Enable ruff's pydocstyle (D) rules and remove docformatter (#2925)

* Enable ruff's pydocstyle (D) rules and set numpy convention

* Fix D406: Section name should end with a newline ('Notes')

* Fix D405L: Section name should be properly capitalized ('See also')

* Fix D104 Missing docstring in public package

* Fix D409: Section underline should match the length of its name

* Ignore a D410/D411 violation

* Fix D103: Missing docstring in public function

* Fix D105: Missing docstring in magic method

* Fix a formatting issue

* Ignore some D rules

```
$ ruff check pygmt doc/conf.py examples --statistics
645	D200	[*] One-line docstring should fit on one line
312	D205	[ ] 1 blank line required between summary line and description
123	D400	[ ] First line should end with a period
 30	D401	[ ] First line of docstring should be in imperative mood: "A mock GMT API function that always returns a given value."
 30	D412	[*] No blank lines allowed between a section header and its content ("Examples")
 12	D202	[*] No blank lines allowed after function docstring (found 1)
```

* Enabel D213 and D410 rules
* Fully remove docformatter
* Update the contributing guides

---------

Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

.github/workflows/format-command.yml

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

.github/workflows/style_checks.yaml

@@ -34,11 +34,11 @@ jobs:
 
       - name: Install packages
         run: |
-          python -m pip install docformatter ruff
+          python -m pip install ruff
           python -m pip list
           sudo apt-get install dos2unix
 
-      - name: Formatting check (docformatter, ruff)
+      - name: Formatting check (ruff)
         run: make check
 
       - name: Ensure files use UNIX line breaks and have 644 permission

Makefile

@@ -15,8 +15,8 @@ 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 docformatter and ruff to automatically format the code"
-	@echo "  check          run code style and quality checks (docformatter and ruff)"
+	@echo "  format         run ruff to automatically format the code"
+	@echo "  check          run ruff to check code style and quality"
 	@echo "  codespell      run codespell to check common misspellings"
 	@echo "  typecheck      run mypy for static type check"
 	@echo "  clean          clean up build and generated files"
@@ -60,12 +60,10 @@ test_no_images: PYTEST_ARGS=-o addopts="--verbose --durations=0 --durations-min=
 test_no_images: _runtest
 
 format:
-	docformatter --in-place $(FORMAT_FILES)
 	ruff check --fix $(FORMAT_FILES)
 	ruff format $(FORMAT_FILES)
 
 check:
-	docformatter --check $(FORMAT_FILES)
 	ruff check $(FORMAT_FILES)
 	ruff format --check $(FORMAT_FILES)
 

doc/contributing.md

@@ -406,7 +406,7 @@ arguments and return values.
 
 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.
+limited to 88 characters** per line.
 
 ### Standards for Example Code
 
@@ -471,14 +471,10 @@ code, be sure to follow the general guidelines in the
 
 ### Code Style
 
-We use some tools to format the code so we don't have to think about it:
-
-- [docformatter](https://github.com/myint/docformatter)
-- [ruff](https://docs.astral.sh/ruff)
-
-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:
+We use the [ruff](https://docs.astral.sh/ruff) tool to format the code, so we
+don't have to think about it. It 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:
 
 ```bash
 make format
@@ -511,7 +507,7 @@ The [`Makefile`](https://github.com/GenericMappingTools/pygmt/blob/main/Makefile
 contains rules for running the linter checks:
 
