STYLE: Transition to ruff for code formatting

Transition to `ruff` for code formatting in line with the rest of the `nipreps` repositories. Drop the flake8 `W503` rule, which is not implemented by `ruff`. Add a GHA workflow to ensure that contributions not complying with the style are detected. Format the source code accordingly.
nipreps · May 10, 2024 · de36988 · de36988
1 parent a8b3927
commit de36988
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Showing 33 changed files with 376 additions and 351 deletions.
diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
@@ -0,0 +1,24 @@
+name: Contribution checks
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  stable:
+    name: Run ruff
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3
+
+      - name: Install and run pre-commit hooks
+        uses: pre-commit/action@v3.0.1
diff --git a/.maint/update_authors.py b/.maint/update_authors.py
@@ -1,8 +1,10 @@
 #!/usr/bin/env python3
 """Update and sort the creators list of the zenodo record."""
+
+import json
 import sys
 from pathlib import Path
-import json
+
 import click
 from fuzzywuzzy import fuzz, process
 
@@ -36,10 +38,7 @@ def read_md_table(md_text):
     retval = []
     for line in md_text.splitlines():
         if line.strip().startswith("| --- |"):
-            keys = (
-                k.replace("*", "").strip()
-                for k in prev.split("|")
-            )
+            keys = (k.replace("*", "").strip() for k in prev.split("|"))
             keys = [k.lower() for k in keys if k]
             continue
         elif not keys:
@@ -60,19 +59,13 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
     last = last or []
     sorted_authors = sorted(entries, key=lambda i: i["name"])
 
-    first_last = [
-        " ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors
-    ]
-    first_last_excl = [
-        " ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []
-    ]
+    first_last = [" ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors]
+    first_last_excl = [" ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []]
 
     unmatched = []
     author_matches = []
     for ele in git_lines:
-        matches = process.extract(
-            ele, first_last, scorer=fuzz.token_sort_ratio, limit=2
-        )
+        matches = process.extract(ele, first_last, scorer=fuzz.token_sort_ratio, limit=2)
         # matches is a list [('First match', % Match), ('Second match', % Match)]
         if matches[0][1] > 80:
             val = sorted_authors[first_last.index(matches[0][0])]
@@ -152,8 +145,9 @@ def cli():
 @cli.command()
 @click.option("-z", "--zenodo-file", type=click.Path(exists=True), default=".zenodo.json")
 @click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
-@click.option("-c", "--contributors", type=click.Path(exists=True),
-              default=".maint/CONTRIBUTORS.md")
+@click.option(
+    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+)
 @click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
 @click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
 def zenodo(
@@ -176,15 +170,13 @@ def zenodo(
     )
 
     zen_contributors, miss_contributors = sort_contributors(
-        _namelast(read_md_table(Path(contributors).read_text())),
-        data,
-        exclude=former
+        _namelast(read_md_table(Path(contributors).read_text())), data, exclude=former
     )
 
     zen_pi = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname"))
+            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
         )
     )
 
@@ -194,8 +186,7 @@ def zenodo(
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ "
-            f"files: {', '.join(misses)}",
+            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
@@ -214,15 +205,14 @@ def zenodo(
         if isinstance(creator["affiliation"], list):
             creator["affiliation"] = creator["affiliation"][0]
 
-    Path(zenodo_file).write_text(
-        "%s\n" % json.dumps(zenodo, indent=2)
-    )
+    Path(zenodo_file).write_text("%s\n" % json.dumps(zenodo, indent=2))
 
