Merge pull request #3038 from nipy/rel/1.2.3

REL: 1.2.3

.zenodo.json

@@ -1,10 +1,5 @@
 {
   "creators": [
-    {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Gorgolewski, Krzysztof J.",
-      "orcid": "0000-0003-3321-7583"
-    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Esteban, Oscar",
@@ -150,15 +145,20 @@
       "affiliation": "Concordia University",
       "name": "Benderoff, Erin"
     },
+    {
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "name": "Halchenko, Yaroslav O.",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
       "orcid": "0000-0001-7037-2449"
     },
     {
-      "affiliation": "Dartmouth College: Hanover, NH, United States",
-      "name": "Halchenko, Yaroslav O.",
-      "orcid": "0000-0003-3456-2493"
+      "affiliation": "The Centre for Addiction and Mental Health",
+      "name": "Joseph, Michael",
+      "orcid": "0000-0002-0068-230X"
     },
     {
       "affiliation": "UC San Diego",
@@ -202,11 +202,6 @@
       "name": "Varoquaux, Gael",
       "orcid": "0000-0003-1076-5122"
     },
-    {
-      "affiliation": "The Centre for Addiction and Mental Health",
-      "name": "Joseph, Michael",
-      "orcid": "0000-0002-0068-230X"
-    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann, Demian",
@@ -250,14 +245,14 @@
       "affiliation": "Nathan s Kline institute for psychiatric research",
       "name": "Sikka, Sharad"
     },
+    {
+      "name": "Forbes, Jessica"
+    },
     {
       "affiliation": "University College London",
       "name": "Mancini, Matteo",
       "orcid": "0000-0001-7194-4568"
     },
-    {
-      "name": "Forbes, Jessica"
-    },
     {
       "affiliation": "Duke University",
       "name": "Iqbal, Shariq",
@@ -295,10 +290,6 @@
     {
       "name": "Kent, James"
     },
-    {
-      "name": "Heinsfeld, Anibal S\u00f3lon",
-      "orcid": "0000-0002-2050-0614"
-    },
     {
       "name": "Watanabe, Aimi"
     },
@@ -325,6 +316,10 @@
       "name": "Eshaghi, Arman",
       "orcid": "0000-0002-6652-3512"
     },
+    {
+      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "orcid": "0000-0002-2050-0614"
+    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -352,14 +347,14 @@
       "affiliation": "UniversityHospital Heidelberg, Germany",
       "name": "Kleesiek, Jens"
     },
-    {
-      "name": "Erickson, Drew"
-    },
     {
       "affiliation": "NIMH IRP",
       "name": "Lee, John A.",
       "orcid": "0000-0001-5884-4247"
     },
+    {
+      "name": "Erickson, Drew"
+    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
@@ -378,6 +373,9 @@
     {
       "name": "K\u00fcttner, Ren\u00e9"
     },
+    {
+      "name": "Perez-Guevara, Martin"
+    },
     {
       "name": "Millman, Jarrod"
     },
@@ -412,6 +410,11 @@
       "name": "Stadler, J\u00f6rg",
       "orcid": "0000-0003-4313-129X"
     },
+    {
+      "affiliation": "Korea Advanced Institute of Science and Technology",
+      "name": "Kim, Sin",
+      "orcid": "0000-0003-4652-3758"
+    },
     {
       "affiliation": "University College London",
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
@@ -524,6 +527,11 @@
     {
       "name": "Matsubara, K"
     },
+    {
+      "affiliation": "University of Pennsylvania",
+      "name": "Junhao WEN",
+      "orcid": "0000-0003-2077-3070"
+    },
     {
       "name": "Cheung, Brian"
     },
@@ -679,9 +687,6 @@
       "name": "Pellman, John",
       "orcid": "0000-0001-6810-4461"
     },
-    {
-      "name": "Perez-Guevara, Martin"
-    },
     {
       "name": "Khanuja, Ranjeet"
     },
@@ -701,6 +706,11 @@
     {
       "name": "Lai, Jeff"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Gorgolewski, Krzysztof J.",
+      "orcid": "0000-0003-3321-7583"
+    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",

doc/changelog/1.X.X-changelog

@@ -1,3 +1,24 @@
+1.2.3 (September 23, 2019)
+==========================
+
+Python 1.2.3 will be the last version to support Python 3.4.
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/35?closed=1)
+
+  * FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037)
+  * FIX: Drop deprecated message argument to ``FileNotFoundError`` (https://github.com/nipy/nipype/pull/3035)
+  * FIX: Handle NIFTI extensions in ``afni.Qwarp`` (https://github.com/nipy/nipype/pull/3028)
+  * FIX: Disallow returning ``None`` in ``pipeline.utils.load_resultfile`` (https://github.com/nipy/nipype/pull/3023)
+  * ENH: Allow afni.CatMatvec to accept empty string opkeys (https://github.com/nipy/nipype/pull/2943)
+  * ENH: Add ``mrrtrix3.MRResize`` interface (https://github.com/nipy/nipype/pull/3031)
+  * ENH: Add version check / telemetry to Nipype (https://github.com/nipy/nipype/pull/3027)
+  * ENH: Update MCFLIRT outputs for FSL 6+ (https://github.com/nipy/nipype/pull/3029)
+  * ENH: Lightweight node cache checking (https://github.com/nipy/nipype/pull/3026)
+  * ENH: Avoid loading result from file when writing reports (https://github.com/nipy/nipype/pull/3024)
+  * ENH: replace portalocker with filelock (https://github.com/nipy/nipype/pull/3025)
+  * MAINT: Set minimum yapf for `checkspecs` to 0.27 (https://github.com/nipy/nipype/pull/3033)
+
+
 1.2.2 (September 07, 2019)
 ==========================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.2.2"
+release = "1.2.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

nipype/info.py

@@ -9,7 +9,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = '1.2.3-dev'
+__version__ = '1.2.3'
 
 
 def get_nipype_gitversion():

tools/feedstock.sh

@@ -108,6 +108,10 @@ Updating feedstock to release branch
 
 * URL = https://github.com/$SRCREPO/archive/$REF.tar.gz
 * SHA256 = \`$SHA256\`
+
+---
+
+@conda-forge-admin, please rerender.
 END
 fi
 

tools/update_zenodo.py

@@ -1,52 +1,21 @@
 #!/usr/bin/env python3
+"""Update and sort the creators list of the zenodo record."""
+import sys
+import shutil
+from pathlib import Path
 import json
 from fuzzywuzzy import fuzz, process
-import shutil
-import os
 import subprocess as sp
 
-if os.path.exists('line-contributions.txt'):
-    with open('line-contributions.txt', 'rt') as fp:
-        lines = fp.readlines()
-else:
-    if shutil.which('git-line-summary'):
-        print("Running git-line-summary on nipype repo")
-        lines = sp.check_output(['git-line-summary']).decode().split('\n')
-    else:
-        raise RuntimeError("Install Git Extras to view git contributors")
-
-data = [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
-
-# load zenodo from master
-with open('.zenodo.json', 'rt') as fp:
-    zenodo = json.load(fp)
-zen_names = [' '.join(val['name'].split(',')[::-1]).strip()
-             for val in zenodo['creators']]
-
-name_matches = []
-
-for ele in data:
-    matches = process.extract(ele, zen_names, scorer=fuzz.token_sort_ratio,
-                              limit=2)
-    # matches is a list [('First match', % Match), ('Second match', % Match)]
-    if matches[0][1] > 80:
-        val = zenodo['creators'][zen_names.index(matches[0][0])]
-    else:
-        # skip unmatched names
-        print("No entry to sort:", ele)
-        continue
-
-    if val not in name_matches:
-        name_matches.append(val)
-
+# These ORCIDs should go last
+CREATORS_LAST = ['Gorgolewski, Krzysztof J.', 'Ghosh, Satrajit']
 # for entries not found in line-contributions
-missing_entries = [
+MISSING_ENTRIES = [
     {"name": "Varada, Jan"},
     {"name": "Schwabacher, Isaac"},
     {"affiliation": "Child Mind Institute / Nathan Kline Institute",
      "name": "Pellman, John",
      "orcid": "0000-0001-6810-4461"},
-    {"name": "Perez-Guevara, Martin"},
     {"name": "Khanuja, Ranjeet"},
     {"affiliation":
         "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.",
@@ -61,31 +30,62 @@
     {"name": "Lai, Jeff"}
 ]
 
-for entry in missing_entries:
-    name_matches.append(entry)
+if __name__ == '__main__':
+    contrib_file = Path('line-contributors.txt')
+    lines = []
+    if contrib_file.exists():
+        print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr)
+        lines = contrib_file.read_text().splitlines()
 
-
-def fix_position(creators):
-    # position first / last authors
-    f_authr = None
-    l_authr = None
-
-    for i, info in enumerate(creators):
-        if info['name'] == 'Gorgolewski, Krzysztof J.':
-            f_authr = i
-        if info['name'] == 'Ghosh, Satrajit':
-            l_authr = i
-
-    if f_authr is None or l_authr is None:
-        raise AttributeError('Missing important people')
-
-    creators.insert(0, creators.pop(f_authr))
-    creators.insert(len(creators), creators.pop(l_authr + 1))
-    return creators
-
-
-zenodo['creators'] = fix_position(name_matches)
-
-with open('.zenodo.json', 'wt') as fp:
-    json.dump(zenodo, fp, indent=2, sort_keys=True)
-    fp.write('\n')
+    git_line_summary_path = shutil.which('git-line-summary')
+    if not lines and git_line_summary_path:
+        print("Running git-line-summary on nipype repo")
+        lines = sp.check_output([git_line_summary_path]).decode().splitlines()
+        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))
+
+    data = [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
+
+    # load zenodo from master
+    zenodo_file = Path('.zenodo.json')
+    zenodo = json.loads(zenodo_file.read_text())
+    zen_names = [' '.join(val['name'].split(',')[::-1]).strip()
+                 for val in zenodo['creators']]
+    total_names = len(zen_names) + len(MISSING_ENTRIES)
+
+    name_matches = []
+    position = 1
+    for ele in data:
+        matches = process.extract(ele, zen_names, scorer=fuzz.token_sort_ratio,
+                                  limit=2)
+        # matches is a list [('First match', % Match), ('Second match', % Match)]
+        if matches[0][1] > 80:
+            val = zenodo['creators'][zen_names.index(matches[0][0])]
+        else:
+            # skip unmatched names
+            print("No entry to sort:", ele)
+            continue
+
+        if val not in name_matches:
+            if val['name'] not in CREATORS_LAST:
+                val['position'] = position
+                position += 1
+            else:
+                val['position'] = total_names + CREATORS_LAST.index(val['name'])
+            name_matches.append(val)
+
+    for missing in MISSING_ENTRIES:
+        missing['position'] = position
+        position += 1
+        name_matches.append(missing)
+
+    zenodo['creators'] = sorted(name_matches, key=lambda k: k['position'])
+    # Remove position
+    for creator in zenodo['creators']:
+        del creator['position']
+
+    zenodo_file.write_text('%s\n' % json.dumps(zenodo, indent=2, sort_keys=True))