Merge pull request #114 from jhlegarreta/TransitionToRuffCodeFormatting

STYLE: Transition to `ruff` for code formatting
nipreps · May 15, 2024 · 43dd874 · 43dd874
2 parents 2437727 + d8f3beb
commit 43dd874
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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:
@@ -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 +1,34 @@
+# 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
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,77 +1,77 @@
 {
-  "title": "NiReports: the NiPreps' reporting and visualization tools",
-  "description": "<p>The visual report system (VRS) of <em>NiPreps</em>.</p>",
-  "creators": [
-    {
-      "orcid": "0000-0001-8435-6191",
-      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
-      "name": "Oscar Esteban"
-    },
-    {
-      "orcid": "0000-0002-3896-6906",
-      "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland",
-      "name": "Elodie Savary"
-    },
-    {
-      "orcid": "0000-0003-3715-7012",
-      "affiliation": "Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK",
-      "name": "Eilidh MacNicol"
-    },
-    {
-      "orcid": "0000-0002-1668-9629",
-      "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland",
-      "name": "C\u00e9line Provins"
-    }
-  ],
   "contributors": [
     {
-      "orcid": "0000-0002-6533-164X",
       "affiliation": "Department of Psychology, Stanford University, CA, USA",
       "name": "Christopher J. Markiewicz",
+      "orcid": "0000-0002-6533-164X",
       "type": "Researcher"
     },
     {
-      "orcid": "0000-0001-7159-1387",
       "affiliation": "Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel",
       "name": "Zvi Baratz",
+      "orcid": "0000-0001-7159-1387",
       "type": "Researcher"
     },
     {
-      "orcid": "0000-0002-7252-7771",
       "affiliation": "Department of Psychology, Stanford University, CA, USA",
       "name": "Mathias Goncalves",
+      "orcid": "0000-0002-7252-7771",
       "type": "Researcher"
     },
     {
-      "orcid": "0000-0003-3007-1056",
       "affiliation": "Department of Psychology, Stanford University, CA, USA",
       "name": "Ross W. Blair",
+      "orcid": "0000-0003-3007-1056",
       "type": "Researcher"
     },
     {
-      "orcid": "0000-0003-4613-6643",
       "affiliation": "Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA",
       "name": "Dylan Nielson",
+      "orcid": "0000-0003-4613-6643",
       "type": "Researcher"
     },
     {
-      "orcid": "0000-0001-8435-6191",
       "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne",
       "name": "Oscar Esteban",
+      "orcid": "0000-0001-8435-6191",
       "type": "Researcher"
     },
     {
-      "orcid": "0000-0001-6755-0259",
       "affiliation": "Department of Psychology, Stanford University, CA, USA",
       "name": "Russell A. Poldrack",
+      "orcid": "0000-0001-6755-0259",
       "type": "Researcher"
     }
   ],
+  "creators": [
+    {
+      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
+      "name": "Oscar Esteban",
+      "orcid": "0000-0001-8435-6191"
+    },
+    {
+      "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland",
+      "name": "Elodie Savary",
+      "orcid": "0000-0002-3896-6906"
+    },
+    {
+      "affiliation": "Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK",
+      "name": "Eilidh MacNicol",
+      "orcid": "0000-0003-3715-7012"
+    },
+    {
+      "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland",
+      "name": "C\u00e9line Provins",
+      "orcid": "0000-0002-1668-9629"
+    }
+  ],
+  "description": "<p>The visual report system (VRS) of <em>NiPreps</em>.</p>",
   "keywords": [
     "neuroimaging",
     "visualization",
     "nipreps"
   ],
   "license": "Apache-2.0",
+  "title": "NiReports: the NiPreps' reporting and visualization tools",
   "upload_type": "software"
 }
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,3 +1,3 @@
 # Contributing to *nireports*
 
-*nireports* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/).
+*nireports* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/).