From 876e8fd1f581e466482f33980769de0d779f039f Mon Sep 17 00:00:00 2001
From: Adam Gayoso <adamgayoso@users.noreply.github.com>
Date: Sun, 1 Sep 2024 17:12:20 +0100
Subject: [PATCH] Add more ruff rules (#177)

* Add more ruff rules

* remove bandit

* Add FA

* fixes

* Remove D400
---
 docs/extensions/typed_returns.py    | 10 +++++----
 pyproject.toml                      | 32 ++++++++++++++---------------
 src/scib_metrics/benchmark/_core.py |  8 ++++----
 3 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index 1135204..8eceeb6 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -1,12 +1,14 @@
 # code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
 # with some minor adjustment
 from __future__ import annotations
-
+from sphinx.ext.napoleon import NumpyDocstring
+from typing import TYPE_CHECKING
 import re
-from collections.abc import Generator, Iterable
 
-from sphinx.application import Sphinx
-from sphinx.ext.napoleon import NumpyDocstring
+if TYPE_CHECKING:
+    from collections.abc import Generator, Iterable
+
+    from sphinx.application import Sphinx
 
 
 def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
diff --git a/pyproject.toml b/pyproject.toml
index d550a21..3c65b09 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,10 +35,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pre-commit",
-    "twine>=4.0.2",
-]
+dev = ["pre-commit", "twine>=4.0.2"]
 doc = [
     "sphinx>=4",
     "sphinx-book-theme>=1.0",
@@ -93,17 +90,20 @@ xfail_strict = true
 src = ["src"]
 line-length = 120
 lint.select = [
-    "F",  # Errors detected by Pyflakes
-    "E",  # Error detected by Pycodestyle
-    "W",  # Warning detected by Pycodestyle
-    "I",  # isort
-    "D",  # pydocstyle
-    "B",  # flake8-bugbear
-    "TID",  # flake8-tidy-imports
-    "C4",  # flake8-comprehensions
-    "BLE",  # flake8-blind-except
-    "UP",  # pyupgrade
-    "RUF100",  # Report unused noqa directives
+    "F",      # Errors detected by Pyflakes
+    "E",      # Error detected by Pycodestyle
+    "W",      # Warning detected by Pycodestyle
+    "I",      # isort
+    "D",      # pydocstyle
+    "B",      # flake8-bugbear
+    "TID",    # flake8-tidy-imports
+    "C4",     # flake8-comprehensions
+    "BLE",    # flake8-blind-except
+    "UP",     # pyupgrade
+    "RUF100", # Report unused noqa directives
+    "ICN",    # flake8-import-conventions
+    "TCH",    # flake8-type-checking
+    "FA",     # flake8-future-annotations
 ]
 lint.ignore = [
     # line too long -> we accept long comment lines; formatter gets rid of long code lines
@@ -122,8 +122,6 @@ lint.ignore = [
     "B008",
     # __magic__ methods are are often self-explanatory, allow missing docstrings
     "D105",
-    # first line should end with a period [Bug: doesn't work with single-line docstrings]
-    "D400",
     # First line should be in imperative mood; try rephrasing
     "D401",
     ## Disable one in each pair of mutually incompatible rules
diff --git a/src/scib_metrics/benchmark/_core.py b/src/scib_metrics/benchmark/_core.py
index c159da9..dcfc259 100644
--- a/src/scib_metrics/benchmark/_core.py
+++ b/src/scib_metrics/benchmark/_core.py
@@ -6,7 +6,7 @@
 from functools import partial
 from typing import Any
 
-import matplotlib
+import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -297,7 +297,7 @@ def plot_results_table(self, min_max_scale: bool = True, show: bool = True, save
             The directory to save the plot to. If `None`, the plot is not saved.
         """
         num_embeds = len(self._embedding_obsm_keys)
-        cmap_fn = lambda col_data: normed_cmap(col_data, cmap=matplotlib.cm.PRGn, num_stds=2.5)
+        cmap_fn = lambda col_data: normed_cmap(col_data, cmap=mpl.cm.PRGn, num_stds=2.5)
         df = self.get_results(min_max_scale=min_max_scale)
         # Do not want to plot what kind of metric it is
         plot_df = df.drop(_METRIC_TYPE, axis=0)
@@ -335,7 +335,7 @@ def plot_results_table(self, min_max_scale: bool = True, show: bool = True, save
                 title=col.replace(" ", "\n", 1),
                 plot_fn=bar,
                 plot_kw={
-                    "cmap": matplotlib.cm.YlGnBu,
+                    "cmap": mpl.cm.YlGnBu,
                     "plot_bg_bar": False,
                     "annotate": True,
                     "height": 0.9,
@@ -347,7 +347,7 @@ def plot_results_table(self, min_max_scale: bool = True, show: bool = True, save
             for i, col in enumerate(score_cols)
         ]
         # Allow to manipulate text post-hoc (in illustrator)
-        with matplotlib.rc_context({"svg.fonttype": "none"}):
+        with mpl.rc_context({"svg.fonttype": "none"}):
             fig, ax = plt.subplots(figsize=(len(df.columns) * 1.25, 3 + 0.3 * num_embeds))
             tab = Table(
                 plot_df,