Merge branch 'refactor/data_kind' into refactor/virtualfile_in

Author: seisman

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -8,49 +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 [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)
-- [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
+- [ ] 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)
   - [ ] 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
+- [ ] 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"
-- [ ] 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
-    - [ ] Update authorship list
-    - [ ] Update DOI (and url for BibTeX)
-    - [ ] Update version
-    - [ ] Update date released
-  - [ ] 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))
+- [ ] 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 SPEC0 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)
+
 ---
 
 - [ ] Party :tada: (don't tick before all other checkboxes are ticked!)

.github/workflows/cache_data.yaml

@@ -58,7 +58,7 @@ jobs:
             xarray
             netCDF4
             packaging
-            build
+            python-build
 
       # Install the package that we want to test
       - name: Install the package
@@ -76,9 +76,10 @@ jobs:
 
       # 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

.github/workflows/check-links.yml

@@ -49,6 +49,8 @@ jobs:
           --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 "^https://github.com/GenericMappingTools/pygmt/releases/tag/%7B%7Bpath%7D%7D"
+          --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
           --exclude "^git"
           --exclude "^file://"
           --exclude "https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"

.github/workflows/ci_docs.yml

@@ -94,7 +94,7 @@ jobs:
           create-args: >-
             python=3.12
             gmt=6.5.0
-            ghostscript=10.03.1
+            ghostscript=10.04.0
             numpy
             pandas
             xarray
@@ -104,10 +104,10 @@ jobs:
             geopandas<1.0
             ipython
             rioxarray
-            build
             make
             pip
-            myst-parser
+            python-build
+            myst-nb
             panel
             sphinx
             sphinx-autodoc-typehints

.github/workflows/ci_doctests.yaml

@@ -62,9 +62,9 @@ jobs:
             ipython
             pyarrow
             rioxarray
-            build
             make
             pip
+            python-build
             pytest
             pytest-doctestplus
             pytest-mpl

.github/workflows/ci_tests.yaml

@@ -72,13 +72,22 @@ jobs:
           - python-version: '3.10'
             numpy-version: '1.24'
             pandas-version: '=1.5'
-            xarray-version: '=2022.06'
+            xarray-version: '=2022.09'
             optional-packages: ''
           - python-version: '3.12'
-            numpy-version: '2.0'
+            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.
+          - os: 'ubuntu-latest'
+            python-version: '3.11'  # Can't be 3.10 or 3.12.
+            numpy-version: '1.24'
+            pandas-version: ''
+            xarray-version: ''
+            optional-packages: ' geopandas<1'
 
     timeout-minutes: 30
     defaults:
@@ -119,16 +128,16 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}
             gmt=6.5.0
-            ghostscript=10.03.1
+            ghostscript=10.04.0
             numpy=${{ matrix.numpy-version }}
             pandas${{ matrix.pandas-version }}
             xarray${{ matrix.xarray-version }}
             netCDF4
             packaging
-            build
             dvc
             make
             pip
+            python-build
             pytest
             pytest-cov
             pytest-doctestplus
@@ -161,7 +170,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.0
         if: failure()
         with:
           name: artifact-${{ runner.os }}-${{ matrix.python-version }}

.github/workflows/ci_tests_dev.yaml

@@ -75,7 +75,7 @@ jobs:
             ninja
             curl
             fftw
-            ghostscript=10.03.1
+            ghostscript=10.04.0
             glib
             hdf5
             libblas
@@ -179,7 +179,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.0
         if: ${{ failure() }}
         with:
           name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}

.github/workflows/ci_tests_legacy.yaml

@@ -61,6 +61,7 @@ jobs:
           create-args: >-
             python=3.10
             gmt=${{ matrix.gmt_version }}
+            ghostscript<10
             numpy
             pandas<2
             xarray
@@ -72,9 +73,9 @@ jobs:
             pyarrow
             rioxarray
             sphinx-gallery
-            build
             make
             pip
+            python-build
             pytest
             pytest-doctestplus
             pytest-mpl

.github/workflows/format-command.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/create-github-app-token@v1.10.3
+      - uses: actions/create-github-app-token@v1.11.0
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}
@@ -25,7 +25,7 @@ jobs:
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/setup-python@v5.1.1
+      - uses: actions/setup-python@v5.2.0
         with:
           python-version: '3.12'
 

.github/workflows/publish-to-pypi.yml

@@ -51,7 +51,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v5.1.1
+      uses: actions/setup-python@v5.2.0
       with:
         python-version: '3.12'
 
@@ -75,10 +75,10 @@ jobs:
         ls -lh dist/
 
     - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.9.0
+      uses: pypa/gh-action-pypi-publish@v1.10.2
       with:
         repository-url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@v1.9.0
+      uses: pypa/gh-action-pypi-publish@v1.10.2