Dep updates and expansion of ruff CI

.github/workflows/test.yml

@@ -58,14 +58,12 @@ jobs:
       # run python style checks
       - name: Poetry Lock Check
         run: poetry check --lock
-      - name: isort
-        run: poetry run isort snakebids -c
-      - name: Black
-        run: poetry run black snakebids --check
+      - name: Formatting
+        run: poetry run ruff format snakebids --check
+      - name: Linting
+        run: poetry run ruff check snakebids
       - name: pyright
         run: poetry run pyright snakebids
-      - name: ruff
-        run: poetry run ruff snakebids
 
   build-cache-env:
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -10,23 +10,16 @@ repos:
       - id: trailing-whitespace
   - repo: local
     hooks:
-      - id: isort
-        entry: poetry run isort
-        name: isort
-        language: system
-        types_or: [cython, pyi, python]
-  - repo: local
-    hooks:
-      - id: black
-        entry: poetry run black
-        name: black
+      - id: format
+        entry: poetry run ruff format
+        name: Ruff Format
         language: system
         types_or: [cython, pyi, python]
   - repo: local
     hooks:
       - id: system
-        name: Ruff
-        entry: poetry run ruff
+        name: Ruff Lint
+        entry: poetry run ruff check
         language: system
         exclude: \._py\}\}$
         types_or: [cython, pyi, python]

pyproject.toml

@@ -70,20 +70,18 @@ jinja2-time = ">=0.2.0"
 requests = ">=2.31.0"
 
 [tool.poetry.group.dev.dependencies]
-black = "^23.1.0"
 pytest = "^7.0.0"
 pytest-mock = "^3.7.0"
-isort = "^5.10.1"
-poethepoet = "^0.22.0"
+poethepoet = "^0.24.0"
 pre-commit = "^3.0.0"
 mkinit = "^1.0.0"
 hypothesis = "^6.34.1"
 pytest-benchmark = "^4.0.0"
 pyfakefs = "^5.1.0"
 pyparsing = "^3.0.9"
 pathvalidate = "^3.0.0"
-pyright = "==1.1.324"
-ruff = "^0.0.290"
+pyright = "^1.1.339"
+ruff = "^0.1.7"
 pytest-xdist = "^3.3.1"
 pytest-split = "^0.8.1"
 tomli = "^2.0.1"
@@ -98,13 +96,13 @@ build-backend = "poetry_dynamic_versioning.backend"
 
 [tool.poe.tasks]
 setup = "pre-commit install"
-quality.shell = "isort snakebids && black snakebids && ruff snakebids && pyright snakebids"
-fix.shell = "ruff --fix snakebids && isort snakebids && black snakebids"
+quality.shell = "ruff format --check snakebids && ruff check snakebids && pyright snakebids"
+fix.shell = "ruff format snakebids && ruff check --fix snakebids"
 test = """
 pytest --doctest-modules --ignore=docs \
     --ignore=snakebids/project_template --benchmark-disable
 """
-mkinit = "mkinit --recursive --nomods --black -i snakebids"
+mkinit.shell = "mkinit --recursive --nomods -i snakebids && ruff format snakebids && ruff check --fix --select I001 snakebids "
 benchmark = "pytest --benchmark-only --benchmark-autosave"
 