 ```bash
-make check   # Runs docformatter and ruff (in check mode)
+make check   # Runs ruff in check mode
 ```
 
 ### Testing your Code

environment.yml

@@ -24,7 +24,6 @@ dependencies:
     - pip
     # Dev dependencies (style checks)
     - codespell
-    - docformatter>=1.7.2
     - ruff>=0.1.9
     # Dev dependencies (unit testing)
     - matplotlib

examples/gallery/3d_plots/grdview_surface.py

@@ -23,6 +23,9 @@
 # Define an interesting function of two variables, see:
 # https://en.wikipedia.org/wiki/Ackley_function
 def ackley(x, y):
+    """
+    Ackley function.
+    """
     return (
         -20 * np.exp(-0.2 * np.sqrt(0.5 * (x**2 + y**2)))
         - np.exp(0.5 * (np.cos(2 * np.pi * x) + np.cos(2 * np.pi * y)))

examples/gallery/lines/vector_styles.py

@@ -4,9 +4,7 @@
 
 The :meth:`pygmt.Figure.plot` method can plot Cartesian, circular, and
 geographic vectors. The ``style`` parameter controls vector attributes.
-See also
-:doc:`Vector attributes example </gallery/lines/vector_heads_tails>`.
-
+See also :doc:`Vector attributes example </gallery/lines/vector_heads_tails>`.
 """
 
 # %%

examples/tutorials/advanced/working_with_panel.py

@@ -73,9 +73,11 @@
 )
 
 
-# Define a function for plotting the single slices
 @pn.depends(central_lon=slider_lon)
 def view(central_lon):
+    """
+    Define a function for plotting the single slices.
+    """
     # Create a new instance or object of the pygmt.Figure() class
     fig = pygmt.Figure()
     fig.coast(
@@ -112,9 +114,11 @@ def view(central_lon):
 )
 
 
-# Define a function for plotting the single slices
 @pn.depends(central_lon=slider_lon)
 def view(central_lon):
+    """
+    Define a function for plotting the single slices.
+    """
     # Create a new instance or object of the pygmt.Figure() class
     fig = pygmt.Figure()
     # Set up a colormap for the elevation in meters

pygmt/figure.py

@@ -88,7 +88,9 @@ def __init__(self):
         self._activate_figure()
 
     def __del__(self):
-        # Clean up the temporary directory that stores the previews
+        """
+        Clean up the temporary directory that stores the previews.
+        """
         if hasattr(self, "_preview_dir"):
             self._preview_dir.cleanup()
 

pygmt/helpers/decorators.py

@@ -445,7 +445,7 @@ def fmt_docstring(module_func):
     - J = projection
     - R = region
     <BLANKLINE>
-    """
+    """  # noqa: D410,D411
     filler_text = {}
 
     if hasattr(module_func, "aliases"):

pygmt/helpers/tempfile.py

@@ -62,9 +62,15 @@ def __init__(self, prefix="pygmt-", suffix=".txt"):
             self.name = tmpfile.name
 
     def __enter__(self):
+        """
+        Do nothing but return the object.
+        """
         return self
 
     def __exit__(self, *args):
+        """
+        Remove the temporary file.
+        """
         if os.path.exists(self.name):
             os.remove(self.name)
 

pygmt/helpers/utils.py

@@ -529,7 +529,7 @@ def args_in_kwargs(args, kwargs):
         short-form aliases of the parameters.
 
     Returns
-    --------
+    -------
     bool
         If one of the required arguments is in ``kwargs``.
 

pygmt/src/config.py

@@ -203,10 +203,15 @@ def __init__(self, **kwargs):
             lib.call_module(module="set", args=arg_str)
 
     def __enter__(self):
+        """
+        Do nothing but return the object.
+        """
         return self
 
     def __exit__(self, exc_type, exc_value, traceback):
-        # revert to initial values
+        """
+        Revert GMT configurations to initial values.
+        """
         arg_str = " ".join(
             [f'{key}="{value}"' for key, value in self.old_defaults.items()]
         )

pygmt/src/grdhisteq.py

@@ -102,7 +102,7 @@ def _grdhisteq(grid, output_type, **kwargs):
               ``outgrid`` or ``outfile``)
 
         See Also
-        -------
+        --------
         :func:`pygmt.grd2cpt`
         """
 
@@ -194,7 +194,7 @@ def equalize_grid(
         >>> grid = pygmt.grdhisteq.equalize_grid(grid=grid, gaussian=True)
 
         See Also
-        -------
+        --------
         :func:`pygmt.grd2cpt`
 
         Note
@@ -306,7 +306,7 @@ def compute_bins(
         4       705.0  2275.5
 
         See Also
-        -------
+        --------
         :func:`pygmt.grd2cpt`
 
         Note

pygmt/src/grdtrack.py

@@ -209,7 +209,7 @@ def grdtrack(grid, points=None, newcolname=None, outfile=None, **kwargs):
         - **+c**\ *fact* : Compute envelope on stacked profile as
           ±\ *fact* \*\ *deviation* [Default fact value is 2].
 
-        Notes:
+        Here are some notes:
 
         1. Deviations depend on *method* and are st.dev (**a**), L1 scale,
            i.e., 1.4826 \* median absolute deviation (MAD) (for **m** and

pygmt/tests/__init__.py

@@ -0,0 +1,3 @@
+"""
+PyGMT test suite.
+"""

pygmt/tests/test_clib_loading.py

@@ -24,6 +24,9 @@ def __init__(self, name):
         self._name = name
 
     def __str__(self):
+        """
+        String representation of the object.
+        """
         return self._name
 
 

pyproject.toml

@@ -75,14 +75,6 @@ ignore-words-list = "astroid,oints,reenable,tripel,trough"
 [tool.coverage.run]
 omit = ["*/tests/*", "*pygmt/__init__.py"]
 
-[tool.docformatter]
-black = true
-recursive = true
-pre-summary-newline = true
-make-summary-multi-line = true
-wrap-summaries = 88
-wrap-descriptions = 88
-
 [tool.mypy]
 exclude = ["pygmt/tests/"]
 ignore_missing_imports = true
@@ -103,6 +95,7 @@ select = [
     "B",    # flake8-bugbear
     "BLE",  # flake8-blind-except
     "C4",   # flake8-comprehensions
+    "D",    # pydocstyle
     "E",    # pycodestyle
     "EXE",  # flake8-executable
     "F",    # pyflakes
@@ -131,7 +124,17 @@ select = [
     "W",    # pycodestyle warnings
     "YTT",  # flake8-2020
 ]
+extend-select = [
+    "D213",  # Summary lines should be positioned on the second physical line of the docstring.
+    "D410",  # A blank line after section headings.
+]
 ignore = [
+    "D200",     # One-line docstring should fit on one line
+    "D202",     # No blank lines allowed after function docstring
+    "D205",     # 1 blank line required between summary line and description
+    "D400",     # First line should end with a period
+    "D401",     # First line of docstring should be in imperative mood
+    "D412",     # No blank lines allowed between a section header and its content
     "E501",     # Avoid enforcing line-length violations
     "ISC001",   # Single-line-implicit-string-concatenation, conflict with formatter
     "PD901",    # Allow using the generic variable name `df` for DataFrames
@@ -153,6 +156,11 @@ known-third-party = ["pygmt"]
 [tool.ruff.lint.pycodestyle]
 max-doc-length = 88
 
+[tool.ruff.lint.pydocstyle]
+# See https://docs.astral.sh/ruff/faq/#does-ruff-support-numpy-or-google-style-docstrings
+# for the enabled/disabled rules for the "numpy" convention.
+convention = "numpy"
+
 [tool.ruff.lint.pylint]
 max-args=10