Merge pull request #130 from oesteban/maint/setup-revision

STY/MAINT: Preparing the first large overhaul of dMRIPrep

.maint/paper_author_list.py

@@ -7,7 +7,7 @@
 
 
 # These authors should go last
-AUTHORS_LAST = ['Rokem, Ariel', 'Esteban, Oscar']
+AUTHORS_LAST = ["Rokem, Ariel", "Esteban, Oscar"]
 
 
 def _aslist(inlist):
@@ -16,34 +16,54 @@ def _aslist(inlist):
     return inlist
 
 
-if __name__ == '__main__':
-    devs = json.loads(Path('.maint/developers.json').read_text())
-    contribs = json.loads(Path('.maint/contributors.json').read_text())
+if __name__ == "__main__":
+    devs = json.loads(Path(".maint/developers.json").read_text())
+    contribs = json.loads(Path(".maint/contributors.json").read_text())
 
     author_matches, unmatched = sort_contributors(
-        devs + contribs, get_git_lines(),
-        exclude=json.loads(Path('.maint/former.json').read_text()),
-        last=AUTHORS_LAST)
+        devs + contribs,
+        get_git_lines(),
+        exclude=json.loads(Path(".maint/former.json").read_text()),
+        last=AUTHORS_LAST,
+    )
     # Remove position
     affiliations = []
     for item in author_matches:
-        del item['position']
-        for a in _aslist(item.get('affiliation', 'Unaffiliated')):
+        del item["position"]
+        for a in _aslist(item.get("affiliation", "Unaffiliated")):
             if a not in affiliations:
                 affiliations.append(a)
 
-    aff_indexes = [', '.join(['%d' % (affiliations.index(a) + 1)
-                              for a in _aslist(author.get('affiliation', 'Unaffiliated'))])
-                   for author in author_matches]
+    aff_indexes = [
+        ", ".join(
+            [
+                "%d" % (affiliations.index(a) + 1)
+                for a in _aslist(author.get("affiliation", "Unaffiliated"))
+            ]
+        )
+        for author in author_matches
+    ]
 
-    print("Some people made commits, but are missing in .maint/ "
-          "files: %s." % ', '.join(unmatched), file=sys.stderr)
+    print(
+        "Some people made commits, but are missing in .maint/ "
+        "files: %s." % ", ".join(unmatched),
+        file=sys.stderr,
+    )
 
-    print('Authors (%d):' % len(author_matches))
-    print("%s." % '; '.join([
-        '%s \\ :sup:`%s`\\ ' % (i['name'], idx)
-        for i, idx in zip(author_matches, aff_indexes)
-    ]))
+    print("Authors (%d):" % len(author_matches))
+    print(
+        "%s."
+        % "; ".join(
+            [
+                "%s \\ :sup:`%s`\\ " % (i["name"], idx)
+                for i, idx in zip(author_matches, aff_indexes)
+            ]
+        )
+    )
 
-    print('\n\nAffiliations:\n%s' % '\n'.join(['{0: >2}. {1}'.format(i + 1, a)
-                                               for i, a in enumerate(affiliations)]))
+    print(
+        "\n\nAffiliations:\n%s"
+        % "\n".join(
+            ["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)]
+        )
+    )

.maint/update_zenodo.py

@@ -6,26 +6,29 @@
 from fuzzywuzzy import fuzz, process
 
 # These ORCIDs should go last
-CREATORS_LAST = ['Rokem, Ariel', 'Esteban, Oscar']
-CONTRIBUTORS_LAST = ['Poldrack, Russell A.']
+CREATORS_LAST = ["Rokem, Ariel", "Esteban, Oscar"]
+CONTRIBUTORS_LAST = ["Poldrack, Russell A."]
 
