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Merge pull request nipreps#1203 from nipreps/sty/ruff
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STY: Add *Ruff* config and fix all warnings and errors
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@oesteban
oesteban authored Mar 19, 2024
2 parents 7bc9ece + 4d76600 commit 544a505
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Showing 65 changed files with 3,238 additions and 3,154 deletions.
155 changes: 78 additions & 77 deletions .maint/update_authors.py
100644 → 100755
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
#!/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

Expand Down Expand Up @@ -35,21 +36,21 @@ def read_md_table(md_text):
keys = None
retval = []
for line in md_text.splitlines():
if line.strip().startswith("| --- |"):
if line.strip().startswith('| --- |'):
keys = (
k.replace("*", "").strip()
for k in prev.split("|")
k.replace('*', '').strip()
for k in prev.split('|')
)
keys = [k.lower() for k in keys if k]
continue
elif not keys:
prev = line
continue

if not line or not line.strip().startswith("|"):
if not line or not line.strip().startswith('|'):
break

values = [v.strip() or None for v in line.split("|")][1:-1]
values = [v.strip() or None for v in line.split('|')][1:-1]
retval.append({k: v for k, v in zip(keys, values) if v})

return retval
Expand All @@ -58,13 +59,13 @@ def read_md_table(md_text):
def sort_contributors(entries, git_lines, exclude=None, last=None):
"""Return a list of author dictionaries, ordered by contribution."""
last = last or []
sorted_authors = sorted(entries, key=lambda i: i["name"])
sorted_authors = sorted(entries, key=lambda i: i['name'])

first_last = [
" ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors
' '.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 []
' '.join(val['name'].split(',')[::-1]).strip() for val in exclude or []
]

unmatched = []
Expand All @@ -85,15 +86,15 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
if val not in author_matches:
author_matches.append(val)

names = {" ".join(val["name"].split(",")[::-1]).strip() for val in author_matches}
names = {' '.join(val['name'].split(',')[::-1]).strip() for val in author_matches}
for missing_name in first_last:
if missing_name not in names:
missing = sorted_authors[first_last.index(missing_name)]
author_matches.append(missing)

position_matches = []
for i, item in enumerate(author_matches):
pos = item.pop("position", None)
pos = item.pop('position', None)
if pos is not None:
position_matches.append((i, int(pos)))

Expand All @@ -105,7 +106,7 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
return author_matches, unmatched


def get_git_lines(fname="line-contributors.txt"):
def get_git_lines(fname='line-contributors.txt'):
"""Run git-line-summary."""
import shutil
import subprocess as sp
Expand All @@ -114,33 +115,33 @@ def get_git_lines(fname="line-contributors.txt"):

lines = []
if contrib_file.exists():
print("WARNING: Reusing existing line-contributors.txt file.", file=sys.stderr)
print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr)
lines = contrib_file.read_text().splitlines()

git_line_summary_path = shutil.which("git-line-summary")
git_line_summary_path = shutil.which('git-line-summary')
if not lines and git_line_summary_path:
print("Running git-line-summary on repo")
print('Running git-line-summary on repo')
lines = sp.check_output([git_line_summary_path]).decode().splitlines()
lines = [l for l in lines if "Not Committed Yet" not in l]
contrib_file.write_text("\n".join(lines))
lines = [line for line in lines if 'Not Committed Yet' not in line]
contrib_file.write_text('\n'.join(lines))

if not lines:
raise RuntimeError(
"""\
Could not find line-contributors from git repository.%s"""
% """ \
git-line-summary not found, please install git-extras. """
_msg = (
': git-line-summary not found, please install git-extras '
* (git_line_summary_path is None)
)
return [" ".join(line.strip().split()[1:-1]) for line in lines if "%" in line]
raise RuntimeError(
f'Could not find line-contributors from git repository{_msg}.'
)
return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]


def _namelast(inlist):
retval = []
for i in inlist:
i["name"] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
if not i["name"]:
i["name"] = i.get("handle", "<Unknown Name>")
i['name'] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
if not i['name']:
i['name'] = i.get('handle', '<Unknown Name>')
retval.append(i)
return retval