 
 @cli.command()
 @click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
-@click.option("-c", "--contributors", type=click.Path(exists=True),
-              default=".maint/CONTRIBUTORS.md")
+@click.option(
+    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+)
 @click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
 @click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
 def publication(
@@ -232,9 +222,8 @@ def publication(
     former_file,
 ):
     """Generate the list of authors and affiliations for papers."""
-    members = (
-        _namelast(read_md_table(Path(maintainers).read_text()))
-        + _namelast(read_md_table(Path(contributors).read_text()))
+    members = _namelast(read_md_table(Path(maintainers).read_text())) + _namelast(
+        read_md_table(Path(contributors).read_text())
     )
 
     hits, misses = sort_contributors(
@@ -246,15 +235,12 @@ def publication(
     pi_hits = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname"))
+            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
         )
     )
 
     pi_names = [pi["name"] for pi in pi_hits]
-    hits = [
-        hit for hit in hits
-        if hit["name"] not in pi_names
-    ] + pi_hits
+    hits = [hit for hit in hits if hit["name"] not in pi_names] + pi_hits
 
     def _aslist(value):
         if isinstance(value, (list, tuple)):
@@ -281,27 +267,19 @@ def _aslist(value):
 
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ "
-            f"files: {', '.join(misses)}",
+            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
     print("Authors (%d):" % len(hits))
     print(
         "%s."
-        % "; ".join(
-            [
-                "%s \\ :sup:`%s`\\ " % (i["name"], idx)
-                for i, idx in zip(hits, aff_indexes)
-            ]
-        )
+        % "; ".join(["%s \\ :sup:`%s`\\ " % (i["name"], idx) for i, idx in zip(hits, aff_indexes)])
     )
 
     print(
         "\n\nAffiliations:\n%s"
-        % "\n".join(
-            ["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)]
-        )
+        % "\n".join(["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)])
     )
 
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,23 +1,26 @@
+# To install the git pre-commit hook run:
+#   pre-commit install
+# To update the pre-commit hooks run:
+#   pre-commit install-hooks
+
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-json
-    -   id: check-toml
-    -   id: check-case-conflict
-    -   id: check-docstring-first
-    -   id: check-merge-conflict
-    -   id: check-vcs-permalinks
-    -   id: pretty-format-json
-        args: ['--autofix']
--   repo: https://github.com/psf/black
-    rev: 22.3.0
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: debug-statements
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-vcs-permalinks
+      - id: pretty-format-json
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
     hooks:
-    -   id: black
--   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
-    hooks:
-    -   id: isort
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
diff --git a/nireports/__init__.py b/nireports/__init__.py
@@ -21,13 +21,15 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Add metadata on import."""
+
 __packagename__ = "nireports"
 __copyright__ = "2023, The NiPreps developers"
 
 try:
     from ._version import __version__
 except ModuleNotFoundError:
-    from importlib.metadata import version, PackageNotFoundError
+    from importlib.metadata import PackageNotFoundError, version
+
     try:
         __version__ = version(__packagename__)
     except PackageNotFoundError:

diff --git a/nireports/assembler/data/__init__.py b/nireports/assembler/data/__init__.py
@@ -10,6 +10,7 @@
 
 .. autoclass:: Loader
 """
+
 from __future__ import annotations
 
 import atexit

diff --git a/nireports/assembler/misc.py b/nireports/assembler/misc.py
@@ -23,10 +23,11 @@
 # STATEMENT OF CHANGES: This file was ported carrying over full git history from niworkflows,
 # another NiPreps project licensed under the Apache-2.0 terms, and has been changed since.
 """Miscellaneous utilities."""
+
 from collections import defaultdict
 from pathlib import Path
-from bids.utils import listify
 
+from bids.utils import listify
 from nipype.utils.filemanip import loadcrash
 
 
@@ -242,7 +243,7 @@ def unfold_columns(indict, prefix=None, delimiter="_"):
 
     """
     prefix = listify(prefix) if prefix is not None else []
-    keys = sorted(set(list(indict.keys())))
+    keys = sorted(set(indict.keys()))
 
     data = []
     subdict = defaultdict(dict, {})
@@ -254,7 +255,7 @@ def unfold_columns(indict, prefix=None, delimiter="_"):
             subdict[col[0]][col[1]] = indict[key]
 
     if subdict:
-        for skey in sorted(list(subdict.keys())):
+        for skey in sorted(subdict.keys()):
             sskeys = list(subdict[skey].keys())
 
