Add new ruff rules and apply rules to codes

Author: moshi4

pyproject.toml

@@ -68,22 +68,36 @@ line-length = 88
 # Lint Rules: https://docs.astral.sh/ruff/rules/
 [tool.ruff.lint]
 select = [
-    "F", # pyflakes
-    "E", # pycodestyle (Error)
-    "W", # pycodestyle (Warning)
-    "I", # isort
-    "D", # pydocstyle
+    "I",   # isort
+    "F",   # pyflakes
+    "E",   # pycodestyle (Error)
+    "W",   # pycodestyle (Warning)
+    "D",   # pydocstyle
+    "UP",  # pyupgrade
+    "PL",  # Pylint
+    "ANN", # flake8-annotations
+    "TC",  # flake8-type-checking
+    "B",   # flake8-bugbear
+    "SIM", # flake8-simplify
+    "ARG", # flake8-unused-arguments
+    "PTH", # flake8-use-pathlib
+    "RUF", # Ruff-specific rules
 ]
 ignore = [
-    "D100", # Missing docstring in public module
-    "D101", # Missing docstring in public class
-    "D104", # Missing docstring in public package
-    "D105", # Missing docstring in magic method
-    "D205", # 1 blank line required between summary line and description
-    "D400", # First line should end with a period
-    "D401", # First line should be in imperative mood
-    "D403", # First word of the first line should be properly capitalized
-    "D415", # First line should end with a period, question mark, or exclamation point
+    "D100",    # Missing docstring in public module
+    "D101",    # Missing docstring in public class
+    "D104",    # Missing docstring in public package
+    "D105",    # Missing docstring in magic method
+    "D205",    # 1 blank line required between summary line and description
+    "D400",    # First line should end with a period
+    "D401",    # First line should be in imperative mood
+    "D403",    # First word of the first line should be properly capitalized
+    "D415",    # First line should end with a period, question mark, or exclamation point
+    "ANN003",  # Missing type annotation for **{name}
+    "PTH123",  # open() should be replaced by Path.open()
+    "PLR0913", # Too many arguments in function definition ({c_args} > {max_args})
+    "PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
+    "UP038",   # Deprecated: Use X | Y in {} call instead of (X, Y)
 ]
 
 [tool.ruff.lint.pydocstyle]

src/pycirclize/annotation.py

@@ -2,16 +2,19 @@
 
 import warnings
 from collections import defaultdict
+from typing import TYPE_CHECKING
 
 import numpy as np
-from matplotlib.projections.polar import PolarAxes
 from matplotlib.text import Annotation, Text
-from matplotlib.transforms import Bbox
-from numpy.typing import NDArray
 
 from pycirclize import config, utils
 from pycirclize.utils.plot import degrees
 
+if TYPE_CHECKING:
+    from matplotlib.projections.polar import PolarAxes
+    from matplotlib.transforms import Bbox
+    from numpy.typing import NDArray
+
 
 def adjust_annotation(ax: PolarAxes) -> None:
     """Adjust annotation text position"""
@@ -20,7 +23,10 @@ def adjust_annotation(ax: PolarAxes) -> None:
     if len(ann_list) == 0 or config.ann_adjust.max_iter <= 0:
         return
     if len(ann_list) > config.ann_adjust.limit:
-        warnings.warn(f"Too many annotations(={len(ann_list)}). Annotation position adjustment is not done.")  # fmt: skip  # noqa: E501
+        warnings.warn(
+            f"Too many annotations(={len(ann_list)}). Annotation position adjustment is not done.",  # noqa: E501
+            stacklevel=2,
+        )
         return
 
     def get_ann_window_extent(ann: Annotation) -> Bbox:
@@ -70,7 +76,7 @@ def _get_sorted_ann_list(ax: PolarAxes) -> list[Annotation]:
         loc = utils.plot.get_loc(ann.xyann[0])
         loc2ann_list[loc].append(ann)
 
-    def sort_by_ann_rad(ann: Annotation):
+    def sort_by_ann_rad(ann: Annotation) -> float:
         return utils.plot.degrees(ann.xyann[0])
 
     return (

src/pycirclize/circos.py

@@ -5,21 +5,17 @@
 import textwrap
 import warnings
 from collections import defaultdict
-from collections.abc import Mapping
+from collections.abc import Callable, Sequence
 from copy import deepcopy
 from pathlib import Path
-from typing import Any, Callable, Sequence
+from typing import TYPE_CHECKING, Any
 
