Merge branch 'main' into pyarrow/string

Author: weiji14

.github/ISSUE_TEMPLATE/bug_report.yaml renamed to .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/feature_request.yaml renamed to .github/ISSUE_TEMPLATE/2-feature_request.yaml

@@ -8,46 +8,51 @@ assignees: ''
 ---
 
 **Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
-**Scheduled Date**: YYYY/MM/DD
-**Pull request due date**: YYYY/MM/DD
+**Scheduled Date**: 20YY/MM/DD
+**Pull request due date**: 20YY/MM/DD
+**DOI**: `10.5281/zenodo.XXXXXXX`
 
 **Priority PRs/issues to complete prior to release**
+
 - [ ] Wrap X ()
 - [ ] 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
-- [ ] 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 [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
   - [ ] 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)
-  - [ ] 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
+  - [ ] All tests pass in the ["Doctests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
+- [ ] Update warnings in `pygmt/_show_versions.py` as well as notes in
+      [Not working transparency](https://www.pygmt.org/dev/install.html#not-working-transparency)
+      regarding GMT-Ghostscript incompatibility
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
-- [ ] 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
-    - [ ] Update authorship list
-    - [ ] 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
-  - [ ] 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))
+- [ ] Finish up the "Changelog entry for v0.x.x" Pull Request (Use the previous changelog PR as a reference)
+- [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
+- [ ] Draft the announcement on https://hackmd.io/@pygmt
 
 **Release**:
+
 - [ ] At the [PyGMT release page on GitHub](https://github.com/GenericMappingTools/pygmt/releases):
   - [ ] Edit the draft release notes with the finalized changelog
   - [ ] Set the tag version and release title to vX.Y.Z
   - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
-- [ ] 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
+- [ ] Download pygmt-X.Y.Z.zip (rename to pygmt-vX.Y.Z.zip) and baseline-images.zip from
+      the release page, and upload the two zip files to https://zenodo.org/deposit,
+      ensure that they are 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. Remember to pin Python and 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)
+  - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! 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/ISSUE_TEMPLATE/module_request.yaml renamed to .github/ISSUE_TEMPLATE/3-module_request.yaml

@@ -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 `required_gmt_version` in `pygmt/clib/__init__.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 renamed to .github/ISSUE_TEMPLATE/4-release_checklist.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/ISSUE_TEMPLATE/bump_gmt_checklist.md renamed to .github/ISSUE_TEMPLATE/5-bump_gmt_checklist.md

@@ -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/PULL_REQUEST_TEMPLATE.md

@@ -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/dependabot.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
 
@@ -11,19 +11,13 @@ 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'
-  # `workflow_dispatch` allows CodSpeed to trigger backtest
-  # performance analysis in order to generate initial data.
+    types: [ opened, reopened, labeled, synchronize ]
+  # '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 }}
@@ -32,66 +26,69 @@ 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}
 
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.2.0
         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 >> $GITHUB_PATH
-          conda install --solver=libmamba gmt=6.4.0 python=3.12 \
-                        numpy pandas xarray netCDF4 packaging \
-                        geopandas pytest pytest-benchmark pytest-mpl
-          python -m pip install -U pytest-codspeed setuptools
+      # Install Micromamba with conda-forge dependencies
+      - name: Setup Micromamba
+        uses: mamba-org/[email protected]
+        with:
+          environment-name: pygmt
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+          cache-downloads: false
+          cache-environment: true
+          # environment cache is persistent for one week.
+          cache-environment-key: micromamba-environment-${{ 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/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
+        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@v2.0.2
+        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/release-drafter.yml

@@ -1,18 +1,26 @@
-# Cache GMT remote data files and uploads as artifacts
+# 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 manually uncomment the 'pull_request:' line
-# below 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
 
 on:
-  # Uncomment the 'pull_request' line below to manually re-cache data artifacts
-  # pull_request:
+  pull_request:
+    # Make any changes to the following files to refresh the cache in PRs
+    paths:
+      - 'pygmt/helpers/caching.py'
+      - '.github/workflows/cache_data.yaml'
+  workflow_dispatch:
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -28,14 +36,14 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.2.0
         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@v1.7.3
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           environment-name: pygmt
           condarc: |
@@ -44,13 +52,13 @@ jobs:
               - nodefaults
           create-args: >-
             python=3.12
-            gmt=6.4.0
+            gmt=6.5.0
             numpy
             pandas
             xarray
             netCDF4
             packaging
-            build
+            python-build
 
       # Install the package that we want to test
       - name: Install the package
@@ -61,13 +69,19 @@ jobs:
       # Download remote files
       - name: Download remote data
         run: |
-          python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
+          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
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: gmt-cache
+          include-hidden-files: true
           path: |
-              ~/.gmt/cache
-              ~/.gmt/server
+            ~/.gmt/cache
+            ~/.gmt/server
+            ~/.gmt/gmt_data_server.txt
+            ~/.gmt/gmt_hash_server.txt