Update linting tool versions and replace isort with ruff (#622)

This PR is a small follow-up to #616 (regarding [comments](#616 (review)) by @bdice)

It also introduces a `.git-blame-ignore-revs` to ignore all of the formatting changes introduced in !616 from git blame views

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Bradley Dice (https://github.com/bdice)
  - Gigon Bae (https://github.com/gigony)
  - https://github.com/jakirkham

URL: #622

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Applied black, isort and ruff globally to the codebase
+d489bb3969d67643ad6c3ff62f516b635206ae2a

.pre-commit-config.yaml

@@ -10,25 +10,20 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: debug-statements
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        files: ^python/cucim/src/.*
-        args: ["--settings-path=python/cucim/pyproject.toml"]
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.10.1
     hooks:
       - id: black
         files: (python|legate)/.*
         args: ["--config", "python/cucim/pyproject.toml"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.278
+    rev: v0.1.3
     hooks:
       - id: ruff
-        files: python/.*$
+        types_or: [python, pyi]
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.6
     hooks:
       - id: codespell
         args: ["--toml", "python/cucim/pyproject.toml"]

CONTRIBUTING.md

@@ -59,32 +59,30 @@ The following instructions are for developers and contributors to cuCIM OSS deve
 #### Python
 
 
-cuCIM uses [isort](https://readthedocs.org/projects/isort/), [ruff](https://docs.astral.sh/ruff/) and [black](https://black.readthedocs.io/en/stable/) to ensure a consistent code format
-throughout the project. `isort`, and `flake8` can be installed with
+cuCIM uses [ruff](https://docs.astral.sh/ruff/) and [black](https://black.readthedocs.io/en/stable/) to ensure a consistent code format
+throughout the project. `ruff`, and `black` can be installed with
 `conda` or `pip`:
 
 ```bash
-conda install isort black ruff
+conda install black ruff
 ```
 
 ```bash
-pip install isort black ruff
+pip install black ruff
 ```
 
 These tools are used to auto-format the Python code in the repository. Additionally, there is a CI check in place to enforce that the committed code follows our standards. To run only for the python/cucim folder, change to that folder and run
 
 ```bash
-isort .
 black .
 ruff .
 ```
 
 To also check formatting in top-level folders like `benchmarks`, `examples` and `experiments`, these tools can also be run from the top level of the repository as follows:
 
 ```bash
-isort --settings-path="python/cucim/pyproject.toml" .
 black --config python/cucim/pyproject.toml .
-ruff .
+ruff --config python/cucim/pyproject.toml .
 ```
 
 In addition to these tools, [codespell](https://github.com/codespell-project/codespell) can be used to help diagnose and interactively fix spelling errors in both Python and C++ code. It can also be run from the top level of the repository in interactive mode using:

benchmarks/skimage/_image_bench.py

@@ -157,7 +157,8 @@ def run_benchmark(self, duration=3, verbose=True):
                 var_kwargs_cpu = self._update_kwargs_arrays(var_kwargs1, "cpu")
                 var_kwargs_gpu = self._update_kwargs_arrays(var_kwargs1, "gpu")
 
-                # Note: brute_force=True on 'gpu' because False is not implemented
+                # Note: brute_force=True on 'gpu' because False is not
+                # implemented
                 if "brute_force" in var_kwargs_gpu:
                     var_kwargs_gpu["brute_force"] = True
 

benchmarks/skimage/cucim_color_bench.py

@@ -251,7 +251,10 @@ def main(args):
         "-i",
         "--img_size",
         type=str,
-        help="Size of input image (omit color channel, it will be appended as needed)",
+        help=(
+            "Size of input image (omit color channel, it will be appended "
+            "as needed)"
+        ),
         required=True,
     )
     parser.add_argument(

benchmarks/skimage/cucim_feature_bench.py

@@ -137,7 +137,7 @@ def main(args):
             False,
             True,
         ),
-        # blob detectors. fixed kwargs here are taken from the docstring examples
+        # blob detectors, fixed kwargs are taken from the docstring examples
         (
             "blob_dog",
             dict(threshold=0.05, min_sigma=10, max_sigma=40),

benchmarks/skimage/cucim_filters_bench.py

@@ -143,8 +143,6 @@ def main(args):
             # image sizes/shapes
             shape = tuple(list(map(int, (args.img_size.split(",")))))
 
