Enable ruff's pylint rules (PL) and remove pylint (#2815)

* Enable ruff's pylint rules (PL) but ignore PLR2004
* Remove pylint settings from pyproject.toml
* Remove all 'pylint: disable' directives
* Use noqa to suppress some ruff errors
* Fix a lint issue in timestamp.py
* Fully remove pylint from Makefile, CI, docs, and environment.yml
* Update doc/contributing.md

Co-authored-by: Wei Ji <[email protected]>

Author: seisman

.github/workflows/style_checks.yaml

@@ -34,16 +34,13 @@ jobs:
 
       - name: Install packages
         run: |
-          python -m pip install blackdoc docformatter pylint ruff
+          python -m pip install blackdoc docformatter ruff
           python -m pip list
           sudo apt-get install dos2unix
 
       - 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

@@ -18,7 +18,6 @@ help:
 	@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 ""
@@ -74,9 +73,6 @@ check:
 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

@@ -505,15 +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 blackdoc, docformatter, ruff (in check mode)
-make lint    # Runs pylint, which is a bit slower
 ```
 
 ### Testing your Code

environment.yml

@@ -25,7 +25,6 @@ dependencies:
     - blackdoc
     - codespell
     - docformatter>=1.7.2
-    - pylint
     - ruff
     # Dev dependencies (unit testing)
     - matplotlib

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/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. "

pygmt/clib/session.py

@@ -175,7 +175,7 @@ def info(self):
         Dictionary with the GMT version and default paths and parameters.
         """
         if not hasattr(self, "_info"):
-            self._info = {  # pylint: disable=attribute-defined-outside-init
+            self._info = {
                 "version": self.get_default("API_VERSION"),
                 "padding": self.get_default("API_PAD"),
                 # API_BINDIR points to the directory of the Python interpreter
@@ -312,7 +312,6 @@ def get_libgmt_func(self, name, argtypes=None, restype=None):
         <class 'ctypes.CDLL.__init__.<locals>._FuncPtr'>
         """
         if not hasattr(self, "_libgmt"):
-            # pylint: disable=attribute-defined-outside-init
             self._libgmt = load_libgmt()
         function = getattr(self._libgmt, name)
         if argtypes is not None:
@@ -349,7 +348,7 @@ def create(self, name):
         """
         try:
             # Won't raise an exception if there is a currently open session
-            self.session_pointer  # pylint: disable=pointless-statement
+            self.session_pointer
             # In this case, fail to create a new session until the old one is
             # destroyed
             raise GMTCLibError(
@@ -369,10 +368,10 @@ def create(self, name):
 
         # Capture the output printed by GMT into this list. Will use it later
         # to generate error messages for the exceptions raised by API calls.
-        self._error_log = []  # pylint: disable=attribute-defined-outside-init
+        self._error_log = []
 
         @ctp.CFUNCTYPE(ctp.c_int, ctp.c_void_p, ctp.c_char_p)
-        def print_func(file_pointer, message):  # pylint: disable=unused-argument
+        def print_func(file_pointer, message):
             """
             Callback function that the GMT C API will use to print log and
             error messages.
@@ -389,7 +388,6 @@ def print_func(file_pointer, message):  # pylint: disable=unused-argument
 
         # Need to store a copy of the function because ctypes doesn't and it
         # will be garbage collected otherwise
-        # pylint: disable=attribute-defined-outside-init
         self._print_callback = print_func
 
         padding = self["GMT_PAD_DEFAULT"]
@@ -1468,7 +1466,7 @@ def virtualfile_from_grid(self, grid):
