Merge branch 'main' into add-coast-alias-F

Author: yvonnefroehlich

.github/workflows/format-command.yml

@@ -32,7 +32,7 @@ jobs:
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          python -m pip install black blackdoc docformatter ruff
+          python -m pip install blackdoc docformatter ruff
           python -m pip list
           sudo apt-get install dos2unix
 

.github/workflows/style_checks.yaml

@@ -34,16 +34,13 @@ jobs:
 
       - name: Install packages
         run: |
-          python -m pip install black blackdoc docformatter pylint ruff
+          python -m pip install blackdoc docformatter ruff
           python -m pip list
           sudo apt-get install dos2unix
 
-      - name: Formatting check (black, blackdoc, docformatter, ruff)
+      - name: Formatting check (blackdoc, docformatter, ruff)
         run: make check
 
-      - name: Linting (pylint)
-        run: make lint
-
       - name: Ensure files use UNIX line breaks and have 644 permission
         run: |
           find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec dos2unix --quiet {} \;

Makefile

@@ -15,10 +15,9 @@ help:
 	@echo "  fulltest       run the test suite (including all doctests)"
 	@echo "  doctest        run the doctests only"
 	@echo "  test_no_images run the test suite (including all doctests) but skip image comparisons"
-	@echo "  format         run black, blackdoc, docformatter and ruff to automatically format the code"
-	@echo "  check          run code style and quality checks (black, blackdoc, docformatter, ruff)"
+	@echo "  format         run blackdoc, docformatter and ruff to automatically format the code"
+	@echo "  check          run code style and quality checks (blackdoc, docformatter, ruff)"
 	@echo "  codespell      run codespell to check common misspellings"
-	@echo "  lint           run pylint for a deeper (and slower) quality check"
 	@echo "  clean          clean up build and generated files"
 	@echo "  distclean      clean up build and generated files, including project metadata files"
 	@echo ""
@@ -61,24 +60,19 @@ test_no_images: _runtest
 
 format:
 	docformatter --in-place $(FORMAT_FILES)
-	black $(FORMAT_FILES)
 	blackdoc $(FORMAT_FILES)
 	ruff check --fix $(FORMAT_FILES)
 	ruff format $(FORMAT_FILES)
 
 check:
 	docformatter --check $(FORMAT_FILES)
-	black --check $(FORMAT_FILES)
 	blackdoc --check $(FORMAT_FILES)
 	ruff check $(FORMAT_FILES)
 	ruff format --check $(FORMAT_FILES)
 
 codespell:
 	@codespell
 
-lint:
-	pylint $(LINT_FILES)
-
 clean:
 	find . -name "*.pyc" -exec rm -v {} +
 	find . -name "*~" -exec rm -v {} +

doc/conf.py

@@ -1,16 +1,11 @@
 """
 Sphinx documentation configuration file.
 """
-# pylint: disable=invalid-name
-
 import datetime
 from importlib.metadata import metadata
 
 # ruff: isort: off
-from sphinx_gallery.sorting import (  # pylint: disable=no-name-in-module
-    ExplicitOrder,
-    ExampleTitleSortKey,
-)
+from sphinx_gallery.sorting import ExplicitOrder, ExampleTitleSortKey
 import pygmt
 from pygmt import __commit__, __version__
 from pygmt.sphinx_gallery import PyGMTScraper
@@ -139,7 +134,7 @@
 # General information about the project
 year = datetime.date.today().year
 project = "PyGMT"
-copyright = f"2017-{year}, The PyGMT Developers"  # pylint: disable=redefined-builtin
+copyright = f"2017-{year}, The PyGMT Developers"
 if len(__version__.split("+")) > 1 or __version__ == "unknown":
     version = "dev"
     # Set base_url for stable version

doc/contributing.md

@@ -404,7 +404,7 @@ the `pygmt/src/` and `pygmt/datasets/` folders. **All docstrings** should follow
 All functions/classes/methods should have docstrings with a full description of all
 arguments and return values.
 
-While the maximum line length for code is automatically set by Black, docstrings
+While the maximum line length for code is automatically set by ruff, docstrings
 must be formatted manually. To play nicely with Jupyter and IPython, **keep docstrings
 limited to 79 characters** per line.
 