Expand All @@ -152,12 +153,12 @@ 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("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
@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('--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(
zenodo_file,
maintainers,
Expand Down Expand Up @@ -185,18 +186,18 @@ def zenodo(

zen_pi = _namelast(reversed(read_md_table(Path(pi).read_text())))

zenodo["creators"] = zen_creators
zenodo["contributors"] = zen_contributors + [
zenodo['creators'] = zen_creators
zenodo['contributors'] = zen_contributors + [
pi for pi in zen_pi if pi not in zen_contributors
]
creator_names = {
c["name"] for c in zenodo["creators"]
if c["name"] != "<Unknown Name>"
c['name'] for c in zenodo['creators']
if c['name'] != '<Unknown Name>'
}

zenodo["contributors"] = [
c for c in zenodo["contributors"]
if c["name"] not in creator_names
zenodo['contributors'] = [
c for c in zenodo['contributors']
if c['name'] not in creator_names
]

misses = set(miss_creators).intersection(miss_contributors)
Expand All @@ -208,35 +209,35 @@ def zenodo(
)

# Remove position
for creator in zenodo["creators"]:
creator.pop("position", None)
creator.pop("handle", None)
if "affiliation" not in creator:
creator["affiliation"] = "Unknown affiliation"
elif isinstance(creator["affiliation"], list):
creator["affiliation"] = creator["affiliation"][0]

for creator in zenodo["contributors"]:
creator.pop("handle", None)
creator["type"] = "Researcher"
creator.pop("position", None)

if "affiliation" not in creator:
creator["affiliation"] = "Unknown affiliation"
elif isinstance(creator["affiliation"], list):
creator["affiliation"] = creator["affiliation"][0]
for creator in zenodo['creators']:
creator.pop('position', None)
creator.pop('handle', None)
if 'affiliation' not in creator:
creator['affiliation'] = 'Unknown affiliation'
elif isinstance(creator['affiliation'], list):
creator['affiliation'] = creator['affiliation'][0]

for creator in zenodo['contributors']:
creator.pop('handle', None)
creator['type'] = 'Researcher'
creator.pop('position', None)

if 'affiliation' not in creator:
creator['affiliation'] = 'Unknown affiliation'
elif isinstance(creator['affiliation'], list):
creator['affiliation'] = creator['affiliation'][0]

Path(zenodo_file).write_text(
"%s\n" % json.dumps(zenodo, indent=2)
'%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("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
@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('--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(
maintainers,
contributors,
Expand All @@ -257,10 +258,10 @@ def publication(
)

pi_hits = _namelast(reversed(read_md_table(Path(pi).read_text())))
pi_names = [pi["name"] for pi in pi_hits]
pi_names = [pi['name'] for pi in pi_hits]
hits = [
hit for hit in hits
if hit["name"] not in pi_names
if hit['name'] not in pi_names
] + pi_hits

def _aslist(value):
Expand All @@ -271,16 +272,16 @@ def _aslist(value):
# Remove position
affiliations = []
for item in hits:
item.pop("position", None)
for a in _aslist(item.get("affiliation", "Unaffiliated")):
item.pop('position', None)
for a in _aslist(item.get('affiliation', 'Unaffiliated')):
if a not in affiliations:
affiliations.append(a)

aff_indexes = [
", ".join(
', '.join(
[
"%d" % (affiliations.index(a) + 1)
for a in _aslist(author.get("affiliation", "Unaffiliated"))
'%d' % (affiliations.index(a) + 1)
for a in _aslist(author.get('affiliation', 'Unaffiliated'))
]
)
for author in hits
Expand All @@ -293,25 +294,25 @@ def _aslist(value):
file=sys.stderr,
)

print("Authors (%d):" % len(hits))
print('Authors (%d):' % len(hits))
print(
"%s."
% "; ".join(
'%s.'
% '; '.join(
[
"%s \\ :sup:`%s`\\ " % (i["name"], idx)
'{} \\ :sup:`{}`\\ '.format(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\nAffiliations:\n%s'
% '\n'.join(
[f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)]
)
)


if __name__ == "__main__":
if __name__ == '__main__':
""" Install entry-point """
cli()
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