nipy · josephmje · Aug 19, 2019 · Aug 20, 2019 · Aug 20, 2019 · Aug 20, 2019
diff --git a/.mailmap b/.mailmap
@@ -151,6 +151,7 @@ Michael Waskom <michael.l.waskom@gmail.com> mwaskom <mwaskom@mit.edu>
 Michael Waskom <michael.l.waskom@gmail.com> mwaskom <mwaskom@nyu.edu>
 Michael Waskom <michael.l.waskom@gmail.com> mwaskom <mwaskom@stanford.edu>
 Miguel Molina-Romero <miguel.molina.romero@gmail.com> Miguel Molina <miguel.molina.romero@gmail.com>
+Murat Bilgel <bilgelm@gmail.com> Murat Bilgel <murat.bilgel@nih.gov>
 Oliver Contier <o.contier@gmail.com> oliver-contier <oliver.contier@ovgu.de>
 Oscar Esteban <code@oscaresteban.es> Oscar Esteban <code@oscaresteban>
 Oscar Esteban <code@oscaresteban.es> oesteban <code@oscaresteban.es>
@@ -160,6 +161,7 @@ Paul Sharp <psharp1289@gmail.com> psharp1289 <psharp1289@gmail.com>
 Ranjit Khanuja <ranjit.jhu@gmail.com> RanjitK <ranjit.jhu@gmail.com>
 Rastko Ćirić <rc042010@mymail.pomona.edu> rciric <rc042010@mymail.pomona.edu>
 Rastko Ćirić <rc042010@mymail.pomona.edu> Rastko Ćirić <rciric@users.noreply.github.com>
+Rastko Ćirić <rc042010@mymail.pomona.edu> rciric <rastko@stanford.edu>
 Ross Markello <rossmarkello@gmail.com> Ross Markello <rdm222@cornell.edu>
 Russell Poldrack <poldrack@gmail.com> Russ Poldrack <poldrack@gmail.com>
 Russell Poldrack <poldrack@gmail.com> poldrack <poldrack@gmail.com>
@@ -182,7 +184,11 @@ Siqi Liu <lsqshr@gmail.com> sql <lsqshr@gmail.com>
 Steven Giavasis <sgiava77@gmail.com> Steven Giavasis <steven.giavasis@cmi-rsch-li001.childmind.org>
 Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiava77@gmail.com>
 Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiavasis@ieee.org>
+Steven Tilley <stilley@hollandbloorview.ca> Steven Tilley <steve@steventilley.com>
 Tristan Glatard <tristan.glatard@mcgill.ca> Tristan Glatard <tristan.glatard@creatis.insa-lyon.fr>
+Victor Férat <victor.ferat@live.fr> Victor <victor.ferat@live.fr>
+Victor Férat <victor.ferat@live.fr> Victor Ferat <vferat@fcbg.ch>
+Victor Férat <victor.ferat@live.fr> Victor Férat <victor.ferat@live.Fr>
 Victor Saase <victor@saase.net> vsaase <victor@saase.net>
 Weijie Huang <hwjbupt@gmail.com> forwho <hwjbupt@gmail.com>
 William Triplett <wtriplett@gmail.com> William Triplett <wtriplett@ufl.edu>

