style: swap out black for ruff-format

ruff-format is a rust implementation of the black formatter that is 10x faster with 99.9% compatiblity. This commit swaps out black for the ruff-format as the pre-commit hook that checks formatting.

.pre-commit-config.yaml

@@ -1,9 +1,8 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.6"
     hooks:
-      - id: black
-        language_version: python3.9
+      - id: ruff-format
         exclude: tutorials/nbconverted/
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v2.7.1"

pycytominer/cyto_utils/DeepProfiler_processing.py

@@ -1,6 +1,7 @@
 """
 Utility function to load and process the output files of a DeepProfiler run.
 """
+
 import os
 import pathlib
 import numpy as np

pycytominer/cyto_utils/cells.py

@@ -787,9 +787,8 @@ def merge_single_cells(
             self.image_df.merge(sc_df, on=self.merge_cols, how="right")
             # pandas rename performance may be improved using copy=False, inplace=False
             # reference: https://ryanlstevens.github.io/2022-05-06-pandasColumnRenaming/
+            .rename(self.linking_col_rename, axis="columns", copy=False, inplace=False)
             .rename(
-                self.linking_col_rename, axis="columns", copy=False, inplace=False
-            ).rename(
                 self.full_merge_suffix_rename, axis="columns", copy=False, inplace=False
             )
         )

pycytominer/cyto_utils/single_cell_ingest_utils.py

@@ -71,8 +71,8 @@ def assert_linking_cols_complete(linking_cols="default", compartments="default")
     # Confirm that every compartment has been specified in the linking_cols
     unique_linking_cols = sorted(list(set(unique_linking_cols)))
     diff_column = set(compartments).difference(unique_linking_cols)
-    assert unique_linking_cols == sorted(
-        compartments
+    assert (
+        unique_linking_cols == sorted(compartments)
     ), "All compartments must be specified in the linking_cols, {miss} is missing".format(
         miss=diff_column
     )

pycytominer/feature_select.py

@@ -1,6 +1,7 @@
 """
 Select features to use in downstream analysis based on specified selection method
 """
+
 from pycytominer.operations import (
     correlation_threshold,
     variance_threshold,

pyproject.toml

@@ -111,9 +111,51 @@ version_files = [
     "CITATION.cff"
 ]
 
-[tool.black]
+[tool.ruff]
+target-version = "py38"
 line-length = 88
-target-version = ['py39']
+fix = true
+select = [
+    # flake8-2020
+    # "YTT",
+    # flake8-bandit
+    #"S",
+    # flake8-bugbear
+    # "B",
+    # flake8-builtins
+    # "A",
+    # flake8-comprehensions
+    # "C4",
+    # flake8-debugger
+    # "T10",
+    # flake8-simplify
+    # "SIM",
+    # isort
+    # "I",
+    # mccabe
+    # "C90",
+    # pycodestyle
+    # "E", "W",
+    # pyflakes
+    # "F",
+    # pygrep-hooks
+    # "PGH",
+    # pyupgrade
+    # "UP",
+    # ruff
+    # "RUF",
+    # tryceratops
+    # "TRY",
+]
+ignore = [
+    # LineTooLong
+    "E501",
+    # DoNotAssignLambda
+    "E731",
+]
+
+[tool.ruff.format]
+preview = true
 
 [tool.pytest.ini_options]
 testpaths = "tests"

tests/test_cyto_utils/test_DeepProfiler_processing.py

@@ -1,6 +1,7 @@
 """
 This tests the output from a DeepProfiler run (May 2021)
 """
+
 import os
 import random
 import pytest