             # If there is only one subkey, merge back

diff --git a/nireports/assembler/report.py b/nireports/assembler/report.py
@@ -23,6 +23,7 @@
 # STATEMENT OF CHANGES: This file was ported carrying over full git history from niworkflows,
 # another NiPreps project licensed under the Apache-2.0 terms, and has been changed since.
 """Core objects representing reports."""
+
 import re
 from collections import defaultdict
 from itertools import compress
@@ -36,7 +37,6 @@
 from nireports.assembler import data
 from nireports.assembler.reportlet import Reportlet
 
-
 # Add a new figures spec
 try:
     add_config_paths(figures=data.load("nipreps.json"))
@@ -270,8 +270,7 @@ def __init__(
         metadata = metadata or {}
         if "filename" not in metadata:
             metadata["filename"] = Path(out_filename).name.replace(
-                "".join(Path(out_filename).suffixes),
-                ""
+                "".join(Path(out_filename).suffixes), ""
             )
 
         # Initialize structuring elements
@@ -287,9 +286,7 @@ def __init__(
             "out_dir": str(out_dir),
             "reportlets_dir": str(root),
         }
-        meta_repl.update({
-            kk: vv for kk, vv in metadata.items() if isinstance(vv, str)
-        })
+        meta_repl.update({kk: vv for kk, vv in metadata.items() if isinstance(vv, str)})
         meta_repl.update(bids_filters)
         expr = re.compile(f'{{({"|".join(meta_repl.keys())})}}')
 
@@ -308,7 +305,8 @@ def __init__(
 
         # Path to the Jinja2 template
         self.template_path = (
-            Path(settings["template_path"]) if "template_path" in settings
+            Path(settings["template_path"])
+            if "template_path" in settings
             else data.load("report.tpl").absolute()
         )
 
@@ -383,7 +381,8 @@ def index(self, config):
                     # do not display entities with the value None.
                     c_filt = [
                         f'{key} <span class="bids-entity">{c_value}</span>'
-                        for key, c_value in zip(entities, c) if c_value is not None
+                        for key, c_value in zip(entities, c)
+                        if c_value is not None
                     ]
                     # Set a common title for this particular combination c
                     title = "Reports for: %s." % ", ".join(c_filt)
@@ -420,11 +419,11 @@ def process_plugins(self, config, metadata=None):
         self.footer = []
 
         plugins = config.get("plugins", None)
-        for plugin in (plugins or []):
+        for plugin in plugins or []:
             env = jinja2.Environment(
-                loader=jinja2.FileSystemLoader(searchpath=str(
-                    Path(__file__).parent / "data" / f"{plugin['type']}"
-                )),
+                loader=jinja2.FileSystemLoader(
+                    searchpath=str(Path(__file__).parent / "data" / f"{plugin['type']}")
+                ),
                 trim_blocks=True,
                 lstrip_blocks=True,
                 autoescape=False,
@@ -434,12 +433,17 @@ def process_plugins(self, config, metadata=None):
             plugin_meta.update((metadata or {}).get(plugin["type"], {}))
             for member in ("header", "navbar", "footer"):
                 old_value = getattr(self, member)
-                setattr(self, member, old_value + [
-                    env.get_template(f"{member}.tpl").render(
-                        config=plugin,
-                        metadata=plugin_meta,
-                    )
-                ])
+                setattr(
+                    self,
+                    member,
+                    old_value
+                    + [
+                        env.get_template(f"{member}.tpl").render(
+                            config=plugin,
+                            metadata=plugin_meta,
+                        )
+                    ],
+                )
 
     def generate_report(self):
         """Once the Report has been indexed, the final HTML can be generated"""
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,7 @@ @@
     .. autoclass:: Loader
     """
     from __future__ import annotations
     import atexit
@@ Expand Down @@