update linters and move their configurations from setup.cfg to pyproj…

…ect.toml (#616)

The first commit here is from #615

This MR makes multiple linting-related changes to cuCIM
- moves existing `isort` config from `setup.cfg` to a new `pyproject.toml` file
- update `isort` conventions to match other RAPIDS projects
- add `black` and apply it (use `fmt::off`/`fmt::on` as needed to preserve formatting of look-up tables and test cases)
- replace use of `flake8` with `ruff`
- add config for `codespell` and apply recommended fixes across both C++ and Python code
- update CONTRIBUTING.md instructions to reflect these changes
- Pre-commit hooks for `black`, `ruff` and `codespell` were added. The pre-commit hook for `flake8` was removed.

The only non-linting change is
- move pytest configuration from `setup.cfg` to `pyproject.toml`

I plan to leave any build-system related changes to `pyproject.toml` to a follow-up MR. This MR focuses only on linting/testing.

It will probably be easiest to review the individual commits. Some, like applying `black` are quite large.

Fixes #23

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

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

URL: #616

.pre-commit-config.yaml

@@ -15,10 +15,23 @@ repos:
     hooks:
       - id: isort
         files: ^python/cucim/src/.*
-        args: ["--settings-path=python/cucim/setup.cfg"]
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+        args: ["--settings-path=python/cucim/pyproject_.toml"]
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
     hooks:
-      - id: flake8
-        args: ["--config=python/cucim/setup.cfg"]
-        files: ^python/cucim/.*
+      - id: black
+        files: (python|legate)/.*
+        args: ["--config", "python/cucim/pyproject_.toml"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.278
+    hooks:
+      - id: ruff
+        files: python/.*$
+        args: ["--exclude", "__init__.py"]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        args: ["--toml", "python/cucim/pyproject_.toml"]
+        additional_dependencies:
+          - tomli

CHANGELOG.md

@@ -95,7 +95,7 @@
 ## 🐛 Bug Fixes
 
 - Fix bug in median filter with non-uniform footprint ([#521](https://github.com/rapidsai/cucim/pull/521)) [@grlee77](https://github.com/grlee77)
-- use cp.around instead of cp.round for CuPy 10.x compatiblity ([#508](https://github.com/rapidsai/cucim/pull/508)) [@grlee77](https://github.com/grlee77)
+- use cp.around instead of cp.round for CuPy 10.x compatibility ([#508](https://github.com/rapidsai/cucim/pull/508)) [@grlee77](https://github.com/grlee77)
 - Fix error in LZ4-compressed Zarr writing demo ([#506](https://github.com/rapidsai/cucim/pull/506)) [@grlee77](https://github.com/grlee77)
 - Normalize whitespace. ([#474](https://github.com/rapidsai/cucim/pull/474)) [@bdice](https://github.com/bdice)
 

CONTRIBUTING.md

@@ -58,27 +58,43 @@ The following instructions are for developers and contributors to cuCIM OSS deve
 
 #### Python
 
-cuCIM uses [isort](https://readthedocs.org/projects/isort/), and
-[flake8](http://flake8.pycqa.org/en/latest/) to ensure a consistent code format
+
+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
 `conda` or `pip`:
 
 ```bash
-conda install isort flake8
+conda install isort black ruff
+```
+
+```bash
+pip install isort 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
-pip install isort flake8
+isort --settings-path="python/cucim/pyproject.toml" .
+black --config python/cucim/pyproject.toml .
+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. You can use the tools to
-automatically format your python code by running:
+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:
 
