Merge branch 'main' into options

Author: seisman

.github/ISSUE_TEMPLATE/bump_gmt_checklist.md

@@ -7,8 +7,9 @@ assignees: ''
 
 ---
 
-:tada: [GMT X.Y.Z](https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z) has been released! It is installable from the
-[conda-forge channel](https://anaconda.org/conda-forge/gmt/files) using the following command:
+:tada: [GMT X.Y.Z](https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z) has been released!
+It is installable from the [conda-forge channel](https://anaconda.org/conda-forge/gmt/files)
+using the following command:
 
 `mamba install -c conda-forge gmt=X.Y.Z`
 
@@ -28,14 +29,15 @@ assignees: ''
   - [ ] Update GMT 6.x minor version for `extlinks` urls in `doc/conf.py`
   - [ ] Update GMT 6.x minor version in `.github/workflows/check-links.yml`
 - [ ] Fix failing tests (1 or more PRs)
+- [ ] Fix failing doctests reported in the ["Doctest" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
 - [ ] Fix [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
 
 **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 `test_get_default` in `pygmt/tests/test_clib.py`
-  - [ ] Update compatibility table in `README.rst`
+  - [ ] Update minimum required versions in `doc/minversions.md`
   - [ ] Remove unsupported GMT version from `.github/workflows/ci_tests_legacy.yaml`
 - [ ] Remove [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
 - [ ] Update deprecated syntax in source code and examples based on the [GMT Changelog](https://docs.generic-mapping-tools.org/latest/changes.html)

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -16,11 +16,12 @@ assignees: ''
 - [ ] Wrap Y ()
 
 **Before release**:
-- [ ] Check [NEP29](https://numpy.org/neps/nep-0029-deprecation_policy.html) to see if we need to bump the minimum Python and NumPy versions
+- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of 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 to ensure that:
   - [ ] 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
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
 - [ ] Finish up 'Changelog entry for v0.x.x' Pull Request:
@@ -30,8 +31,8 @@ assignees: ''
     - [ ] Update DOI (and url for BibTeX)
     - [ ] Update version
     - [ ] Update date released
-  - [ ] Add the documentation link https://github.com/GenericMappingTools/pygmt#compatibility-with-gmtpythonnumpy-versions
-  - [ ] Add compatibility information https://github.com/GenericMappingTools/pygmt#compatibility-with-gmtpythonnumpy-versions
+  - [ ] 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))
 
 **Release**:
@@ -47,7 +48,6 @@ assignees: ''
 - [ ] 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)
-  - [ ] [Twitter](https://twitter.com/gmt_dev) (after forum announcement)
 ---
 
 - [ ] Party :tada: (don't tick before all other checkboxes are ticked!)

.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/release-drafter.yml

@@ -53,7 +53,7 @@ template: |
 
   $CHANGES
 
-  **Full Changelog**: https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION
+  **Full Changelog**: <https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION>
 
   ### Contributors
 

.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}
@@ -59,14 +57,14 @@ 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
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v3.0.0
+        uses: dawidd6/action-download-artifact@v3.1.1
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -79,7 +77,7 @@ jobs:
           mkdir -p ~/.gmt
           mv .gmt/* ~/.gmt
           # Change modification times of the two files, so GMT won't refresh it
-          touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
+          touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
       # Install the package that we want to test
@@ -88,7 +86,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v2.0.2
+        uses: CodSpeedHQ/action@v2.1.1
         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'
@@ -38,7 +38,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.7.3
+        uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: pygmt
           condarc: |
@@ -47,7 +47,7 @@ jobs:
               - nodefaults
           create-args: >-
             python=3.12
-            gmt=6.4.0
+            gmt=6.5.0
             numpy
             pandas
             xarray
@@ -66,6 +66,9 @@ jobs:
         run: |
           python -c "from pygmt.helpers.caching import cache_data; cache_data()"
 
+      - name: List downloaded remote files
+        run: ls -lhR ~/.gmt
+
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
         uses: actions/upload-artifact@v4
@@ -74,3 +77,5 @@ jobs:
           path: |
               ~/.gmt/cache
               ~/.gmt/server
+              ~/.gmt/gmt_data_server.txt
+              ~/.gmt/gmt_hash_server.txt

.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@v1.9.3
       with:
         # 429: Too many requests
         args: >
@@ -47,29 +48,26 @@ 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"
           --exclude "^https://www.researchgate.net/project/"
           --exclude "^https://test.pypi.org/simple/"
-          --exclude "^https://twitter.com/"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"
           "repository/**/*.py"
           "documentation/dev/**/*.html"
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Get current date
       id: date
       run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
 
     - name: Create Issue From File
       if: env.lychee_exit_code != 0
-      uses: peter-evans/create-issue-from-file@v4
+      uses: peter-evans/create-issue-from-file@v5
       with:
         title: Link Checker Report on ${{ steps.date.outputs.date }}
         content-filepath: ./lychee/out.md

.github/workflows/ci_docs.yml

@@ -18,13 +18,22 @@ name: Docs
 on:
   push:
     branches: [ main ]
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - 'doc/**'
+      - 'examples/**'
+      - 'README.md'
+      - '.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.md'
+      - '.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:
@@ -65,7 +75,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.7.3
+        uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: pygmt
           condarc: |
@@ -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
@@ -101,7 +111,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v3.0.0
+        uses: dawidd6/action-download-artifact@v3.1.1
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -114,7 +124,7 @@ jobs:
           mkdir -p ~/.gmt
           mv .gmt/* ~/.gmt
           # Change modification times of the two files, so GMT won't refresh it
-          touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
+          touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
       # Install the package that we want to test

.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:
@@ -40,7 +41,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.7.3
+        uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: pygmt
           condarc: |
@@ -49,7 +50,7 @@ jobs:
               - nodefaults
           create-args: >-
             python=3.12
-            gmt=6.4.0
+            gmt=6.5.0
             numpy
             pandas
             xarray
@@ -69,7 +70,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v3.0.0
+        uses: dawidd6/action-download-artifact@v3.1.1
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -82,7 +83,7 @@ jobs:
           mkdir -p ~/.gmt
           mv .gmt/* ~/.gmt
           # Change modification times of the two files, so GMT won't refresh it
-          touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
+          touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
       # Install the package that we want to test