             yield vfile
 
     @fmt_docstring
-    def virtualfile_from_data(
+    def virtualfile_from_data(  # noqa: PLR0912
         self,
         check_kind=None,
         data=None,

pygmt/datasets/tile_map.py

@@ -107,7 +107,6 @@ def load_tile_map(region, zoom="auto", source=None, lonlat=True, wait=0, max_ret
       * y            (y) float64 -7.081e-10 -7.858e+04 ... -1.996e+07 ...
       * x            (x) float64 -2.004e+07 -1.996e+07 ... 1.996e+07 2.004e+07
     """
-    # pylint: disable=too-many-locals
     if contextily is None:
         raise ImportError(
             "Package `contextily` is required to be installed to use this function. "

pygmt/figure.py

@@ -9,8 +9,7 @@
 try:
     import IPython
 except ImportError:
-    IPython = None  # pylint: disable=invalid-name
-
+    IPython = None
 
 from pygmt.clib import Session
 from pygmt.exceptions import GMTError, GMTInvalidInput
@@ -34,7 +33,7 @@
 
 # Show figures in Jupyter notebooks if available
 if IPython:
-    get_ipython = IPython.get_ipython()  # pylint: disable=invalid-name
+    get_ipython = IPython.get_ipython()
     if get_ipython and "IPKernelApp" in get_ipython.config:  # Jupyter Notebook enabled
         SHOW_CONFIG["method"] = "notebook"
 
@@ -82,9 +81,7 @@ class Figure:
 
     def __init__(self):
         self._name = unique_name()
-        self._preview_dir = TemporaryDirectory(  # pylint: disable=consider-using-with
-            prefix=f"{self._name}-preview-"
-        )
+        self._preview_dir = TemporaryDirectory(prefix=f"{self._name}-preview-")
         self._activate_figure()
 
     def __del__(self):
@@ -251,7 +248,7 @@ def psconvert(self, **kwargs):
                 module="psconvert", args=f"{prefix_arg} {build_arg_string(kwargs)}"
             )
 
-    def savefig(
+    def savefig(  # noqa: PLR0912
         self,
         fname,
         transparent=False,
@@ -320,7 +317,6 @@ def savefig(
             :meth:`pygmt.Figure.psconvert`. Valid parameters are ``gs_path``,
             ``gs_option``, ``resize``, ``bb_style``, and ``verbose``.
         """
-        # pylint: disable=too-many-branches
         # All supported formats
         fmts = {
             "bmp": "b",
@@ -518,7 +514,7 @@ def _repr_html_(self):
         html = '<img src="data:image/png;base64,{image}" width="{width}px">'
         return html.format(image=base64_png.decode("utf-8"), width=500)
 
-    from pygmt.src import (  # pylint: disable=import-outside-toplevel
+    from pygmt.src import (
         basemap,
         coast,
         colorbar,

pygmt/helpers/tempfile.py

@@ -126,7 +126,6 @@ def tempfile_from_geojson(geojson):
         E.g. '1a2b3c4d5e6.gmt'.
     """
     with GMTTempFile(suffix=".gmt") as tmpfile:
-        # pylint: disable=import-outside-toplevel
         import geopandas as gpd
 
         os.remove(tmpfile.name)  # ensure file is deleted first

pygmt/helpers/testing.py

@@ -73,12 +73,10 @@ def check_figures_equal(*, extensions=("png",), tol=0.0, result_dir="result_imag
     ...
     >>> shutil.rmtree(path="tmp_result_images")  # cleanup folder if tests pass
     """
-    # pylint: disable=invalid-name
     ALLOWED_CHARS = set(string.digits + string.ascii_letters + "_-[]()")
     KEYWORD_ONLY = inspect.Parameter.KEYWORD_ONLY
 
     def decorator(func):
-        # pylint: disable=import-outside-toplevel
         import pytest
         from matplotlib.testing.compare import compare_images
 

pygmt/helpers/utils.py

@@ -499,7 +499,7 @@ def launch_external_viewer(fname, waiting=0):
     elif os_name == "darwin":  # Darwin is macOS
         subprocess.run(["open", fname], check=False, **run_args)
     elif os_name == "win32":
-        os.startfile(fname)  # pylint: disable=no-member
+        os.startfile(fname)
     else:
         webbrowser.open_new_tab(f"file://{fname}")
     if waiting > 0:

pygmt/sphinx_gallery.py

@@ -9,7 +9,7 @@
 from pygmt.figure import SHOWED_FIGURES
 
 
-class PyGMTScraper:  # pylint: disable=too-few-public-methods
+class PyGMTScraper:
     """
     Save ``pygmt.Figure`` objects that had their ``show`` method called.
 

pygmt/src/__init__.py

@@ -1,8 +1,6 @@
 """
 Source code for PyGMT methods.
 """
-# pylint: disable=import-outside-toplevel
-
 from pygmt.src.basemap import basemap
 from pygmt.src.binstats import binstats
 from pygmt.src.blockm import blockmean, blockmedian, blockmode

pygmt/src/basemap.py

@@ -82,6 +82,6 @@ def basemap(self, **kwargs):
     {perspective}
     {transparency}
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         lib.call_module(module="basemap", args=build_arg_string(kwargs))

pygmt/src/coast.py

@@ -201,7 +201,7 @@ def coast(self, **kwargs):
     >>> # Show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     if not args_in_kwargs(args=["C", "G", "S", "I", "N", "E", "Q", "W"], kwargs=kwargs):
         raise GMTInvalidInput(
             """At least one of the following parameters must be specified:

pygmt/src/colorbar.py

@@ -144,6 +144,6 @@ def colorbar(self, **kwargs):
     >>> # Show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         lib.call_module(module="colorbar", args=build_arg_string(kwargs))

pygmt/src/config.py

@@ -6,7 +6,7 @@
 from pygmt.clib import Session
 
 
-class config:  # pylint: disable=invalid-name
+class config:
     """
     Set GMT defaults globally or locally.
 

pygmt/src/contour.py

@@ -112,7 +112,7 @@ def contour(self, data=None, x=None, y=None, z=None, **kwargs):
     {perspective}
     {transparency}
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
 
     with Session() as lib:
         file_context = lib.virtualfile_from_data(

pygmt/src/grdcontour.py

@@ -121,7 +121,7 @@ def grdcontour(self, grid, **kwargs):
     >>> # show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
         with file_context as fname:

pygmt/src/grdhisteq.py

@@ -19,7 +19,7 @@
 __doctest_skip__ = ["grdhisteq.*"]
 
 
-class grdhisteq:  # pylint: disable=invalid-name
+class grdhisteq:
     r"""
     Perform histogram equalization for a grid.
 

pygmt/src/grdimage.py

@@ -173,7 +173,7 @@ def grdimage(self, grid, **kwargs):
     >>> # show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
 
     with Session() as lib:
         with lib.virtualfile_from_data(

pygmt/src/grdview.py

@@ -144,7 +144,7 @@ def grdview(self, grid, **kwargs):
     >>> # show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         with lib.virtualfile_from_data(
             check_kind="raster", data=grid

pygmt/src/histogram.py

@@ -132,7 +132,7 @@ def histogram(self, data, **kwargs):
     {transparency}
     {wrap}
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
         with file_context as infile:

pygmt/src/image.py

@@ -66,6 +66,6 @@ def image(self, imagefile, **kwargs):
     {perspective}
     {transparency}
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         lib.call_module(module="image", args=build_arg_string(kwargs, infile=imagefile))

pygmt/src/inset.py

@@ -132,7 +132,7 @@ def inset(self, **kwargs):
     >>> fig.logo(position="jBR+o0.2c+w3c")
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
     with Session() as lib:
         try:
             lib.call_module(module="inset", args=f"begin {build_arg_string(kwargs)}")

pygmt/src/legend.py

@@ -67,7 +67,7 @@ def legend(self, spec=None, position="JTR+jTR+o0.2c", box="+gwhite+p1p", **kwarg
     {perspective}
     {transparency}
     """
-    kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
+    kwargs = self._preprocess(**kwargs)
 
     if kwargs.get("D") is None:
         kwargs["D"] = position