-            # for shape in [(512, 512), (3840, 2160), (3840, 2160, 3), (192, 192, 192)]:
-
         if function_name in ["gaussian", "unsharp_mask"]:
             fixed_kwargs["channel_axis"] = -1 if shape[-1] == 3 else None
 

benchmarks/skimage/cucim_measure_bench.py

@@ -184,7 +184,7 @@ def main(args):
         # _moments.py
         ("moments", dict(), dict(order=[1, 2, 3, 4]), False, False),
         ("moments_central", dict(), dict(order=[1, 2, 3]), False, True),
-        # omitted from benchmarks (only tiny arrays): moments_normalized, moments_hu
+        # omitted from benchmarks (only tiny arrays): moments_normalized, moments_hu  # noqa: E501
         ("centroid", dict(), dict(), False, True),
         ("inertia_tensor", dict(), dict(), False, True),
         ("inertia_tensor_eigvals", dict(), dict(), False, True),

benchmarks/skimage/cucim_morphology_bench.py

@@ -318,7 +318,10 @@ def main(args):
         "-i",
         "--img_size",
         type=str,
-        help="Size of input image (omit color channel, it will be appended as needed)",
+        help=(
+            "Size of input image (omit color channel, it will be appended "
+            "as needed)"
+        ),
         required=True,
     )
     parser.add_argument(

benchmarks/skimage/cucim_registration_bench.py

@@ -178,7 +178,10 @@ def main(args):
         "-i",
         "--img_size",
         type=str,
-        help="Size of input image (omit color channel, it will be appended as needed)",
+        help=(
+            "Size of input image (omit color channel, it will be appended "
+            "as needed)"
+        ),
         required=True,
     )
     parser.add_argument(

benchmarks/skimage/cucim_restoration_bench.py

@@ -215,7 +215,10 @@ def main(args):
         "-i",
         "--img_size",
         type=str,
-        help="Size of input image (omit color channel, it will be appended as needed)",
+        help=(
+            "Size of input image (omit color channel, it will be appended "
+            "as needed)"
+        ),
         required=True,
     )
     parser.add_argument(

benchmarks/skimage/cucim_segmentation_bench.py

@@ -346,7 +346,10 @@ def main(args):
         "-i",
         "--img_size",
         type=str,
-        help="Size of input image (omit color channel, it will be appended as needed)",
+        help=(
+            "Size of input image (omit color channel, it will be appended "
+            "as needed)"
+        ),
         required=True,
     )
     parser.add_argument(

benchmarks/skimage/cucim_transform_bench.py

@@ -203,7 +203,10 @@ def main(args):
         "-i",
         "--img_size",
         type=str,
-        help="Size of input image (omit color channel, it will be appended as needed)",
+        help=(
+            "Size of input image (omit color channel, it will be appended "
+            "as needed)"
+        ),
         required=True,
     )
     parser.add_argument(

benchmarks/skimage/cupyx_scipy_ndimage_morphology_bench.py

@@ -1,7 +1,6 @@
 import os
 import pickle
 
-import cupy
 import cupy as cp
 import cupyx.scipy.ndimage
 import numpy as np
@@ -143,7 +142,7 @@ def set_args(self, dtype):
                 structure=structure,
                 mask=None,
                 index_str=index_str,
-                # Note: Benchmark runner will change brute_force to True for the GPU
+                # Note: Benchmark runner will change brute_force to True for the GPU  # noqa: E501
                 fixed_kwargs=dict(output=None),
                 var_kwargs=var_kwargs,
             )

examples/python/gds_whole_slide/lz4_nvcomp.py

@@ -42,13 +42,13 @@ def ensure_contiguous_ndarray(buf, max_buffer_size=None, flatten=True):
 
     Notes
     -----
-    This function will not create a copy under any circumstances, it is guaranteed to
-    return a view on memory exported by `buf`.
+    This function will not create a copy under any circumstances, it is
+    guaranteed to return a view on memory exported by `buf`.
     """
     arr = ensure_ndarray(buf)
 
-    # check for object arrays, these are just memory pointers, actual memory holding
-    # item data is scattered elsewhere
+    # check for object arrays, these are just memory pointers, actual memory
+    # holding item data is scattered elsewhere
     if arr.dtype == object:
         raise TypeError("object arrays are not supported")
 

experiments/Supporting_Aperio_SVS_Format/benchmark.py

@@ -148,7 +148,7 @@ def experiment_thread(
         print(f"  hit: {cache.hit_count}   miss: {cache.miss_count}")
         print("  ", psutil.virtual_memory())
 
-        output_text = f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')},thread,{cache_strategy},{input_file},{start_location},{patch_size},{num_workers},{openslide_time},{cucim_time},{rasterio_time},{openslide_time / cucim_time},{rasterio_time / cucim_time},{cache_size},{cache.hit_count},{cache.miss_count}\n"   # noqa: E501
+        output_text = f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')},thread,{cache_strategy},{input_file},{start_location},{patch_size},{num_workers},{openslide_time},{cucim_time},{rasterio_time},{openslide_time / cucim_time},{rasterio_time / cucim_time},{cache_size},{cache.hit_count},{cache.miss_count}\n"  # noqa: E501
         with open("experiment.txt", "a+") as f:
             f.write(output_text)
         print(output_text)

python/cucim/pyproject.toml

@@ -107,46 +107,6 @@ where = ["src"]
 [tool.setuptools.package-data]
 mypkg = ["*.pyi", "*.h", "*.cu"]
 
-[tool.isort]
-profile = "black"
-force_single_line = false
-line_length = 80
-forced_separate = "test_cucim"
-force_grid_wrap = 0
-multi_line_output = 3
-order_by_type = true
-combine_as_imports = true
-include_trailing_comma = true
-known_first_party = [
-    "cucim",
-]
-default_section = "THIRDPARTY"
-sections = [
-    "FUTURE",
-    "STDLIB",
-    "THIRDPARTY",
-    "FIRSTPARTY",
-    "LOCALFOLDER",
-]
-skip = [
-    "3rdparty",
-    "thirdparty",
-    ".eggs",
-    ".git",
-    ".hg",
-    ".mypy_cache",
-    ".tox",
-    ".venv",
-    "ci",
-    "cpp",
-    "_build",
-    "build",
-    "build-debug",
-    "build-release",
-    "_deps",
-    "dist",
-]
-
 [tool.pytest.ini_options]
 # If a pytest section is found in one of the possible config files
 # (pytest.ini, tox.ini or setup.cfg), then pytest will not look for any others,
@@ -173,7 +133,7 @@ testpaths = [
 
 [tool.ruff]
 # see: https://docs.astral.sh/ruff/rules/
-select = ["E", "F", "W"]
+select = ["E", "F", "W", "I"]
 fixable = ["ALL"]
 exclude = [
     # TODO: Remove this in a follow-up where we fix __all__.
@@ -189,10 +149,17 @@ exclude = [
     "__init__.py",
 ]
 line-length = 80
+fix = true
 
 [tool.ruff.per-file-ignores]
 # "src/cucim/skimage/util/tests/test_shape.py" = ["E201", "E202"]
 
+[tool.ruff.isort]
+combine-as-imports = true
+force-single-line = false
+known-first-party = ["cucim"]
+order-by-type = true
+
 [tool.black]
 line-length = 80
 target-version = ["py39"]
@@ -225,9 +192,9 @@ exclude = '''
 # this is only to allow you to run codespell interactively
 # e.g. via
 #   codespell --toml python/cucim/pyproject.toml . -i 3 -w
-skip = "build*,dist,.cache,html,_build,_deps,3rdparty,_static,generated,latex,.git,*.ipynb,test_data/input/LICENSE-3rdparty,jitify_testing"
+skip = "build*,dist,.cache,html,_build,_deps,3rdparty/*,_static,generated,latex,.git,*.ipynb,test_data/input/LICENSE-3rdparty,jitify_testing"
 # ignore-regex = ""
-ignore-words-list = "ans,coo,boun,bui,gool,hart,lond,nd,paeth,unser,wronly"
+ignore-words-list = "ans,coo,boun,bui,gool,hart,lond,manuel,nd,paeth,unser,wronly"
 quiet-level = 3
 
 # to undo: ./test_data/input/LICENSE-3rdparty

python/cucim/src/cucim/skimage/segmentation/_chan_vese.py

@@ -258,7 +258,7 @@ def _cv_small_disk(image_size):
 
 def _cv_init_level_set(init_level_set, image_shape, dtype=cp.float64):
     """Generates an initial level set function conditional on input arguments."""  # noqa: E501
-    if type(init_level_set) == str:
+    if isinstance(init_level_set, str):
         if init_level_set == "checkerboard":
             res = _cv_checkerboard(image_shape, 5, dtype)
         elif init_level_set == "disk":

python/cucim/src/cucim/skimage/segmentation/tests/test_expand_labels.py

@@ -17,7 +17,7 @@
 # to avoid bias, but as we are relying on the index map returned
 # by the scipy.ndimage distance transform, what actually happens
 # is determined by the upstream implementation of the distance
-# tansform, thus we don't give any guarantees for the edge case pixels.
+# transform, thus we don't give any guarantees for the edge case pixels.
 #
 # Regardless, it seems prudent to have a test including an edge case
 # so we can detect whether future upstream changes in scipy.ndimage

python/cucim/src/cucim/skimage/transform/_warps.py

@@ -805,7 +805,7 @@ def warp_coords(coord_map, shape, dtype=cp.float64):
     images used by `warp()`.
 
     It is provided separately from `warp` to give additional flexibility to
-    users who would like, for example, to re-use a particular coordinate
+    users who would like, for example, to reuse a particular coordinate
     mapping, to use specific dtypes at various points along the the
     image-warping process, or to implement different post-processing logic
     than `warp` performs after the call to `ndi.map_coordinates`.

scripts/auditwheel_repair.py

@@ -83,7 +83,7 @@ def inwheelctx_enter(self):
     # with open(wheel_path, 'r') as f:
     #     wheel_text = f.read()
 
-    # wheel_text = wheel_text.replace('Root-Is-Purelib: true', 'Root-Is-Purelib: false')
+    # wheel_text = wheel_text.replace('Root-Is-Purelib: true', 'Root-Is-Purelib: false')  # noqa: E501
 
     # with open(wheel_path, 'w') as f:
     #     f.write(wheel_text)