 ```bash
-isort --atomic python/**/*.py
+codespell --toml python/cucim/pyproject.toml . -i 3 -w
 ```
 
+If codespell is finding false positives in newly added code, the `ignore-words-list` entry of the `tool.codespell` section in `pyproject.toml` can be updated as needed.
+
 ### Get libcucim Dependencies
 
 Compiler requirements:

benchmarks/skimage/_image_bench.py

@@ -1,17 +1,18 @@
 import itertools
 import math
+import re
+import subprocess
 import time
 import types
 from collections import abc
-import re
-import subprocess
 
 import cupy as cp
 import cupyx.scipy.ndimage
 import numpy as np
 import pandas as pd
 import scipy.ndimage
 import skimage.data
+
 from cucim.time import repeat
 
 
@@ -32,13 +33,11 @@ def __init__(
         fixed_kwargs={},
         var_kwargs={},
         index_str=None,  # extra string to append to dataframe index
-        # set_args_kwargs={},  # for passing additional arguments to custom set_args method
         module_cpu=scipy.ndimage,
         module_gpu=cupyx.scipy.ndimage,
         function_is_generator=False,
-        run_cpu=True
+        run_cpu=True,
     ):
-
         self.shape = shape
         self.function_name = function_name
         self.fixed_kwargs_cpu = self._update_kwargs_arrays(fixed_kwargs, "cpu")
@@ -171,17 +170,23 @@ def run_benchmark(self, duration=3, verbose=True):
                     self.func_gpu, self.args_gpu, kw_gpu, duration, cpu=False
                 )
                 print("Number of Repetitions : ", rep_kwargs_gpu)
-                perf_gpu = repeat(self.func_gpu, self.args_gpu, kw_gpu, **rep_kwargs_gpu)
+                perf_gpu = repeat(
+                    self.func_gpu, self.args_gpu, kw_gpu, **rep_kwargs_gpu
+                )
 
                 df.at[index, "shape"] = f"{self.shape}"
                 # df.at[index,  "description"] = index
                 df.at[index, "function_name"] = self.function_name
                 df.at[index, "dtype"] = np.dtype(dtype).name
                 df.at[index, "ndim"] = len(self.shape)
 
-                if self.run_cpu == True:
-                    perf = repeat(self.func_cpu, self.args_cpu, kw_cpu, **rep_kwargs_cpu)
-                    df.at[index, "GPU accel"] = perf.cpu_times.mean() / perf_gpu.gpu_times.mean()
+                if self.run_cpu is True:
+                    perf = repeat(
+                        self.func_cpu, self.args_cpu, kw_cpu, **rep_kwargs_cpu
+                    )
+                    df.at[index, "GPU accel"] = (
+                        perf.cpu_times.mean() / perf_gpu.gpu_times.mean()
+                    )
                     df.at[index, "CPU: host (mean)"] = perf.cpu_times.mean()
                     df.at[index, "CPU: host (std)"] = perf.cpu_times.std()
 
@@ -191,14 +196,22 @@ def run_benchmark(self, duration=3, verbose=True):
                 df.at[index, "GPU: device (std)"] = perf_gpu.gpu_times.std()
                 with cp.cuda.Device() as device:
                     props = cp.cuda.runtime.getDeviceProperties(device.id)
-                    gpu_name = props['name'].decode()
+                    gpu_name = props["name"].decode()
 
-                df.at[index, "GPU: DEV Name"] = [gpu_name for i in range(len(df))]
+                df.at[index, "GPU: DEV Name"] = [
+                    gpu_name for i in range(len(df))
+                ]
                 cmd = "cat /proc/cpuinfo"
                 cpuinfo = subprocess.check_output(cmd, shell=True).strip()
-                cpu_name = re.search("\nmodel name.*\n", cpuinfo.decode()).group(0).strip('\n')
-                cpu_name = cpu_name.replace('model name\t: ', '')
-                df.at[index, "CPU: DEV Name"] = [cpu_name for i in range(len(df))]
+                cpu_name = (
+                    re.search("\nmodel name.*\n", cpuinfo.decode())
+                    .group(0)
+                    .strip("\n")
+                )
+                cpu_name = cpu_name.replace("model name\t: ", "")
+                df.at[index, "CPU: DEV Name"] = [
+                    cpu_name for i in range(len(df))
+                ]
 
                 # accelerations[arr_index] = df.at[index,  "GPU accel"]
                 if verbose: