+          cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
+          create-args: >-
+            gmt=6.5.0
+            python=3.12
+            numpy
+            pandas
+            xarray
+            netCDF4
+            packaging
+            geopandas
+            pyarrow
+            pytest
+            pytest-codspeed
+            pytest-mpl
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/[email protected]
-        with:
-          workflow: cache_data.yaml
-          workflow_conclusion: success
-          name: gmt-cache
-          path: .gmt
-
-      # Move downloaded files to ~/.gmt directory and list them
-      - name: Move and list downloaded remote files
         run: |
-          mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          # Download cached files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package
         run: make install
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v2.2.1
+        uses: CodSpeedHQ/action@v3.0.0
         with:
-          run: |
-            python -c "import pygmt; pygmt.show_versions()"
-            PYGMT_USE_EXTERNAL_DISPLAY="false" python -m pytest -r P --pyargs pygmt --codspeed
-        env:
-          GMT_LIBRARY_PATH: /usr/share/miniconda/lib/
+          # '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"

.github/workflows/cache_data.yaml

@@ -1,12 +1,16 @@
 # Cache GMT remote data files and upload as artifacts
 #
-# This workflow downloads data files needed by PyGMT tests/documentation from
-# the GMT data server and uploads as workflow artifacts which can be accessed
-# by other GitHub Actions workflows.
+# This workflow downloads data files needed by PyGMT tests/documentation from the GMT
+# data server and uploads them as workflow artifacts, which can then be accessed 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 the
-# 'pygmt/helpers/caching.py' file to refresh the cache.
+# It is scheduled to run every Sunday at 12:00 (UTC). If new remote files are needed
+# urgently, maintainers can refresh the cache by one of the following methods:
+#
+# 1. Update this workflow file
+# 2. Update the `pygmt/helpers/caching.py` file
+# 3. Go to https://github.com/GenericMappingTools/pygmt/actions/workflows/cache_data.yaml
+#    and click the "Run workflow" button
 #
 name: Cache data
 
@@ -16,6 +20,7 @@ on:
     paths:
       - 'pygmt/helpers/caching.py'
       - '.github/workflows/cache_data.yaml'
+  workflow_dispatch:
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -31,14 +36,14 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
         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@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-name: pygmt
           condarc: |
@@ -75,7 +80,7 @@ jobs:
         with:
           name: gmt-cache
           path: |
-              ~/.gmt/cache
-              ~/.gmt/server
-              ~/.gmt/gmt_data_server.txt
-              ~/.gmt/gmt_hash_server.txt
+            ~/.gmt/cache
+            ~/.gmt/server
+            ~/.gmt/gmt_data_server.txt
+            ~/.gmt/gmt_hash_server.txt

.github/workflows/check-links.yml

@@ -10,6 +10,7 @@ name: Check Links
 on:
   # Uncomment the 'pull_request' line below to trigger the workflow in PR
   # pull_request:
+  workflow_dispatch:
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -22,38 +23,41 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].1
+      uses: actions/[email protected].7
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].1
+      uses: actions/[email protected].7
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.9.3
+      uses: lycheeverse/lychee-action@v1.10.0
       with:
+        output: /tmp/lychee-out.md
         # 429: Too many requests
         args: >
           --accept 429
-          --exclude-mail
           --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]*$"
           --exclude "^https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z$"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/edit"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/new"
           --exclude "^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/project/"
+          --exclude "^https://www.researchgate.net/"
           --exclude "^https://test.pypi.org/simple/"
           --verbose
           "repository/**/*.rst"
@@ -67,7 +71,9 @@ jobs:
 
     - name: Create Issue From File
       if: env.lychee_exit_code != 0
-      uses: peter-evans/create-issue-from-file@v5
-      with:
-        title: Link Checker Report on ${{ steps.date.outputs.date }}
-        content-filepath: ./lychee/out.md
+      run: |
+        cd repository/
+        title="Link Checker Report on ${{ steps.date.outputs.date }}"
+        gh issue create --title "$title" --body-file /tmp/lychee-out.md
+      env:
+        GH_TOKEN: ${{ github.token }}

.github/workflows/ci_docs.yml

@@ -34,6 +34,7 @@ on:
       - 'examples/**'
       - 'README.md'
       - '.github/workflows/ci_docs.yml'
+  workflow_dispatch:
   release:
     types:
       - published
@@ -68,14 +69,18 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
+      - name: Get current week number of year
+        id: date
+        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT  # e.g., 2024-W19
+
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.8.0
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-name: pygmt
           condarc: |
@@ -84,17 +89,19 @@ jobs:
               - nodefaults
           cache-downloads: false
           cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
             python=3.12
             gmt=6.5.0
-            ghostscript=10.02.1
+            ghostscript=10.03.1
             numpy
             pandas
             xarray
             netCDF4
             packaging
             contextily
-            geopandas
+            geopandas<1.0
             ipython
             rioxarray
             build
@@ -111,21 +118,14 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/[email protected]
-        with:
-          workflow: cache_data.yaml
-          workflow_conclusion: success
-          name: gmt-cache
-          path: .gmt
-
-      # Move downloaded files to ~/.gmt directory and list them
-      - name: Move and list downloaded remote files
         run: |
-          mkdir -p ~/.gmt
-          mv .gmt/* ~/.gmt
+          # Download cached files to ~/.gmt directory and list them
+          gh run download --name gmt-cache --dir ~/.gmt/
           # Change modification times of the two files, so GMT won't refresh it
           touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       # Install the package that we want to test
       - name: Install the package
@@ -138,7 +138,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one
@@ -161,7 +161,7 @@ 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
+          # 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
           echo -e "\nRemoving old files from previous builds of ${version}:"