 
 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]
-    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 = []
     position = 1
     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])]
@@ -36,86 +39,97 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
             continue
 
         if val not in author_matches:
-            val['position'] = position
+            val["position"] = position
             author_matches.append(val)
             position += 1
 
-    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)]
-            missing['position'] = position
+            missing["position"] = position
             author_matches.append(missing)
             position += 1
 
-    all_names = [val['name'] for val in author_matches]
+    all_names = [val["name"] for val in author_matches]
     for last_author in last:
-        author_matches[all_names.index(last_author)]['position'] = position
+        author_matches[all_names.index(last_author)]["position"] = position
         position += 1
 
-    author_matches = sorted(author_matches, key=lambda k: k['position'])
+    author_matches = sorted(author_matches, key=lambda k: k["position"])
 
     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
+
     contrib_file = Path(fname)
 
     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")
         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))
+        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. """ * (git_line_summary_path is None))
-    return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
+        raise RuntimeError(
+            """\
+Could not find line-contributors from git repository.%s"""
+            % """ \
+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]
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     data = get_git_lines()
 
-    zenodo_file = Path('.zenodo.json')
+    zenodo_file = Path(".zenodo.json")
     zenodo = json.loads(zenodo_file.read_text())
 
-    creators = json.loads(Path('.maint/developers.json').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())
+        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)
+        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))
+    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))

dmriprep/__about__.py

@@ -2,17 +2,20 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Base module variables."""
 from ._version import get_versions
-__version__ = get_versions()['version']
+
+__version__ = get_versions()["version"]
 del get_versions
 
-__packagename__ = 'dmriprep'
-__copyright__ = 'Copyright 2019, The dMRIPrep developers'
-__credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder'
-               'of the repository')
-__url__ = 'https://github.com/nipreps/dmriprep'
+__packagename__ = "dmriprep"
+__copyright__ = "Copyright 2019, The dMRIPrep developers"
+__credits__ = (
+    "Contributors: please check the ``.zenodo.json`` file at the top-level folder"
+    "of the repository"
+)
+__url__ = "https://github.com/nipreps/dmriprep"
 
-DOWNLOAD_URL = (
-    'https://github.com/nipreps/{name}/archive/{ver}.tar.gz'.format(
-        name=__packagename__, ver=__version__))
+DOWNLOAD_URL = "https://github.com/nipreps/{name}/archive/{ver}.tar.gz".format(
+    name=__packagename__, ver=__version__
+)
 
 __ga_id__ = "UA-156165436-1"

dmriprep/__init__.py

@@ -7,8 +7,8 @@
 )
 
 __all__ = [
-    '__version__',
-    '__copyright__',
-    '__credits__',
-    '__packagename__',
+    "__version__",
+    "__copyright__",
+    "__credits__",
+    "__packagename__",
 ]

dmriprep/cli/parser.py

@@ -34,7 +34,7 @@ def _min_one(value, parser):
     def _to_gb(value):
         scale = {"G": 1, "T": 10 ** 3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
         digits = "".join([c for c in value if c.isdigit()])
-        units = value[len(digits):] or "M"
+        units = value[len(digits) :] or "M"
         return int(digits) * scale[units[0]]
 
     def _drop_sub(value):
@@ -115,9 +115,12 @@ def _bids_filter(value):
         "(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)",
     )
     g_bids.add_argument(
-        "--anat-derivatives", action='store', metavar="PATH", type=PathExists,
+        "--anat-derivatives",
+        action="store",
+        metavar="PATH",
+        type=PathExists,
         help="Reuse the anatomical derivatives from another fMRIPrep run or calculated "
-             "with an alternative processing tool (NOT RECOMMENDED)."
+        "with an alternative processing tool (NOT RECOMMENDED).",
     )
 
     g_perfm = parser.add_argument_group("Options to handle performance")

dmriprep/cli/run.py

@@ -102,7 +102,7 @@ def main():
                 25,
                 "Works derived from this dMRIPrep execution should "
                 "include the following boilerplate: "
-                f"{config.execution.output_dir / 'dmriprep' / 'logs' / 'CITATION.md'}."
+                f"{config.execution.output_dir / 'dmriprep' / 'logs' / 'CITATION.md'}.",
             )
 
         if config.workflow.run_reconall: