Merge branch 'main' into refactor-build_arg_string

Author: seisman

.github/workflows/check-links.yml

@@ -26,7 +26,7 @@ jobs:
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.3.2
+      uses: lycheeverse/lychee-action@v1.4.1
       with:
         # 429: Too many requests
         args: >
@@ -56,7 +56,7 @@ jobs:
       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
 
     - name: Create Issue From File
-      uses: peter-evans/create-issue-from-file@v3
+      uses: peter-evans/create-issue-from-file@v4
       with:
         title: Link Checker Report on ${{ steps.date.outputs.date }}
         content-filepath: ./lychee/out.md

.github/workflows/ci_tests_dev.yaml

@@ -67,7 +67,7 @@ jobs:
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.event.client_payload.pull_request.head.ref }}
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
@@ -162,7 +162,7 @@ jobs:
           path: tmp-test-dir-with-unique-name
 
       - name: Add reaction
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         if: github.event_name == 'repository_dispatch'
         with:
           token: ${{ steps.generate-token.outputs.token }}

.github/workflows/dvc-diff.yml

@@ -95,7 +95,7 @@ jobs:
         echo ::set-output name=report::$report
 
     - name: Find comment with image diff report
-      uses: peter-evans/find-comment@v1.3.0
+      uses: peter-evans/find-comment@v2.0.0
       id: fc
       with:
         issue-number: ${{ github.event.pull_request.number }}
@@ -104,14 +104,14 @@ jobs:
 
     - name: Create comment with image diff report
       if: steps.fc.outputs.comment-id == ''
-      uses: peter-evans/create-or-update-comment@v1.4.4
+      uses: peter-evans/create-or-update-comment@v2
       with:
         issue-number: ${{ github.event.pull_request.number }}
         body: ${{ steps.image-diff.outputs.report }}
 
     - name: Update comment with new image diff report
       if: steps.fc.outputs.comment-id != ''
-      uses: peter-evans/create-or-update-comment@v1.4.4
+      uses: peter-evans/create-or-update-comment@v2
       with:
         comment-id: ${{ steps.fc.outputs.comment-id }}
         body: ${{ steps.image-diff.outputs.report }}

.github/workflows/format-command.yml

@@ -18,7 +18,7 @@ jobs:
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
       - uses: actions/setup-python@v3.0.0
@@ -43,7 +43,7 @@ jobs:
           fi
 
       - name: Add reaction
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

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

@@ -43,7 +43,7 @@ jobs:
         # Change setuptools-scm local_scheme to "no-local-version" so the
         # local part of the version isn't included, making the version string
         # compatible with PyPI.
-        sed --in-place "s/node-and-date/no-local-version/g" setup.py
+        sed --in-place "s/node-and-date/no-local-version/g" pyproject.toml
 
     - name: Build source and wheel distributions
       run: |

.github/workflows/slash-command-dispatch.yml

@@ -17,7 +17,7 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
       - name: Slash Command Dispatch
-        uses: peter-evans/slash-command-dispatch@v2
+        uses: peter-evans/slash-command-dispatch@v3
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commands: |

AUTHORS.md

@@ -9,16 +9,16 @@ The following people have contributed code and/or documentation to the project
 (alphabetical by name) and are considered to be "PyGMT Developers":
 
