Merge pull request #31 from khanlab/fix-flake8

Update quality workflow to check instead of modify

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 79

.github/workflows/quality.yml

@@ -51,16 +51,16 @@ jobs:
         run: poetry install --no-interaction --no-root --with dev
 
       - name: yamlfix
-        run: poetry run poe yamlfix
+        run: poetry run poe yamlfix-check
 
       - name: isort
-        run: poetry run poe isort
+        run: poetry run poe isort-check
 
       - name: black
-        run: poetry run poe black
+        run: poetry run poe black-check
 
       - name: flake8
         run: poetry run poe flake8
 
       - name: snakefmt
-        run: poetry run poe snakefmt
+        run: poetry run poe snakefmt-check

labelmerge/workflow/rules/label_harmonization.smk

@@ -77,8 +77,12 @@ rule merge_labels:
             **base_inputs["labelmap"].input_wildcards,
         ),
     params:
-        base_exceptions=f"--base_exceptions {' '.join(config['base_exceptions'])}" if config.get("base_exceptions") else "",
-        overlay_exceptions=f"--overlay_exceptions {' '.join(config['overlay_exceptions'])}" if config.get("overlay_exceptions") else "",
+        base_exceptions=f"--base_exceptions {' '.join(config['base_exceptions'])}"
+        if config.get("base_exceptions")
+        else "",
+        overlay_exceptions=f"--overlay_exceptions {' '.join(config['overlay_exceptions'])}"
+        if config.get("overlay_exceptions")
+        else "",
     resources:
         script=str(Path(workflow.basedir) / "scripts" / "labelmerge.py"),
     shell:

labelmerge/workflow/scripts/labelmerge.py

@@ -1,14 +1,15 @@
 #!/usr/bin/env python
 from __future__ import annotations
+
 from argparse import ArgumentParser
 from os import PathLike
 from pathlib import Path
 
 import nibabel as nib
 import numpy as np
-from numpy.typing import ArrayLike
 import pandas as pd
 import xarray as xr
+from numpy.typing import ArrayLike
 
 
 def load_atlas(atlas_path: PathLike):
@@ -35,7 +36,8 @@ def assemble_mask(
         name: str = metadata[metadata["index"] == label].name.iloc[0]
     except IndexError as err:
         raise MetadataError(
-            f"Label with index {label} from {prefix}atlas not found in metadata table."
+            f"Label with index {label} from {prefix}atlas not found in "
+            "metadata table."
         ) from err
     return (
         f"{prefix}{name}",
@@ -121,16 +123,17 @@ def gen_parser() -> ArgumentParser:
         "--base_exceptions",
         nargs="*",
         help=(
-            "Space separated list of integer labels from the base image to keep over "
-            "overlay labels at the same voxels."
+            "Space separated list of integer labels from the base image to "
+            "keep over overlay labels at the same voxels."
         ),
         type=int,
     )
     parser.add_argument(
         "--overlay_exceptions",
         nargs="*",
         help=(
-            "Space separated list of integer labels from the overlay image to discard."
+            "Space separated list of integer labels from the overlay image to "
+            "discard."
         ),
         type=int,
     )
@@ -145,7 +148,9 @@ def main():
     overlay_data, _, _ = load_atlas(Path(args.overlay_map))
     overlay_metadata = pd.read_csv(args.overlay_metadata, sep="\t")
     base_exceptions = args.base_exceptions if args.base_exceptions else []
-    overlay_exceptions = args.overlay_exceptions if args.overlay_exceptions else []
+    overlay_exceptions = (
+        args.overlay_exceptions if args.overlay_exceptions else []
+    )
     base_datasets = split_labels(
         base_data,
         base_metadata,

pyproject.toml

@@ -40,11 +40,22 @@ build-backend = "poetry.core.masonry.api"
 [tool.poe.tasks]
 setup = "pre-commit install"
 yamlfix = { shell = "find . -type f \\( -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* ! -iname snakebids* \\) -exec yamlfix {} \\;" }
-isort = "isort labelmerge/*.py"
+yamlfix-check = { shell = "find . -type f \\( -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* ! -iname snakebids* \\) -exec yamlfix --check {} \\;" }
+isort = "isort labelmerge"
+isort-check = "isort -c labelmerge"
 black = "black labelmerge"
+black-check = "black --check labelmerge"
 flake8 = "flake8 labelmerge"
 snakefmt = "snakefmt labelmerge"
+snakefmt-check = "snakefmt --check labelmerge"
 quality = ["yamlfix", "isort", "black", "flake8", "snakefmt"]
+quality-check = [
+    "yamlfix-check",
+    "isort-check",
+    "black-check",
+    "flake8",
+    "snakefmt-check",
+]
 
 [tool.isort]
 profile = "black"
@@ -53,9 +64,6 @@ multi_line_output = 3
 [tool.black]
 line-length = 79
 
-[tool.flake8]
-ignore = 'E501'
-
 [tool.snakefmt]
 line_length = 79
 include = '\.smk$|^Snakefile'