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-from Bio.Phylo.BaseTree import Tree
-from matplotlib.axes import Axes
 from matplotlib.collections import PatchCollection
 from matplotlib.colorbar import Colorbar
 from matplotlib.colors import Colormap, Normalize
-from matplotlib.figure import Figure
-from matplotlib.patches import Patch
 from matplotlib.projections.polar import PolarAxes
 
 from pycirclize import config, utils
@@ -39,9 +35,18 @@
     to_cytoband_tooltip,
     to_link_tooltip,
 )
-from pycirclize.track import Track
 from pycirclize.tree import TreeViz
-from pycirclize.typing import Numeric
+
+if TYPE_CHECKING:
+    from collections.abc import Mapping
+
+    from Bio.Phylo.BaseTree import Tree
+    from matplotlib.axes import Axes
+    from matplotlib.figure import Figure
+    from matplotlib.patches import Patch
+
+    from pycirclize.track import Track
+    from pycirclize.typing import Numeric
 
 
 class Circos:
@@ -57,7 +62,7 @@ def __init__(
         endspace: bool = True,
         sector2clockwise: dict[str, bool] | None = None,
         show_axis_for_debug: bool = False,
-    ):
+    ) -> None:
         """
         Parameters
         ----------
@@ -87,7 +92,7 @@ def __init__(
         if isinstance(space, Sequence):
             if len(space) != space_num:
                 raise ValueError(f"{space=} is invalid.\nLength of space list must be {space_num}.")  # fmt: skip  # noqa: E501
-            space_list = list(space) + [0]
+            space_list = [*list(space), 0]
             space_deg_size = sum(space)
         else:
             space_list = [space] * space_num + [0]
@@ -181,22 +186,22 @@ def ax(self) -> PolarAxes:
     ############################################################
 
     @classmethod
-    def set_tooltip_enabled(cls, enabled: bool = True):
+    def set_tooltip_enabled(cls, enabled: bool = True) -> None:
         """Enable/disable tooltip annotation using ipympl"""
         if enabled:
             try:
-                import ipympl  # noqa: F401
-                from IPython import get_ipython  # type: ignore
+                import ipympl  # noqa: F401, PLC0415
+                from IPython import get_ipython  # noqa: PLC0415
 
                 get_ipython().run_line_magic("matplotlib", "widget")
                 config.tooltip.enabled = True
             except Exception:
-                warnings.warn("Failed to enable tooltip. To enable tooltip, an interactive python environment such as jupyter and ipympl installation are required.")  # fmt: skip  # noqa: E501
+                warnings.warn("Failed to enable tooltip. To enable tooltip, an interactive python environment such as jupyter and ipympl installation are required.", stacklevel=2)  # fmt: skip  # noqa: E501
         else:
             config.tooltip.enabled = False
 
     @staticmethod
-    def radar_chart(
+    def radar_chart(  # noqa: PLR0912, PLR0915
         table: str | Path | pd.DataFrame | RadarTable,
         *,
         r_lim: tuple[float, float] = (0, 100),
@@ -267,6 +272,7 @@ def radar_chart(
         circos : Circos
             Circos instance initialized for radar chart
         """
+        # TODO: Refactor complex codes
         if not vmin < vmax:
             raise ValueError(f"vmax must be larger than vmin ({vmin=}, {vmax=})")
         size = vmax - vmin
@@ -306,8 +312,8 @@ def radar_chart(
                     if grid_label_formatter:
                         text = grid_label_formatter(v)
                     else:
-                        v = float(f"{v:.9f}")  # Correct rounding error
-                        text = f"{v:.0f}" if math.isclose(int(v), float(v)) else str(v)
+                        v2 = float(f"{v:.9f}")  # Correct rounding error
+                        text = f"{v2:.0f}" if math.isclose(int(v2), v2) else str(v2)
                     track.text(text, 0, r, **grid_label_kws)
             # Plot vertical grid line
             for p in x[:-1]:
@@ -319,7 +325,7 @@ def radar_chart(
         else:
             row_name2color = cmap
         for row_name, values in radar_table.row_name2values.items():
-            y = values + [values[0]]
+            y = [*values, values[0]]
             color = row_name2color[row_name]
             line_kws = line_kws_handler(row_name) if line_kws_handler else {}
             line_kws.setdefault("lw", 1.0)
@@ -441,13 +447,12 @@ def chord_diagram(
         if isinstance(cmap, str):
             utils.ColorCycler.set_cmap(cmap)
             colors = utils.ColorCycler.get_color_list(len(names))
-            name2color = dict(zip(names, colors))
+            name2color = dict(zip(names, colors, strict=True))
+        elif isinstance(cmap, defaultdict):
+            name2color = cmap
         else:
-            if isinstance(cmap, defaultdict):
-                name2color = cmap
-            else:
-                name2color: dict[str, str] = defaultdict(lambda: "grey")
-                name2color.update(cmap)
+            name2color: dict[str, str] = defaultdict(lambda: "grey")
+            name2color.update(cmap)
 
         # Initialize circos sectors
         circos = Circos(matrix.to_sectors(), start, end, space=space, endspace=endspace)
@@ -876,10 +881,8 @@ def link(
         if "lw" not in kwargs and "linewidth" not in kwargs:
             kwargs.update(dict(lw=0.1))
 
