[MAINT] use ruff

.pre-commit-config.yaml

@@ -79,19 +79,12 @@ repos:
     -   id: prettier
         types_or: [css]
 
--   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.1.0
+    # Lint and format Python code
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.1
     hooks:
-    -   id: black
-
--   repo: https://github.com/pycqa/isort
-    rev: 8.0.0
-    hooks:
-    -   id: isort
-
--   repo: https://github.com/PyCQA/flake8
-    rev: 7.3.0
-    hooks:
-    -   id: flake8
-        args: [--config, .flake8, --verbose, tools]
-        additional_dependencies: [flake8-bugbear]
+    -   id: ruff-check
+        # args: [--statistics]
+        args: [--fix, --show-fixes, --unsafe-fixes]
+    -   id: ruff-format
+        # args: [--diff]

macros/__init__.py

@@ -12,12 +12,12 @@
 
 __all__ = [
     "define_env",
-    "generate_converter_table",
-    "generate_tools_table",
-    "generate_members_table",
+    "generate_apps_table",
     "generate_beps_table",
+    "generate_converter_table",
+    "generate_filename_templates",
     "generate_grants_table",
-    "generate_apps_table",
+    "generate_members_table",
+    "generate_tools_table",
     "generate_working_groups_table",
-    "generate_filename_templates",
 ]

macros/macros.py

@@ -86,7 +86,6 @@ def generate_apps_table():
 
 def generate_filename_templates():
     """Create filename templates for all datatypes of all modalities."""
-
     schema_obj = schema.load_schema()
 
     modalities = schema_obj.rules.modalities

macros/main.py

@@ -1,17 +1,17 @@
-"""This package is used to build elements from data into
+"""Package used to build elements from data into
 MarkDown format for the specification text.
 
 Functions decorated in "define_env()" are callable throughout the
 specification and are run/rendered with the mkdocs plugin "macros".
 """
 
-import os
 import sys
+from pathlib import Path
 
-code_path = os.path.abspath(os.path.join(os.path.dirname(__file__)))
+code_path = str(Path(__file__).parent.resolve())
 sys.path.append(code_path)
 
-import macros  # noqa E402
+import macros  # noqa: E402
 
 
 def define_env(env):

pyproject.toml

@@ -38,15 +38,6 @@ builtin = "clear,rare,en-GB_to_en-US"
 ignore-words-list = "Acknowledgements,als,ans,asai,nd,manuel,te,acknowledgements,Varian,mis"
 skip = ".git,env,specification,starter_kit,examples,apps,execution,pyproject.toml,data/**.tsv,data/**.json,docs/collaboration/contributors.md,package-lock.json"
 
-[tool.black]
-line-length = 79
-
-[tool.isort]
-combine_as_imports = true
-line_length = 79
-profile = "black"
-skip_gitignore = true
-
 [tool.djlint]
 profile = "django"
 blank_line_after_tag = "load,extends,include,endblock,set"
@@ -58,3 +49,95 @@ use_gitignore = true
 
 [tool.djlint.css]
 indent_size = 4
+
+[tool.ruff]
+extend-exclude = ["data/datasets/examples", "nilearn/_version.py"]
+include = [
+    "pyproject.toml",
+    "macros/**/*.py",
+    "tools/**/*.py",
+]
+indent-width = 4
+line-length = 79
+
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
+indent-style = "space"
+line-ending = "auto"
+quote-style = "double"
+skip-magic-trailing-comma = false
+
+[tool.ruff.lint]
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+fixable = ["ALL"]
+ignore = [
+    "D100",
+    "D103",
+    "D104",
+    "D205",
+    "E741",
+    "ERA001",
+    "N806",
+    "PERF401",
+    "PLR2004",
+    # Avoid linter rules conflicting with the formatter
+    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+    "COM812",
+    "COM819",
+    "E111",
+    "E114",
+    "E117",
+    "Q000",
+    "Q001",
+    "Q002",
+    "Q003",
+    "W191",
+]
+# List of all the ruff rules (includes why the rule matters)
+# https://docs.astral.sh/ruff/rules/
+select = [
+    "ARG",
+    "B",
+    "C4",
+    "C90",
+    "D",
+    "E",
+    "ERA",
+    "F",
+    "FLY",
+    "FURB",
+    "I",
+    "N",
+    "NPY",
+    "PERF",
+    "PIE",
+    "PTH",
+    "PD",
+    "PGH",
+    "PLR",
+    "RUF",
+    "SIM",
+    "UP",
+    "W",
+]
+unfixable = []
+
+[tool.ruff.lint.mccabe]
+max-complexity = 15
+
+[tool.ruff.lint.per-file-ignores]
+"**/{doc}/*" = ["B018", "D103"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.pylint]
+# https://docs.astral.sh/ruff/settings/#lint_pylint_max-args
+max-args = 15
+# https://docs.astral.sh/ruff/settings/#lint_pylint_max-branches
+max-branches = 15
+# https://docs.astral.sh/ruff/settings/#lint_pylint_max-returns
+max-returns = 5
+# https://docs.astral.sh/ruff/settings/#lint_pylint_max-statements
+max-statements = 100

tools/MRIQC_WepAPI_analysis.py

@@ -29,10 +29,9 @@
 # MRIQC web API doc: https://mriqc.nimh.nih.gov/docs/api
 
 import datetime
-
-# %%
 import json
 from json import JSONDecodeError
+from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -87,21 +86,22 @@ def fix_scannername(model):
     return modelname
 
