Merge branch 'main' into alias-system-v1

Author: seisman

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -11,6 +11,7 @@ assignees: ''
 **Scheduled Date**: 20YY/MM/DD
 **Pull request due date**: 20YY/MM/DD
 **DOI**: `10.5281/zenodo.XXXXXXX`
+**Announcement draft**: https://hackmd.io/@pygmt/xxxxxxxx
 
 **Priority PRs/issues to complete prior to release**
 
@@ -39,11 +40,15 @@ assignees: ''
   - [ ] 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
+- [ ] Verify that [all workflows triggered by the release](https://github.com/GenericMappingTools/pygmt/actions?query=event%3Arelease) pass
+  - [ ] The latest version is correct on [PyPI](https://pypi.org/project/pygmt/)
+  - [ ] The latest version is correct on https://www.pygmt.org/latest/
+  - [ ] The [release page](https://github.com/GenericMappingTools/pygmt/releases) has five assets, including `baseline-images.zip`, `pygmt-docs.zip` and `pygmt-docs.pdf`
 - [ ] 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. Remember to pin GMT, Python and SPEC0 versions]
+- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) (Done automatically by conda-forge's bot. If you don't want to wait, open a new issue in the `conda-forge/pygmt-feedstock` repository with the title `@conda-forge-admin, please update version`. This will trigger the bot immediately. Remember to pin GMT, 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! Requires moderator status)

.github/workflows/check-links.yml

@@ -66,11 +66,8 @@ jobs:
           --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
           --exclude "^https://www.researchgate.net/"
           --exclude "^https://zenodo.org/badge/DOI/"
-          --exclude-path "repository/doc/**/*.rst"
-          --exclude-path "repository/doc/**/*.md"
           --verbose
-          "repository/**/*.rst"
-          "repository/**/*.md"
+          "repository/*.md"
           "repository/**/*.py"
           "documentation/dev/**/*.html"
 

.github/workflows/ci_tests.yaml

@@ -49,7 +49,7 @@ concurrency:
 
 jobs:
   test:
-    name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
+    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     permissions:
       id-token: write  # This is required for requesting OIDC token for codecov
@@ -152,7 +152,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/[email protected].0
+        uses: astral-sh/[email protected].1
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/format-command.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/create-github-app-token@v1.11.6
+      - uses: actions/create-github-app-token@v1.12.0
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}

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: 2025-02-15
-doi: 10.5281/zenodo.14868324
+date-released: 2025-03-31
+doi: 10.5281/zenodo.15071586
 license: BSD-3-Clause
 repository-code: https://github.com/GenericMappingTools/pygmt
 type: software
-version: 0.14.2
+version: 0.15.0

README.md

@@ -137,7 +137,7 @@ Feel free to cite our work in your research using the following BibTeX:
 
 ```
 @software{
-  pygmt_2025_14868324,
+  pygmt_2025_15071586,
   author       = {Tian, Dongdong and
                   Uieda, Leonardo and
                   Leong, Wei Ji and
@@ -157,12 +157,12 @@ Feel free to cite our work in your research using the following BibTeX:
                   Quinn, Jamie and
                   Wessel, Paul},
   title        = {{PyGMT: A Python interface for the Generic Mapping Tools}},
-  month        = feb,
+  month        = mar,
   year         = 2025,
   publisher    = {Zenodo},
-  version      = {0.14.2},
-  doi          = {10.5281/zenodo.14868324},
-  url          = {https://doi.org/10.5281/zenodo.14868324}
+  version      = {0.15.0},
+  doi          = {10.5281/zenodo.15071586},
+  url          = {https://doi.org/10.5281/zenodo.15071586}
 }
 ```
 

doc/_static/version_switch.js

@@ -12,6 +12,7 @@
   var all_versions = {
     'latest': 'latest',
     'dev': 'dev',
+    'v0.15.0': 'v0.15.0',
     'v0.14.2': 'v0.14.2',
     'v0.14.1': 'v0.14.1',
     'v0.14.0': 'v0.14.0',