-        if not allow_twist:
-            # Resolve twist
-            if (rad_end1 - rad_start1) * (rad_end2 - rad_start2) > 0:
-                rad_start2, rad_end2 = rad_end2, rad_start2
+        if not allow_twist and (rad_end1 - rad_start1) * (rad_end2 - rad_start2) > 0:
+            rad_start2, rad_end2 = rad_end2, rad_start2
 
         # Set tooltip content
         gid = gen_gid("link")

src/pycirclize/parser/__init__.py

@@ -5,9 +5,9 @@
 from pycirclize.parser.table import RadarTable, StackedBarTable
 
 __all__ = [
+    "Bed",
     "Genbank",
     "Gff",
-    "Bed",
     "Matrix",
     "RadarTable",
     "StackedBarTable",

src/pycirclize/parser/bed.py

@@ -2,13 +2,16 @@
 
 import csv
 from dataclasses import dataclass
-from pathlib import Path
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from pathlib import Path
 
 
 class Bed:
     """BED Parser Class"""
 
-    def __init__(self, bed_file: str | Path):
+    def __init__(self, bed_file: str | Path) -> None:
         """
         Parameters
         ----------

src/pycirclize/parser/genbank.py

@@ -28,7 +28,7 @@ def __init__(
         name: str | None = None,
         min_range: None = None,
         max_range: None = None,
-    ):
+    ) -> None:
         """
         Parameters
         ----------
@@ -63,7 +63,10 @@ def __init__(
             raise ValueError("Failed to get genbank name.")
 
         if min_range or max_range:
-            warnings.warn("min_range & max_range is no longer used in Genbank parser.")
+            warnings.warn(
+                "min_range & max_range is no longer used in Genbank parser.",
+                stacklevel=2,
+            )
 
         if len(self.records) == 0:
             raise ValueError(f"Failed to parse {gbk_source} as Genbank file.")
@@ -161,7 +164,7 @@ def calc_gc_skew(
             step_size = int(len(seq) / 1000)
         if window_size == 0 or step_size == 0:
             window_size, step_size = len(seq), int(len(seq) / 2)
-        pos_list = list(range(0, len(seq), step_size)) + [len(seq)]
+        pos_list = [*list(range(0, len(seq), step_size)), len(seq)]
         for pos in pos_list:
             window_start_pos = pos - int(window_size / 2)
             window_end_pos = pos + int(window_size / 2)
@@ -215,7 +218,7 @@ def calc_gc_content(
             step_size = int(len(seq) / 1000)
         if window_size == 0 or step_size == 0:
             window_size, step_size = len(seq), int(len(seq) / 2)
-        pos_list = list(range(0, len(seq), step_size)) + [len(seq)]
+        pos_list = [*list(range(0, len(seq), step_size)), len(seq)]
         for pos in pos_list:
             window_start_pos = pos - int(window_size / 2)
             window_end_pos = pos + int(window_size / 2)
@@ -326,7 +329,7 @@ def extract_features(
             Extracted features
         """
         seqid2features = self.get_seqid2features(feature_type, target_strand)
-        first_record_features = list(seqid2features.values())[0]
+        first_record_features = next(iter(seqid2features.values()))
         if target_range:
             target_features = []
             for feature in first_record_features:
@@ -415,10 +418,9 @@ def _parse_gbk_source(
                 with bz2.open(gbk_source, mode="rt", encoding="utf-8") as f:
                     return list(SeqIO.parse(f, "genbank"))
             elif Path(gbk_source).suffix == ".zip":
-                with zipfile.ZipFile(gbk_source) as zip:
-                    with zip.open(zip.namelist()[0]) as f:
-                        io = TextIOWrapper(f, encoding="utf-8")
-                        return list(SeqIO.parse(io, "genbank"))
+                with zipfile.ZipFile(gbk_source) as z, z.open(z.namelist()[0]) as f:
+                    io = TextIOWrapper(f, encoding="utf-8")
+                    return list(SeqIO.parse(io, "genbank"))
             else:
                 with open(gbk_source, encoding="utf-8") as f:
                     return list(SeqIO.parse(f, "genbank"))
@@ -445,9 +447,9 @@ def _is_straddle_feature(self, feature: SeqFeature) -> bool:
         else:
             start = int(feature.location.parts[0].start)  # type: ignore
             end = int(feature.location.parts[-1].end)  # type: ignore
-        return True if start > end else False
+        return start > end
 
-    def __str__(self):
+    def __str__(self) -> str:
         text = f"{self.name}: {len(self.records)} records\n"
         for num, (seqid, size) in enumerate(self.get_seqid2size().items(), 1):
             text += f"{num:02d}. {seqid} ({size:,} bp)\n"