Merge branch 'main' into plot_carpet

nipreps · May 16, 2024 · be2df83 · be2df83
2 parents 2e1be1d + 60fd854
commit be2df83
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Showing 39 changed files with 457 additions and 396 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/[email protected]
diff --git a/.mailmap b/.mailmap
@@ -14,8 +14,8 @@ Christopher J. Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
 Conrad Ma <[email protected]>
-Conrad Ma <[email protected]> Conrad 
-Conrad Ma <[email protected]> 394822740 
+Conrad Ma <[email protected]> Conrad
+Conrad Ma <[email protected]> 394822740
 Conrad Ma <[email protected]> <[email protected]>
 Conrad Ma <[email protected]> <[email protected]>
 Dylan Nielson <[email protected]>

diff --git a/.maint/PIs.md b/.maint/PIs.md
@@ -11,4 +11,4 @@ If you are participating because of your affiliation with another organization (
 | **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** | **Position** |
 | --- | --- | --- | --- | --- | --- |
 | Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Department of Radiology, Lausanne University Hospital and University of Lausanne | -1 |
-| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA | -2 |
+| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA | -2 |
diff --git a/.maint/requirements.txt b/.maint/requirements.txt
@@ -1,2 +1,2 @@
 click
-fuzzywuzzy
+fuzzywuzzy
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:
@@ -50,29 +49,16 @@ def read_md_table(md_text):
             break
 
         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})
+        retval.append({k: v for k, v in zip(keys, values, strict=True) if v})
 
     return retval
 
 
-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"])
-
-    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 []
-    ]
-
+def _extract_git_contributor_matches(git_lines, sorted_authors, first_last, first_last_excl):
     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])]
@@ -85,18 +71,39 @@ 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}
-    for missing_name in first_last:
-        if missing_name not in names:
-            missing = sorted_authors[first_last.index(missing_name)]
-            author_matches.append(missing)
+    return author_matches, unmatched
+
 
+def _get_position_matches(author_matches):
     position_matches = []
     for i, item in enumerate(author_matches):
         pos = item.pop("position", None)
         if pos is not None:
             position_matches.append((i, int(pos)))
 
+    return position_matches
+
+
+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"])
+
+    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 []]
+
+    author_matches, unmatched = _extract_git_contributor_matches(
+        git_lines, sorted_authors, first_last, first_last_excl
+    )
+
+    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 = _get_position_matches(author_matches)
+
     for i, pos in position_matches:
         if pos < 0:
             pos += len(author_matches) + 1
@@ -121,7 +128,7 @@ def get_git_lines(fname="line-contributors.txt"):
     if not lines and git_line_summary_path:
         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]
+        lines = [ele for ele in lines if "Not Committed Yet" not in ele]
         contrib_file.write_text("\n".join(lines))
 
     if not lines:
@@ -152,8 +159,12 @@ 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(
+    "-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 +187,13 @@ 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 +203,7 @@ 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 +222,17 @@ 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 +242,8 @@ 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 +255,12 @@ 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)):
@@ -281,8 +287,7 @@ 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,
         )
 
@@ -292,16 +297,14 @@ def _aslist(value):
         % "; ".join(
             [
                 "%s \\ :sup:`%s`\\ " % (i["name"], idx)
-                for i, idx in zip(hits, aff_indexes)
+                for i, idx in zip(hits, aff_indexes, strict=True)
             ]
         )
     )
 
     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 +1,34 @@
+# To install the git pre-commit hook run:
+#   pre-commit install
+# To update the pre-commit hooks run:
+#   pre-commit install-hooks
+
+exclude: |
+    (?x)^(
+        docs/_static/.*|
+        nireports/tests/data/.*|
+        nireports/assembler/data/tests/work/.*|
+        nireports/assembler/data/tests/crashfile.txt|
+        nireports/assembler/data/.*\.tpl
+    )$
 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