[skip ci] Merge branch 'master' of https://github.com/poldracklab/fmriprep into code_server

Author: jdkent

.github/stale.yml

@@ -1,7 +1,7 @@
 # Number of days of inactivity before an issue becomes stale
-daysUntilStale: 300
+daysUntilStale: 900
 # Number of days of inactivity before a stale issue is closed
-daysUntilClose: 20
+daysUntilClose: 200
 # Issues with these labels will never be considered stale
 exemptLabels:
   - pinned

.zenodo.json

@@ -136,6 +136,11 @@
       "affiliation": "Department of Psychology, Stanford University",
       "orcid": "0000-0002-0533-6035"
     },
+    {
+      "name": "Tooley, Ursula A.",
+      "affiliation": "Department of Neuroscience, University of Pennsylvania, PA, USA",
+      "orcid": "0000-0001-6377-3885"
+    },
     {
       "name": "Poldrack, Russell A.",
       "affiliation": "Department of Psychology, Stanford University",

CHANGES.rst

@@ -12,16 +12,21 @@ with M. Cieslak, A. Adebimpe, and T. Satterthwaite.
 Some other bugfixes, improvements to the documentation and minor features are also
 shipped with the new release.
 
-
-* ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
-* REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
-* MAINT: Remove old ``extensions`` entity selector for PyBIDS queries (#1707) @oesteban
 * FIX: Postpone ``pandoc`` conversion of boilerplate after workflow has fully run (#1710) @oesteban
-* DOC: adding recon-all issue to faq (#1622) @franklin-feingold
 * FIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (#1703) @effigies
 * FIX: Correct BOLD-T1w registration description if DoF != 9 (#1701) @effigies
-* MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies
+* ENH: Make fmriprep print defaults for arguments with help (#1735) @gdevenyi
+* ENH: Add check for updates and check whether version has been flagged. (#1715) @oesteban
+* ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
+* REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
+* DOC: Update .zenodo.json (#1732) @utooley
+* DOC: Add link to documentation in help of ``--output-spaces`` argument (#1722) @oesteban
+* DOC: adding recon-all issue to faq (#1622) @franklin-feingold
 * DOC: Add copyright waiver to boilerplate and reviewer note to docs (#1691) @effigies
+* MAINT: Bump pybids and nipype dependencies (#1744) @effigies
+* MAINT: Move regression tests of EPI masks over to Niworkflows (#1716) @oesteban
+* MAINT: Remove old ``extensions`` entity selector for PyBIDS queries (#1707) @oesteban
+* MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies
 
 1.4.1 (July 9, 2019)
 ====================

fmriprep/cli/run.py

@@ -14,7 +14,7 @@
 import uuid
 import warnings
 from argparse import ArgumentParser
-from argparse import RawTextHelpFormatter
+from argparse import ArgumentDefaultsHelpFormatter
 from multiprocessing import cpu_count
 from time import strftime
 
@@ -46,9 +46,11 @@ def get_parser():
     from .version import check_latest, is_flagged
 
     verstr = 'fmriprep v{}'.format(__version__)
+    currentv = Version(__version__)
+    is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
 
     parser = ArgumentParser(description='FMRIPREP: fMRI PREProcessing workflows',
-                            formatter_class=RawTextHelpFormatter)
+                            formatter_class=ArgumentDefaultsHelpFormatter)
 
     # Arguments as specified by BIDS-Apps
     # required, positional arguments
@@ -140,8 +142,11 @@ def get_parser():
 Non-standard spaces (valid keywords: %s) imply specific orientations and sampling \
 grids. \
 Important to note, the ``res-*`` modifier does not define the resolution used for \
-the spatial normalization """ % (', '.join('"%s"' % s for s in templates()),
-                                 ', '.join(NONSTANDARD_REFERENCES)))
+the spatial normalization.
+For further details, please check out \
+https://fmriprep.readthedocs.io/en/%s/spaces.html""" % (
+            ', '.join('"%s"' % s for s in templates()), ', '.join(NONSTANDARD_REFERENCES),
+            currentv.base_version if is_release else 'latest'))
 
     g_conf.add_argument(
         '--output-space', required=False, action='store', type=str, nargs='+',
@@ -276,9 +281,7 @@ def get_parser():
     g_other.add_argument('--sloppy', action='store_true', default=False,
                          help='Use low-quality tools for speed - TESTING ONLY')
 
-    currentv = Version(__version__)
     latest = check_latest()
-
     if latest is not None and currentv < latest:
         print("""\
 You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.

setup.cfg

@@ -26,9 +26,9 @@ install_requires =
     nibabel >=2.2.1
     indexed_gzip >=0.8.8
     nilearn !=0.5.0, !=0.5.1
-    nipype >=1.2.0
+    nipype >=1.2.1
     psutil >=5.4
-    pybids ~= 0.9.2
+    pybids ~= 0.9.3
     tedana >=0.0.5
     nitime
     numpy