 * [Abhishek Anant](https://twitter.com/itsabhianant) | [0000-0002-5751-2010](https://orcid.org/0000-0002-5751-2010) | Unaffiliated
-* [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | China University of Geosciences
-* [Jamie Quinn](http://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London
-* [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University
-* [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey
-* [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool
-* [Liam Toney](https://liam.earth/) | [0000-0003-0167-9433](https://orcid.org/0000-0003-0167-9433) | University of Alaska Fairbanks
-* [Malte Ziebarth](https://github.com/mjziebarth) | [0000-0002-5190-4478](https://orcid.org/0000-0002-5190-4478) | GFZ German Research Centre for Geosciences
-* [Meghan Jones](https://github.com/meghanrjones) | [0000-0003-0180-8928](https://orcid.org/0000-0003-0180-8928) | University of Hawai'i at Mānoa
-* [Michael Grund](https://github.com/michaelgrund) | [0000-0001-8759-2018](https://orcid.org/0000-0001-8759-2018) | Innoplexia GmbH
-* [Tyler Newton](http://www.tnewton.com/) | [0000-0002-1560-6553](https://orcid.org/0000-0002-1560-6553) | University of Oregon
-* [Wei Ji Leong](https://github.com/weiji14) | [0000-0003-2354-1988](https://orcid.org/0000-0003-2354-1988) | The Ohio State University
+* [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | China University of Geosciences, China
+* [Jamie Quinn](http://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London, United Kingdom
+* [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University, Singapore
+* [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey, USA
+* [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool, United Kingdom
+* [Liam Toney](https://liam.earth/) | [0000-0003-0167-9433](https://orcid.org/0000-0003-0167-9433) | University of Alaska Fairbanks, USA
+* [Malte Ziebarth](https://github.com/mjziebarth) | [0000-0002-5190-4478](https://orcid.org/0000-0002-5190-4478) | GFZ German Research Centre for Geosciences, Germany
+* [Meghan Jones](https://github.com/meghanrjones) | [0000-0003-0180-8928](https://orcid.org/0000-0003-0180-8928) | University of Hawai'i at Mānoa, USA
+* [Michael Grund](https://github.com/michaelgrund) | [0000-0001-8759-2018](https://orcid.org/0000-0001-8759-2018) | Innoplexia GmbH, Germany
+* [Tyler Newton](http://www.tnewton.com/) | [0000-0002-1560-6553](https://orcid.org/0000-0002-1560-6553) | University of Oregon, USA
+* [Wei Ji Leong](https://github.com/weiji14) | [0000-0003-2354-1988](https://orcid.org/0000-0003-2354-1988) | The Ohio State University, USA
 * [William Schlitzer](https://github.com/willschlitzer) | [0000-0002-5843-2282](https://orcid.org/0000-0002-5843-2282) | Unaffiliated
-* [Yohai Magen](https://github.com/yohaimagen) | [0000-0002-4892-4013](https://orcid.org/0000-0002-4892-4013) | Tel Aviv University
+* [Yohai Magen](https://github.com/yohaimagen) | [0000-0002-4892-4013](https://orcid.org/0000-0002-4892-4013) | Tel Aviv University, Israel

CITATION.cff

@@ -38,7 +38,7 @@ authors:
   orcid: https://orcid.org/0000-0001-7036-4238
 - given-names: Yohai
   family-names: Magen
-  affiliation: Tel Aviv University
+  affiliation: Tel Aviv University, Israel
   orcid: https://orcid.org/0000-0002-4892-4013
 - given-names: Kathryn
   family-names: Materna
@@ -58,7 +58,7 @@ authors:
   orcid: https://orcid.org/0000-0002-5190-4478
 - given-names: Jamie
   family-names: Quinn
-  affiliation: University College London
+  affiliation: University College London, United Kingdom
   orcid: https://orcid.org/0000-0002-0268-7032
 - given-names: Paul
   family-names: Wessel

pygmt/__init__.py

@@ -160,7 +160,7 @@ def _get_gmt_version():
         "machine": platform.platform(),
     }
 
-    deps = ["numpy", "pandas", "xarray", "netCDF4", "packaging"]
+    deps = ["numpy", "pandas", "xarray", "netCDF4", "packaging", "geopandas"]
 
     print("PyGMT information:")
     print(f"  version: {__version__}")

pygmt/tests/test_grdfill.py

@@ -6,11 +6,15 @@
 import numpy as np
 import pytest
 import xarray as xr
-from pygmt import grdfill, load_dataarray
+from packaging.version import Version
+from pygmt import clib, grdfill, load_dataarray
 from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import GMTTempFile
 from pygmt.helpers.testing import load_static_earth_relief
 
+with clib.Session() as _lib:
+    gmt_version = Version(_lib.info["version"])
+
 
 @pytest.fixture(scope="module", name="grid")
 def fixture_grid():
@@ -82,6 +86,28 @@ def test_grdfill_dataarray_out(grid, expected_grid):
     xr.testing.assert_allclose(a=result, b=expected_grid)
 
 
+@pytest.mark.skipif(
+    gmt_version < Version("6.4.0"),
+    reason="Upstream bug/crash fixed in https://github.com/GenericMappingTools/gmt/pull/6418.",
+)
+def test_grdfill_asymmetric_pad(grid, expected_grid):
+    """
+    Test grdfill using a region that includes the edge of the grid.
+
+    Regression test for
+    https://github.com/GenericMappingTools/pygmt/issues/1745.
+    """
+    result = grdfill(grid=grid, mode="c20", region=[-55, -50, -24, -16])
+    # check information of the output grid
+    assert isinstance(result, xr.DataArray)
+    assert result.gmt.gtype == 1  # Geographic grid
+    assert result.gmt.registration == 1  # Pixel registration
+    # check information of the output grid
+    xr.testing.assert_allclose(
+        a=result, b=expected_grid.sel(lon=slice(-55, -50), lat=slice(-24, -16))
+    )
+
+
 def test_grdfill_file_out(grid, expected_grid):
     """
     Test grdfill with an outgrid set.