Merge branch 'main' into datatypes/gmtcube

GenericMappingTools · Sep 19, 2024 · 9b87e6d · 9b87e6d
2 parents 087912d + 5196ae6
commit 9b87e6d
Show file tree

Hide file tree

Showing 70 changed files with 1,151 additions and 654 deletions.
diff --git a/.github/ISSUE_TEMPLATE/4-release_checklist.md b/.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!)
diff --git a/.github/workflows/cache_data.yaml b/.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

diff --git a/.github/workflows/ci_docs.yml b/.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
@@ -104,9 +104,9 @@ jobs:
             geopandas<1.0
             ipython
             rioxarray
-            build
             make
             pip
+            python-build
             myst-nb
             panel
             sphinx

diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -62,9 +62,9 @@ jobs:
             ipython
             pyarrow
             rioxarray
-            build
             make
             pip
+            python-build
             pytest
             pytest-doctestplus
             pytest-mpl

diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -119,16 +119,16 @@ 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 +161,7 @@ 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 }}

diff --git a/.github/workflows/ci_tests_dev.yaml b/.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 }}

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
@@ -72,9 +72,9 @@ jobs:
             pyarrow
             rioxarray
             sphinx-gallery
-            build
             make
             pip
+            python-build
             pytest
             pytest-doctestplus
             pytest-mpl

diff --git a/.github/workflows/format-command.yml b/.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'
 

diff --git a/.github/workflows/publish-to-pypi.yml b/.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@v1.10.1
       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@v1.10.1
diff --git a/.github/workflows/slash-command-dispatch.yml b/.github/workflows/slash-command-dispatch.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Slash Command Dispatch
-        uses: peter-evans/slash-command-dispatch@v4
+        uses: peter-evans/slash-command-dispatch@v4.0.0
         with:
           token: ${{ github.token }}
           commands: |

diff --git a/.github/workflows/style_checks.yaml b/.github/workflows/style_checks.yaml
@@ -28,7 +28,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.1.1
+        uses: actions/setup-python@v5.2.0
         with:
           python-version: '3.12'
 

diff --git a/.github/workflows/type_checks.yml b/.github/workflows/type_checks.yml
@@ -37,7 +37,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.1.1
+        uses: actions/setup-python@v5.2.0
         with:
           python-version: '3.12'
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,3 +15,9 @@ repos:
     - id: remove-crlf
     - id: chmod
       args: ['644']
+
+# https://pre-commit.ci/#configuration
+ci:
+  skip: [chmod]
+  autofix_prs: false
+  autoupdate_schedule: quarterly
diff --git a/CITATION.cff b/CITATION.cff
@@ -76,9 +76,9 @@ authors:
   family-names: Wessel
   affiliation: University of Hawaiʻi at Mānoa, USA
   orcid: https://orcid.org/0000-0001-5708-7336
-date-released: 2024-05-01
-doi: 10.5281/zenodo.11062720
+date-released: 2024-09-05
+doi: 10.5281/zenodo.13679420
 license: BSD-3-Clause
 repository-code: https://github.com/GenericMappingTools/pygmt
 type: software
-version: 0.12.0
+version: 0.13.0
diff --git a/README.md b/README.md
@@ -132,7 +132,7 @@ research using the following BibTeX:
 
 ```
 @software{
-  pygmt_2024_11062720,
+  pygmt_2024_13679420,
   author       = {Tian, Dongdong and
                   Uieda, Leonardo and
                   Leong, Wei Ji and
@@ -152,12 +152,12 @@ research using the following BibTeX:
                   Quinn, Jamie and
                   Wessel, Paul},
   title        = {{PyGMT: A Python interface for the Generic Mapping Tools}},
-  month        = may,
+  month        = sep,
   year         = 2024,
   publisher    = {Zenodo},
-  version      = {0.12.0},
-  doi          = {10.5281/zenodo.11062720},
-  url          = {https://doi.org/10.5281/zenodo.11062720}
+  version      = {0.13.0},
+  doi          = {10.5281/zenodo.13679420},
+  url          = {https://doi.org/10.5281/zenodo.13679420}
 }
 ```
 
@@ -186,12 +186,6 @@ Other official wrappers for GMT:
 - [GMT.jl](https://github.com/GenericMappingTools/GMT.jl): A Julia wrapper for GMT.
 - [gmtmex](https://github.com/GenericMappingTools/gmtmex): A Matlab/Octave wrapper for GMT.
 
-Other non-official Python wrappers for GMT (not maintained):
-
-- [gmtpy](https://github.com/emolch/gmtpy) by [Sebastian Heimann](https://github.com/emolch)
-- [pygmt](https://github.com/ian-r-rose/pygmt) by [Ian Rose](https://github.com/ian-r-rose)
-- [PyGMT](https://github.com/glimmer-cism/PyGMT) by [Magnus Hagdorn](https://github.com/mhagdorn)
-
 <!-- doc-index-end-before -->
 
 ## Minimum supported versions

diff --git a/ci/requirements/docs.yml b/ci/requirements/docs.yml
@@ -6,7 +6,7 @@ dependencies:
     # Required dependencies
     - python=3.12
     - gmt=6.5.0
-    - ghostscript=10.03.1
+    - ghostscript=10.04.0
     - numpy
     - pandas
     - xarray
@@ -18,9 +18,9 @@ dependencies:
     - ipython
     - rioxarray
     # Development dependencies (general)
-    - build
     - make
     - pip
+    - python-build
     # Dev dependencies (building documentation)
     - myst-nb
     - panel

diff --git a/doc/_static/style.css b/doc/_static/style.css
@@ -203,3 +203,19 @@ a.copybtn {
 .sphx-glr-single-img {
     max-width: 80%!important;
 }
+
+/*
+ * Styles for aligning table cells.
+ * https://myst-parser.readthedocs.io/en/latest/syntax/tables.html#markdown-syntax
+ */
+th.text-left, td.text-left {
+    text-align: left !important;
+}
+
+th.text-center, td.text-center {
+    text-align: center !important;
+}
+
+th.text-right, td.text-right {
+    text-align: right !important;
+}
diff --git a/doc/_static/version_switch.js b/doc/_static/version_switch.js
@@ -12,6 +12,7 @@
   var all_versions = {
     'latest': 'latest',
     'dev': 'dev',
+    'v0.13.0': 'v0.13.0',
     'v0.12.0': 'v0.12.0',
     'v0.11.0': 'v0.11.0',
     'v0.10.0': 'v0.10.0',

diff --git a/doc/_templates/breadcrumbs.html b/doc/_templates/breadcrumbs.html
@@ -14,7 +14,7 @@
                 {% set gallery_path = gallery_dir[pagename.split("/")[0]] %}
                 {% set example_script = pagename|replace(pagename.split("/")[0], gallery_dir[pagename.split("/")[0]]) %}
                 {% if pagename.split("/")[-1] == "index" %}
-                    {% set example_script = example_script|replace("index", "README.txt") %}
+                    {% set example_script = example_script|replace("index", "GALLERY_HEADER.rst") %}
                 {% else %}
                     {% set example_script = example_script + ".py" %}
                 {% endif %}

diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -317,5 +317,6 @@ Low level access (these are mostly used by the :mod:`pygmt.clib` package):
     clib.Session.get_libgmt_func
     clib.Session.virtualfile_from_data
     clib.Session.virtualfile_from_grid
+    clib.Session.virtualfile_from_stringio
     clib.Session.virtualfile_from_matrix
     clib.Session.virtualfile_from_vectors