@@ -473,12 +473,11 @@ code, be sure to follow the general guidelines in the
 
 We use some tools to format the code so we don't have to think about it:
 
-- [Black](https://github.com/psf/black)
 - [blackdoc](https://github.com/keewis/blackdoc)
 - [docformatter](https://github.com/myint/docformatter)
 - [ruff](https://docs.astral.sh/ruff)
 
-Black and blackdoc loosely follows the [PEP8](http://pep8.org) guide but with a few
+These tools loosely follow the [PEP8](http://pep8.org) guide but with a few
 differences. Regardless, you won't have to worry about formatting the code yourself.
 Before committing, run it to automatically format your code:
 
@@ -506,15 +505,14 @@ editors or IDEs. We consistently use `# %%` as code block separators (please
 refer to [issue #2660](https://github.com/GenericMappingTools/pygmt/issues/2660)
 for the discussions) and require at least one separator in all example files.
 
-We also use [ruff](https://docs.astral.sh/ruff) and
-[pylint](https://pylint.pycqa.org/) to check the quality of the code and quickly catch
-common errors.
+We also use [ruff](https://docs.astral.sh/ruff) to check the quality of the code
+and quickly catch common errors.
+
 The [`Makefile`](https://github.com/GenericMappingTools/pygmt/blob/main/Makefile)
-contains rules for running both checks:
+contains rules for running the linter checks:
 
 ```bash
-make check   # Runs black, blackdoc, docformatter, ruff (in check mode)
-make lint    # Runs pylint, which is a bit slower
+make check   # Runs blackdoc, docformatter, ruff (in check mode)
 ```
 
 ### Testing your Code

environment.yml

@@ -3,6 +3,7 @@ channels:
     - conda-forge
     - nodefaults
 dependencies:
+    - python=3.12
     # Required dependencies
     - gmt=6.4.0
     - numpy>=1.22
@@ -22,11 +23,9 @@ dependencies:
     - make
     - pip
     # Dev dependencies (style checks)
-    - black
     - blackdoc
     - codespell
     - docformatter>=1.7.2
-    - pylint
     - ruff
     # Dev dependencies (unit testing)
     - matplotlib

examples/gallery/images/rgb_image.py

@@ -28,7 +28,7 @@
     # Subset to area of Lāhainā in EPSG:32604 coordinates
     image = img.rio.clip_box(minx=738000, maxx=755000, miny=2300000, maxy=2318000)
     image = image.load()  # Force loading the DataArray into memory
-image
+image  # noqa: B018
 
 # %%
 # Plot the RGB imagery:

pygmt/__init__.py

@@ -83,7 +83,7 @@ def print_clib_info(file=sys.stdout):
     Includes the GMT version, default values for parameters, the path to the
     ``libgmt`` shared library, and GMT directories.
     """
-    from pygmt.clib import Session  # pylint: disable=import-outside-toplevel
+    from pygmt.clib import Session
 
     lines = ["GMT library information:"]
     with Session() as ses:
@@ -104,7 +104,7 @@ def show_versions(file=sys.stdout):
     - Core dependency versions (NumPy, Pandas, Xarray, etc)
     - GMT library information
     """
-    # pylint: disable=import-outside-toplevel
+
     import importlib
     import platform
     import subprocess

pygmt/clib/conversion.py

@@ -103,7 +103,7 @@ def dataarray_to_matrix(grid):
                 "but GMT only supports regular spacing. Calculated regular spacing "
                 f"{coord_inc} is assumed in the '{dim}' dimension."
             )
-            warnings.warn(msg, category=RuntimeWarning)
+            warnings.warn(msg, category=RuntimeWarning, stacklevel=2)
         if coord_inc == 0:
             raise GMTInvalidInput(
                 f"Grid has a zero increment in the '{dim}' dimension."

pygmt/clib/loading.py

@@ -163,7 +163,6 @@ def check_libgmt(libgmt):
     functions = ["Create_Session", "Get_Enum", "Call_Module", "Destroy_Session"]
     for func in functions:
         if not hasattr(libgmt, "GMT_" + func):
-            # pylint: disable=protected-access
             msg = (
                 f"Error loading '{libgmt._name}'. Couldn't access function GMT_{func}. "
                 "Ensure that you have installed an up-to-date GMT version 6 library. "