MAINT: Add authorship

.mailmap

@@ -0,0 +1,8 @@
+Christopher J. Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Mathias Goncalves <[email protected]>
+Mathias Goncalves <[email protected]> <[email protected]>
+Mathias Goncalves <[email protected]> <[email protected]>
+Oscar Esteban <[email protected]>
+Oscar Esteban <[email protected]> <[email protected]>

.maint/contributors.json

@@ -0,0 +1 @@
+[]

.maint/developers.json

@@ -0,0 +1,30 @@
+[
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Goncalves, Mathias",
+    "orcid": "0000-0002-7252-7771"
+  },
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Markiewicz, Christopher J.",
+    "orcid": "0000-0002-6533-164X"
+  },
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Poldrack, Russell A.",
+    "orcid": "0000-0001-6755-0259"
+  },
+  {
+    "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
+    "name": "Esteban, Oscar",
+    "orcid": "0000-0001-8435-6191"
+  },
+  {
+    "affiliation": "University of Minnesota",
+    "name": "Feczko, Eric"
+  },
+  {
+    "affiliation": "University of Minnesota",
+    "name": "Fair, Damien A."
+  }
+]

.maint/former.json

@@ -0,0 +1 @@
+[]

.maint/update_zenodo.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+"""Update and sort the creators list of the zenodo record."""
+import sys
+from pathlib import Path
+import json
+from fuzzywuzzy import fuzz, process
+
+# These ORCIDs should go last
+CREATORS_LAST = ['Poldrack, Russell A.', 'Fair, Damien A.']
+CONTRIBUTORS_LAST = []
+
+
+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 []]
+
+    unmatched = []
+    author_matches = []
+    position = 1
+    for ele in git_lines:
+        matches = process.extract(ele, first_last, scorer=fuzz.token_sort_ratio,
+                                  limit=2)
+        if not matches:
+            return [], []
+        # matches is a list [('First match', % Match), ('Second match', % Match)]
+        if matches[0][1] > 80:
+            val = sorted_authors[first_last.index(matches[0][0])]
+        else:
+            # skip unmatched names
+            if ele not in first_last_excl:
+                unmatched.append(ele)
+            continue
+
+        if val not in author_matches:
+            val['position'] = position
+            author_matches.append(val)
+            position += 1
+
+    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)]
+            missing['position'] = position
+            author_matches.append(missing)
+            position += 1
+
+    all_names = [val['name'] for val in author_matches]
+    for last_author in last:
+        author_matches[all_names.index(last_author)]['position'] = position
+        position += 1
+
+    author_matches = sorted(author_matches, key=lambda k: k['position'])
+
+    return author_matches, unmatched
+
+
+def get_git_lines(fname='line-contributors.txt'):
+    """Run git-line-summary."""
+    import shutil
+    import subprocess as sp
+    contrib_file = Path(fname)
+
+    lines = []
+    if contrib_file.exists():
+        print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr)
+        lines = contrib_file.read_text().splitlines()
+
+    cmd = [shutil.which('git-line-summary')]
+    if cmd == [None]:
+        cmd = [shutil.which('git-summary'), "--line"]
+    if not lines and cmd[0]:
+        print(f"Running {' '.join(cmd)!r} on repo")
+        lines = sp.check_output(cmd).decode().splitlines()
+        lines = [l for l in lines if "Not Committed Yet" not in l]
+        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. """ * (cmd[0] is None))
+    return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
+
+
+if __name__ == '__main__':
+    data = get_git_lines()
+
+    zenodo_file = Path('.zenodo.json')
+    zenodo = json.loads(zenodo_file.read_text())
+
+    creators = json.loads(Path('.maint/developers.json').read_text())
+    zen_creators, miss_creators = sort_contributors(
+        creators, data,
+        exclude=json.loads(Path('.maint/former.json').read_text()),
+        last=CREATORS_LAST)
+    contributors = json.loads(Path('.maint/contributors.json').read_text())
+    zen_contributors, miss_contributors = sort_contributors(
+        contributors, data,
+        exclude=json.loads(Path('.maint/former.json').read_text()),
+        last=CONTRIBUTORS_LAST)
+    zenodo['creators'] = zen_creators
+    zenodo['contributors'] = zen_contributors
+
+    print("Some people made commits, but are missing in .maint/ "
+          "files: %s." % ', '.join(set(miss_creators).intersection(miss_contributors)),
+          file=sys.stderr)
+
+    # Remove position
+    for creator in zenodo['creators']:
+        del creator['position']
+        if isinstance(creator['affiliation'], list):
+            creator['affiliation'] = creator['affiliation'][0]
+
+    for creator in zenodo['contributors']:
+        creator['type'] = 'Researcher'
+        del creator['position']
+        if isinstance(creator['affiliation'], list):
+            creator['affiliation'] = creator['affiliation'][0]
+
+    zenodo_file.write_text('%s\n' % json.dumps(zenodo, indent=2))

.pre-commit-config.yaml

@@ -10,7 +10,9 @@ repos:
     rev: 22.3.0
     hooks:
     -   id: black
+        files: ^nibabies/
 -   repo: https://github.com/pycqa/isort
     rev: 5.10.1
     hooks:
-    - id: isort
+    -   id: isort
+        files: ^nibabies/

.zenodo.json

@@ -0,0 +1,58 @@
+{
+  "title": "NiBabies: a robust preprocessing pipeline for infant functional MRI",
+  "description": "<p>NiBabies is a robust and easy-to-use pipeline for preprocessing of diverse infant and neonate fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.</p>",
+  "contributors": [],
+  "creators": [
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Goncalves, Mathias",
+      "orcid": "0000-0002-7252-7771"
+    },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Markiewicz, Christopher J.",
+      "orcid": "0000-0002-6533-164X"
+    },
+    {
+      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
+      "name": "Esteban, Oscar",
+      "orcid": "0000-0001-8435-6191"
+    },
+    {
+      "affiliation": "University of Minnesota",
+      "name": "Feczko, Eric"
+    },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Poldrack, Russell A.",
+      "orcid": "0000-0001-6755-0259"
+    },
+    {
+      "affiliation": "University of Minnesota",
+      "name": "Fair, Damien A."
+    }
+  ],
+  "keywords": [
+    "neuroimaging",
+    "workflow",
+    "pipeline",
+    "preprocessing",
+    "fMRI",
+    "BIDS",
+    "infant"
+  ],
+  "license": "Apache-2.0",
+  "related_identifiers": [
+    {
+      "identifier": "https://github.com/nipreps/nibabies",
+      "relation": "documents",
+      "scheme": "url"
+    },
+    {
+      "identifier": "10.5281/zenodo.6418986",
+      "relation": "isPartOf",
+      "scheme": "doi"
+    }
+  ],
+  "upload_type": "software"
+}

setup.cfg

@@ -74,6 +74,9 @@ docs =
 duecredit =
     duecredit
     citeproc-py != 0.5.0
+maint =
+    fuzzywuzzy
+    python-Levenshtein
 pointclouds =
     pyntcloud
 style =
@@ -90,6 +93,7 @@ all =
     %(aroma)s
     %(doc)s
     %(duecredit)s
+    %(maint)s
     %(pointclouds)s
     %(style)s
     %(test)s