 
-def get_data(datafile, drop_duplicates=True):
+def get_data(datafile):
 
     datatype = "bold" if "bold" in datafile else "T1w"
     results = []
     problems = 0
 
-    with open(datafile) as f:
-        for line in f.readlines():
+    with Path(datafile).open() as f:
+        for line in f:
             try:
                 results.append(json.loads(line.strip()))
             except JSONDecodeError:
                 problems += 1
 
     print(
-        f"found {len(results)} results in json, problems decoding {problems} records"
+        f"found {len(results)} results in json, "
+        f"problems decoding {problems} records"
     )
     return results, datatype
 
@@ -134,13 +134,11 @@ def clean_data(results, datatype, drop_duplicates=True):
     )
 
     results_df = results_df.sort_values(by="month")
-    # clean up
-    # results_df = results_df.query('MagneticFieldStrength < 15')
 
     results_df = results_df.assign(
         Scanner=[fix_scannername(i) for i in results_df.ManufacturersModelName]
     )
-    fs = np.array(results_df["MagneticFieldStrength"].values.tolist())
+    fs = np.array(results_df["MagneticFieldStrength"].to_numpy().tolist())
 
     results_df["MagneticFieldStrength"] = np.where(
         fs > 100, fs / 10000, fs
@@ -173,7 +171,6 @@ def clean_data(results, datatype, drop_duplicates=True):
 # %%
 all_results_df = pd.concat((bold_results_df, t1w_results_df))
 all_results_df = all_results_df.sort_values(by="month").reset_index()
-all_results_df.shape
 all_results_df.to_csv("mriqc_results_summary.csv")
 
 # %%

tools/bep_gantt_mermaid_insert.py

@@ -1,4 +1,4 @@
-"""Creates a Gantt chart for the completed BEPs"""
+"""Creates a Gantt chart for the completed BEPs."""
 
 from __future__ import annotations
 
@@ -22,7 +22,7 @@ def target_file() -> Path:
 def get_bep_timeline() -> pd.DataFrame:
     completd_beps = data_dir() / "beps" / "beps_completed.yml"
 
-    with open(completd_beps, "r") as f:
+    with Path(completd_beps).open() as f:
         yaml = YAML(typ="safe", pure=True)
         data = yaml.load(f)
 
@@ -38,30 +38,30 @@ def get_bep_timeline() -> pd.DataFrame:
 
         if StartDoc and StartPR:
             df.append(
-                dict(
-                    BEP=BEP,
-                    Start=StartDoc,
-                    Finish=StartPR,
-                    Resource="Google Doc",
-                )
+                {
+                    "BEP": BEP,
+                    "Start": StartDoc,
+                    "Finish": StartPR,
+                    "Resource": "Google Doc",
+                }
             )
         if StartPR and Finish:
             df.append(
-                dict(
-                    BEP=BEP,
-                    Start=StartPR,
-                    Finish=Finish,
-                    Resource="Pull Request",
-                )
+                {
+                    "BEP": BEP,
+                    "Start": StartPR,
+                    "Finish": Finish,
+                    "Resource": "Pull Request",
+                }
             )
         if not StartPR:
             df.append(
-                dict(
-                    BEP=BEP,
-                    Start=StartDoc,
-                    Finish=Finish,
-                    Resource="Google Doc",
-                )
+                {
+                    "BEP": BEP,
+                    "Start": StartDoc,
+                    "Finish": Finish,
+                    "Resource": "Google Doc",
+                }
             )
 
     df = pd.DataFrame(df)
@@ -81,18 +81,22 @@ def main():
 """
 
     for bep in df.BEP.unique():
-        bep_df = df[df.BEP == bep]
-        google_start = bep_df[bep_df.Resource == "Google Doc"].Start.values[0]
-        google_end = bep_df[bep_df.Resource == "Google Doc"].Finish.values[0]
+        bep_df = df[bep == df.BEP]
+        google_start = bep_df[
+            bep_df.Resource == "Google Doc"
+        ].Start.to_numpy()[0]
+        google_end = bep_df[bep_df.Resource == "Google Doc"].Finish.to_numpy()[
+            0
+        ]
 
         text += f"""    section BEP{bep[:3]}
             Google doc    :{google_start}, {google_end}
 """
 
         pr_df = bep_df[bep_df.Resource == "Pull Request"]
         if len(pr_df) > 0:
-            pr_start = pr_df.Start.values[0]
-            pr_end = pr_df.Finish.values[0]
+            pr_start = pr_df.Start.to_numpy()[0]
+            pr_end = pr_df.Finish.to_numpy()[0]
 
             text += f"""            Pull request  :{pr_start}, {pr_end}
 """
@@ -102,11 +106,11 @@ def main():
     print(text)
 
     # insert into target file
-    with open(target_file(), "r") as f:
+    with Path(target_file()).open() as f:
         lines = f.readlines()
 
     inser_mermaid_here = False
-    with open(target_file(), "w") as f:
+    with Path(target_file()).open("w") as f:
         for line in lines:
             if line.startswith("<!-- MERMAID GANTT CHART STARTS -->"):
                 inser_mermaid_here = True