 [tool.poe.tasks._get_version]
@@ -139,11 +137,100 @@ reportImportCycles = false
 [tool.ruff]
 select = [
     "E",    # pycodestyle error
+    "W",    # pycodestyle warning
     "F",    # pyflakes
+    "N",    # pep8-naming
+    "UP",   # pyupgrade
+    "YTT",  # flake8-2020
+    "S",    # flake8-bandit
+    "BLE",  # flake8-blind-except
+    "B",    # flake8-bugbear
+    "A",    # flake8-builtins
+    "COM",  # flake8-commas
+    "C4",   # flake8-comprehensions
+    "T10",  # flake8-debugger
+    "EM",   # flake8-errmsg
+    "FA",   # flake8-future-annotations
+    "ISC",  # flake8-implicit-str-concat
+    "ICN",  # flake8-import-conventions
+    "G",    # flake8-logging-format
+    "INP",  # flake8-no-pep420
+    "PIE",  # flake8-pie
+    "PT",   # flake8-pytest-style
+    "RSE",  # flake8-raise
+    "RET",  # flake8-return
+    "SLF",  # flake8-self
+    "SIM",  # flake8-simplify
+    # We use os.path a lot in "legitimate" ways, so this ruleset has too many
+    # false positives
+    # "PTH",  # flake8-use-pathlib
+    "TRY",  # tryceratops
+    "FLY",  # flynt
+    "D",    # pydocstyle
     "PL",   # pylint
     "RUF",  # ruff
-    "UP",   #pyupgrade
     "T100", # debugger
+    "I",    # isort
+    # Other perf rules give more false positives than benefits
+    "PERF101", # do not cast iterable to list
 ]
-ignore = ["PLR0913"]
+ignore = [
+    "PLR0913",
+    "D105",     # missing docstring in magic method
+    "D100",     # Require docstring in public modules
+    "D104",     # Require docstring in public packages
+    "S603",     # Subprocess without shell equals true
+    "S607",     # start-process-with-partial-path
+    # recommended ignores for ruff format
+    "W191",
+    "E111",
+    "E114",
+    "E117",
+    "D206",
+    "D300",
+    "Q000",
+    "Q001",
+    "Q002",
+    "Q003",
+    "COM812",
+    "COM819",
+    "ISC001",
+    "ISC002",
+]
+
+
 target-version = "py38"
+
+namespace-packages = ["snakebids/plugins"]
+
+[tool.ruff.per-file-ignores]
+"snakebids/project_template/**" = ["N999"]
+"snakebids/tests/**" = [
+    "D",
+    "S101",     # assert
+    "S307",     # Use of eval
+    "SLF",
+]
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
+ignore-decorators = ["snakebids.utils.utils.property_alias"]
+
+[tool.ruff.flake8-builtins]
+builtins-ignorelist = ["filter"]
+
+[tool.ruff.flake8-import-conventions.extend-aliases]
+itertools = "it"
+functools = "ft"
+operator = "op"
+subprocess = "sp"
+importlib_resources = "impr"
+"importlib.resources" = "impr"
+"importlib.metadata" = "impm"
+more_itertools = "itx"
+"hypothesis.strategies" = "st"
+"snakebids.tests.strategies" = "sb_st"
+"snakebids.utils.sb_itertools" = "sb_it"
+
+[tool.ruff.flake8-pytest-style]
+fixture-parentheses = false

snakebids/__init__.py

@@ -19,7 +19,9 @@
     get_wildcard_constraints,
     write_derivative_json,
 )
-from snakebids.paths import bids
+from snakebids.paths import (
+    bids,
+)
 
 __all__ = [
     "BidsComponent",
@@ -35,5 +37,4 @@
     "get_wildcard_constraints",
     "write_derivative_json",
 ]
-
 # </AUTOGEN_INIT>

snakebids/admin.py

@@ -15,6 +15,7 @@
 
 
 def create_app(args: argparse.Namespace) -> None:
+    """Implement the ``snakebids create`` command."""
     output = Path(args.output_dir).resolve()
     if not output.parent.exists():
         print(
@@ -47,13 +48,15 @@ def create_app(args: argparse.Namespace) -> None:
 
 
 def create_descriptor(args: argparse.Namespace) -> None:
+    """Implement the ``snakebids boutiques`` command."""
     app = SnakeBidsApp(args.app_dir.resolve())
     add_dynamic_args(app.parser, app.config["parse_args"], app.config["pybids_inputs"])
     app.create_descriptor(args.out_path)
     print(f"Boutiques descriptor created at {args.out_path}")
 