doc/changes.md

@@ -1,14 +1,69 @@
 # Changelog
 
+## Release v0.15.0 (2025/03/31)
+
+[![Digital Object Identifier for PyGMT v0.15.0](https://zenodo.org/badge/DOI/10.5281/zenodo.15071586.svg)](https://doi.org/10.5281/zenodo.15071586)
+
+### Highlights
+
+* 🎉 **Fifteenth minor release of PyGMT** 🎉
+* One new gallery example and two new tutorials
+* Figure.shift_origin: Support shifting origins temporarily when used as a context manager ([#2509](https://github.com/GenericMappingTools/pygmt/pull/2509))
+* Documentation as HTML ZIP archive and in PDF format for offline reference
+
+### Enhancements
+
+* **BREAKING** Support typesetting apostrophe (') and backtick (`) ([#3105](https://github.com/GenericMappingTools/pygmt/pull/3105))
+* **BREAKING** pygmt.grdcut: Refactor to store output in virtualfiles for grids ([#3115](https://github.com/GenericMappingTools/pygmt/pull/3115))
+* GMTDataArrayAccessor: Support passing values using enums GridRegistration and GridType for grid registration and type ([#3696](https://github.com/GenericMappingTools/pygmt/pull/3696))
+* pygmt.grdfill: Add new parameters 'constantfill'/'gridfill'/'neighborfill'/'splinefill' for filling holes ([#3855](https://github.com/GenericMappingTools/pygmt/pull/3855))
+* pygmt.grdfill: Add new parameter 'inquire' to inquire the bounds of holes ([#3880](https://github.com/GenericMappingTools/pygmt/pull/3880))
+* pygmt.grdfill: Add alias 'coltypes' (-f) ([#3869](https://github.com/GenericMappingTools/pygmt/pull/3869))
+
+### Deprecations
+
+* pygmt.grdfill: Deprecate parameter 'no_data' to 'hole' (remove in v0.19.0) ([#3852](https://github.com/GenericMappingTools/pygmt/pull/3852))
+* pygmt.grdfill: Deprecate parameter 'mode', use parameters 'constantfill'/'gridfill'/'neighborfill'/'splinefill' instead (remove in v0.19.0) ([#3855](https://github.com/GenericMappingTools/pygmt/pull/3855))
+* pygmt.grdclip: Deprecate parameter 'new' to 'replace' (remove in v0.19.0) ([#3884](https://github.com/GenericMappingTools/pygmt/pull/3884))
+* clib.Session: Remove deprecated open_virtual_file method, use open_virtualfile instead (Deprecated since v0.11.0) ([#3738](https://github.com/GenericMappingTools/pygmt/pull/3738))
+* clib.Session: Remove deprecated virtualfile_from_data method, use virtualfile_in instead (Deprecated since v0.13.0) ([#3739](https://github.com/GenericMappingTools/pygmt/pull/3739))
+
+### Documentation
+
+* Add an advanced tutorial for plotting focal mechanisms (beachballs) ([#2550](https://github.com/GenericMappingTools/pygmt/pull/2550))
+* Add an advanced tutorial for creating legends ([#3594](https://github.com/GenericMappingTools/pygmt/pull/3594))
+* Add a gallery example for Figure.hlines and Figure.vlines ([#3755](https://github.com/GenericMappingTools/pygmt/pull/3755))
+
+### Maintenance
+
+* Use the 'release-branch-semver' version scheme for setuptools_scm ([#3828](https://github.com/GenericMappingTools/pygmt/pull/3828))
+* Rename _GMT_DATASET.to_dataframe to .to_pandas and _GMT_GRID.to_dataarray/_GMT_IMAGE.to_dataarray to .to_xarray ([#3798](https://github.com/GenericMappingTools/pygmt/pull/3798))
+* Bump to ruff 0.9.0, apply ruff 2025 style, and ignore A005 (stdlib-module-shadowing) violations ([#3763](https://github.com/GenericMappingTools/pygmt/pull/3763))
+* Use well-known labels in project URLs following PEP753 ([#3743](https://github.com/GenericMappingTools/pygmt/pull/3743))
+* clib.conversion: Remove the unused array_to_datetime function ([#3507](https://github.com/GenericMappingTools/pygmt/pull/3507))
+* CI: Test on Linux arm64 runners ([#3778](https://github.com/GenericMappingTools/pygmt/pull/3778))
+* CI: Build PDF documentation using tectonic ([#3765](https://github.com/GenericMappingTools/pygmt/pull/3765))
+
+**Full Changelog**: <https://github.com/GenericMappingTools/pygmt/compare/v0.14.0...v0.15.0>
+
+### Contributors
+
+* [Dongdong Tian](https://github.com/seisman)
+* [Yvonne Fröhlich](https://github.com/yvonnefroehlich)
+* [Wei Ji Leong](https://github.com/weiji14)
+* [Michael Grund](https://github.com/michaelgrund)
+
+---
+
 ## Release v0.14.2 (2025/02/15)
 
 [![Digital Object Identifier for PyGMT v0.14.2](https://zenodo.org/badge/DOI/10.5281/zenodo.14868324.svg)](https://doi.org/10.5281/zenodo.14868324)
 
 
 ### Bug Fixes
 
-- **Patch release fixing a critical bug introduced in PyGMT v0.14.1**
-- Fix the bug for passing text strings with numeric values ([#3804](https://github.com/GenericMappingTools/pygmt/pull/3804))
+* **Patch release fixing a critical bug introduced in PyGMT v0.14.1**
+* Fix the bug for passing text strings with numeric values ([#3804](https://github.com/GenericMappingTools/pygmt/pull/3804))
 
 **Full Changelog**: <https://github.com/GenericMappingTools/pygmt/compare/v0.14.1...v0.14.2>
 
@@ -24,16 +79,16 @@
 
 ### Highlights
 
-- **Patch release fixing critical bugs in PyGMT v0.14.0**
-- Fix the bug of converting Python sequence of datetime-like objects ([#3760](https://github.com/GenericMappingTools/pygmt/pull/3760))
+* **Patch release fixing critical bugs in PyGMT v0.14.0**
+* Fix the bug of converting Python sequence of datetime-like objects ([#3760](https://github.com/GenericMappingTools/pygmt/pull/3760))
 
 ### Maintenance
 
-- CI: Separate jobs for publishing to TestPyPI and PyPI ([#3742](https://github.com/GenericMappingTools/pygmt/pull/3742))
-- clib.conversion._to_numpy: Add tests for Python sequence of datetime-like objects ([#3758](https://github.com/GenericMappingTools/pygmt/pull/3758))
-- Fix an image in README.md (broken on PyPI) and rewrap to 88 characters ([#3740](https://github.com/GenericMappingTools/pygmt/pull/3740))
-- Fix the dataset link in the RGB image gallery example ([#3781](https://github.com/GenericMappingTools/pygmt/pull/3781))
-- Update License year to 2025 ([#3737](https://github.com/GenericMappingTools/pygmt/pull/3737))
+* CI: Separate jobs for publishing to TestPyPI and PyPI ([#3742](https://github.com/GenericMappingTools/pygmt/pull/3742))
+* clib.conversion._to_numpy: Add tests for Python sequence of datetime-like objects ([#3758](https://github.com/GenericMappingTools/pygmt/pull/3758))
+* Fix an image in README.md (broken on PyPI) and rewrap to 88 characters ([#3740](https://github.com/GenericMappingTools/pygmt/pull/3740))
+* Fix the dataset link in the RGB image gallery example ([#3781](https://github.com/GenericMappingTools/pygmt/pull/3781))
+* Update License year to 2025 ([#3737](https://github.com/GenericMappingTools/pygmt/pull/3737))
 
 **Full Changelog**: <https://github.com/GenericMappingTools/pygmt/compare/v0.14.0...v0.14.1>
 

doc/minversions.md

@@ -47,6 +47,7 @@ compatibility reasons.
 | PyGMT Version | Documentation | GMT | Python | NumPy | pandas | Xarray |
 |---|---|---|---|---|---|---|
 | [Dev][]* | <doc:dev>, [HTML+ZIP](doc:dev/pygmt-docs.zip), [PDF](doc:dev/pygmt-docs.pdf) | {{ requires.gmt }} | {{ requires.python }} | {{ requires.numpy }} | {{ requires.pandas }} | {{ requires.xarray }} |
+| <tag:v0.15.0> | <doc:v0.15.0>, <html:v0.15.0>, <pdf:v0.15.0> | >=6.4.0 | >=3.11 | >=1.25 | >=2.0 | >=2023.04 |
 | <tag:v0.14.2> | <doc:v0.14.2>, <html:v0.14.2> | >=6.4.0 | >=3.11 | >=1.25 | >=2.0 | >=2023.04 |
 | <tag:v0.14.1> | <doc:v0.14.1>, <html:v0.14.1> | >=6.4.0 | >=3.11 | >=1.25 | >=2.0 | >=2023.04 |
 | <tag:v0.14.0> | <doc:v0.14.0>, <html:v0.14.0> | >=6.4.0 | >=3.11 | >=1.25 | >=2.0 | >=2023.04 |

pygmt/src/grdclip.py

@@ -4,18 +4,26 @@
 
 import xarray as xr
 from pygmt.clib import Session
-from pygmt.helpers import build_arg_list, fmt_docstring, kwargs_to_strings, use_alias
+from pygmt.helpers import (
+    build_arg_list,
+    deprecate_parameter,
+    fmt_docstring,
+    kwargs_to_strings,
+    use_alias,
+)
 
 __doctest_skip__ = ["grdclip"]
 
 
+# TODO(PyGMT>=0.19.0): Remove the deprecated "new" parameter.
 @fmt_docstring
+@deprecate_parameter("new", "replace", "v0.15.0", remove_version="v0.19.0")
 @use_alias(
     R="region",
     Sa="above",
     Sb="below",
     Si="between",
-    Sr="new",
+    Sr="replace",
     V="verbose",
 )
 @kwargs_to_strings(
@@ -55,7 +63,7 @@ def grdclip(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None:
     between : str or list
         [*low*, *high*, *between*].
         Set all data[i] >= *low* and <= *high* to *between*.
-    new : str or list
+    replace : str or list
         [*old*, *new*].
         Set all data[i] == *old* to *new*. This is mostly useful when
         your data are known to be integer values.