 
 def gen_parser() -> argparse.ArgumentParser:
+    """Generate the CLI parser for ``snakebids``."""
     parser = argparse.ArgumentParser(
         description="Perform administrative Snakebids tasks."
     )
@@ -85,7 +88,6 @@ def gen_parser() -> argparse.ArgumentParser:
 
 def main() -> None:
     """Invoke Snakebids cli."""
-
     parser = gen_parser()
     args = parser.parse_args()
     args.func(args)

snakebids/app.py

@@ -4,7 +4,7 @@
 import argparse
 import logging
 import sys
-from importlib import metadata
+from importlib import metadata as impm
 from os import PathLike
 from pathlib import Path
 from typing import Any, Callable
@@ -67,9 +67,8 @@ def wrapper(self: SnakeBidsApp):
                 # else, snakefile
                 return Path(self.snakemake_dir, path)
 
-        raise ConfigError(
-            f"Error: no {file_name} file found, tried {', '.join(choices)}."
-        )
+        msg = f"Error: no {file_name} file found, tried {', '.join(choices)}."
+        raise ConfigError(msg)
 
     return wrapper
 
@@ -85,8 +84,8 @@ def _get_app_version(self: SnakeBidsApp) -> str | None:
        SnakeBidsApp's snakemake_dir
     """
     try:
-        return metadata.version(self.snakemake_dir.name)
-    except metadata.PackageNotFoundError:
+        return impm.version(self.snakemake_dir.name)
+    except impm.PackageNotFoundError:
         logger.warning(
             "App version not found; will be recorded in output as 'unknown'. "
             "If this is unexpected, please contact the app maintainer."
@@ -158,8 +157,7 @@ class SnakeBidsApp:
     args: SnakebidsArgs | None = None
 
     def run_snakemake(self) -> None:
-        """Run snakemake with the given config, after applying plugins"""
-
+        """Run snakemake with the given config, after applying plugins."""
         # If no SnakebidsArgs were provided on class instantiation, we compute args
         # using the provided parser
         if not self.args:
@@ -240,8 +238,8 @@ def run_snakemake(self) -> None:
             config_file=new_config_file,
             data=dict(
                 app.config,
-                snakemake_version=metadata.version("snakemake"),
-                snakebids_version=metadata.version("snakebids"),
+                snakemake_version=impm.version("snakemake"),
+                snakebids_version=impm.version("snakebids"),
                 app_version=app.version or "unknown",
             ),
             force_overwrite=True,
@@ -286,7 +284,7 @@ def update_config(config: dict[str, Any], snakebids_args: SnakebidsArgs) -> None
     # filter_{input_type} dict
     pybids_inputs = config["pybids_inputs"]
     args = snakebids_args.args_dict
-    for input_type in pybids_inputs.keys():
+    for input_type in pybids_inputs:
         arg_filter_dict = args[f"filter_{input_type}"]
         if arg_filter_dict is not None:
             pybids_inputs[input_type].setdefault("filters", {})
@@ -299,7 +297,7 @@ def update_config(config: dict[str, Any], snakebids_args: SnakebidsArgs) -> None
 
     # add cmdline defined wildcards from the list:
     # wildcards_{input_type}
-    for input_type in pybids_inputs.keys():
+    for input_type in pybids_inputs:
         wildcards_list = args[f"wildcards_{input_type}"]
         if wildcards_list is not None:
             pybids_inputs[input_type].setdefault("wildcards", [])
@@ -308,7 +306,7 @@ def update_config(config: dict[str, Any], snakebids_args: SnakebidsArgs) -> None
 
     # add custom input paths to
     # config['pybids_inputs'][input_type]['custom_path']
-    for input_type in pybids_inputs.keys():
+    for input_type in pybids_inputs:
         custom_path = args[f"path_{input_type}"]
         if custom_path is not None:
             pybids_inputs[input_type]["custom_path"] = Path(custom_path).resolve()