diff --git a/.zenodo.json b/.zenodo.json
@@ -78,10 +78,6 @@
       "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
       "name": "Wong, Jason"
     },
-    {
-      "affiliation": "Concordia University",
-      "name": "Benderoff, Erin"
-    },
     {
       "name": "Modat, Marc"
     },
@@ -150,6 +146,10 @@
     {
       "name": "Berleant, Shoshana"
     },
+    {
+      "affiliation": "Concordia University",
+      "name": "Benderoff, Erin"
+    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
@@ -293,11 +293,11 @@
       "orcid": "0000-0002-7796-8795"
     },
     {
-      "name": "Heinsfeld, Anibal S\u00f3lon",
-      "orcid": "0000-0002-2050-0614"
+      "name": "Kent, James"
     },
     {
-      "name": "Kent, James"
+      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "orcid": "0000-0002-2050-0614"
     },
     {
       "name": "Watanabe, Aimi"
@@ -355,15 +355,15 @@
     {
       "name": "Erickson, Drew"
     },
-    {
-      "affiliation": "Child Mind Institute",
-      "name": "Giavasis, Steven"
-    },
     {
       "affiliation": "NIMH IRP",
       "name": "Lee, John A.",
       "orcid": "0000-0001-5884-4247"
     },
+    {
+      "affiliation": "Child Mind Institute",
+      "name": "Giavasis, Steven"
+    },
     {
       "name": "Correa, Carlos"
     },
@@ -381,9 +381,6 @@
     {
       "name": "Millman, Jarrod"
     },
-    {
-      "name": "Lai, Jeff"
-    },
     {
       "name": "Zhou, Dale"
     },
@@ -393,23 +390,28 @@
     {
       "name": "Haselgrove, Christian"
     },
+    {
+      "affiliation": "Holland Bloorview Kids Rehabilitation Hospital",
+      "name": "Tilley II, Steven",
+      "orcid": "0000-0003-4853-5082"
+    },
     {
       "name": "Renfro, Mandy"
     },
     {
       "affiliation": "The University of Sydney",
       "name": "Liu, Siqi"
     },
-    {
-      "affiliation": "Leibniz Institute for Neurobiology",
-      "name": "Stadler, J\u00f6rg",
-      "orcid": "0000-0003-4313-129X"
-    },
     {
       "affiliation": "University of Pennsylvania",
       "name": "Kahn, Ari E.",
       "orcid": "0000-0002-2127-0507"
     },
+    {
+      "affiliation": "Leibniz Institute for Neurobiology",
+      "name": "Stadler, J\u00f6rg",
+      "orcid": "0000-0003-4313-129X"
+    },
     {
       "affiliation": "University College London",
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
@@ -502,31 +504,26 @@
       "name": "Perkins, L. Nathan"
     },
     {
-      "affiliation": "University of Amsterdam",
-      "name": "Lukas Snoek",
-      "orcid": "0000-0001-8972-204X"
+      "name": "Marina, Ana"
     },
     {
-      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
-      "name": "Weninger, Leon"
+      "name": "Mattfeld, Aaron"
     },
     {
-      "affiliation": "Stanford University",
-      "name": "Lerma-Usabiaga, Garikoitz",
-      "orcid": "0000-0001-9800-4816"
+      "name": "Noel, Maxime"
     },
     {
-      "name": "Marina, Ana"
+      "affiliation": "University of Amsterdam",
+      "name": "Lukas Snoek",
+      "orcid": "0000-0001-8972-204X"
     },
     {
-      "name": "Mattfeld, Aaron"
+      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
+      "name": "Weninger, Leon"
     },
     {
       "name": "Matsubara, K"
     },
-    {
-      "name": "Noel, Maxime"
-    },
     {
       "name": "Cheung, Brian"
     },
@@ -573,9 +570,6 @@
     {
       "name": "Weinstein, Alejandro"
     },
-    {
-      "name": "Tambini, Arielle"
-    },
     {
       "affiliation": "Duke University",
       "name": "Broderick, William",
@@ -598,6 +592,11 @@
     {
       "name": "Khanuja, Ranjeet"
     },
+    {
+      "affiliation": "National Institute on Aging, Baltimore, MD, USA",
+      "name": "Bilgel, Murat",
+      "orcid": "0000-0001-5042-7422"
+    },
     {
       "name": "Schlamp, Kai"
     },
@@ -612,6 +611,9 @@
     {
       "name": "Tarbert, Claire"
     },
+    {
+      "name": "Tambini, Arielle"
+    },
     {
       "name": "Nickson, Thomas"
     },
@@ -636,6 +638,11 @@
     {
       "name": "Flandin, Guillaume"
     },
+    {
+      "affiliation": "Stanford University",
+      "name": "Lerma-Usabiaga, Garikoitz",
+      "orcid": "0000-0001-9800-4816"
+    },
     {
       "affiliation": "Vrije Universiteit Amsterdam",
       "name": "Ort, Eduard"
@@ -691,6 +698,9 @@
       "name": "Mihai, Paul Glad",
       "orcid": "0000-0001-5715-6442"
     },
+    {
+      "name": "Lai, Jeff"
+    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",

diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog
@@ -1,3 +1,19 @@
+1.2.2 (September 07, 2019)
+==========================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/33?closed=1)
+
+  * FIX: Ensure ``loadpkl`` returns a not None value (https://github.com/nipy/nipype/pull/3020)
+  * FIX: ``loadpkl`` failed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017)
+  * FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007)
+  * FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010)
+  * ENH: Add interface for AFNI ``3dTsmooth`` (https://github.com/nipy/nipype/pull/2948)
+  * ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012)
+  * ENH: Add ``--rescale-intensities`` and name_source to N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3011)
+  * ENH: Add index_mask_file input to ImageStats (https://github.com/nipy/nipype/pull/3005)
+  * RF: Remove versioning from ``loadpkl`` (https://github.com/nipy/nipype/pull/3019)
+  * MAINT: Add ``python_requires`` to package metadata (https://github.com/nipy/nipype/pull/3006)
+
 1.2.1 (August 19, 2019)
 =======================
 

diff --git a/doc/conf.py b/doc/conf.py
@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.2.1"
+release = "1.2.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/documentation.rst b/doc/documentation.rst
@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.2.1 <http://nipype.readthedocs.io/en/1.2.1/>`_ `1.2.0 <http://nipype.readthedocs.io/en/1.2.0/>`_
+Previous versions: `1.2.2 <http://nipype.readthedocs.io/en/1.2.2/>`_ `1.2.1 <http://nipype.readthedocs.io/en/1.2.1/>`_
 
 
 .. container:: doc2

diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py
@@ -799,11 +799,11 @@ def _run_interface(self, runtime):
                             '(http://pandas.pydata.org/) to run.'), e)
 
         try:
-            import lockfile as pl
+            from filelock import SoftFileLock
             self._have_lock = True
         except ImportError:
             from warnings import warn
-            warn(('Python module lockfile was not found: AddCSVRow will not be'
+            warn(('Python module filelock was not found: AddCSVRow will not be'
                   ' thread-safe in multi-processor execution'))
 
         input_dict = {}
@@ -822,7 +822,7 @@ def _run_interface(self, runtime):
         df = pd.DataFrame([input_dict])
 
         if self._have_lock:
-            self._lock = pl.FileLock(self.inputs.in_file)
+            self._lock = SoftFileLock('%s.lock' % self.inputs.in_file)
 
             # Acquire lock
             self._lock.acquire()
@@ -837,13 +837,6 @@ def _run_interface(self, runtime):
         if self._have_lock:
             self._lock.release()
 
-        # Using nipype.external.portalocker this might be something like:
-        # with pl.Lock(self.inputs.in_file, timeout=1) as fh:
-        #     if op.exists(fh):
-        #         formerdf = pd.read_csv(fh, index_col=0)
-        #         df = pd.concat([formerdf, df], ignore_index=True)
-        #         df.to_csv(fh)
-
         return runtime
 
     def _list_outputs(self):

diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py
@@ -6,7 +6,10 @@
 def test_AddCSVRow_inputs():
     input_map = dict(
         _outputs=dict(usedefault=True, ),
-        in_file=dict(mandatory=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
     )
     inputs = AddCSVRow.input_spec()
 

diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py
@@ -4,11 +4,10 @@
 
 
 def test_Gunzip_inputs():
-    input_map = dict(
-        in_file=dict(
-            extensions=None,
-            mandatory=True,
-        ), )
+    input_map = dict(in_file=dict(
+        extensions=None,
+        mandatory=True,
+    ), )
     inputs = Gunzip.input_spec()
 
     for key, metadata in list(input_map.items()):

diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py
@@ -4,11 +4,10 @@
 
 
 def test_NonSteadyStateDetector_inputs():
-    input_map = dict(
-        in_file=dict(
-            extensions=None,
-            mandatory=True,
-        ), )
+    input_map = dict(in_file=dict(
+        extensions=None,
+        mandatory=True,
+    ), )
     inputs = NonSteadyStateDetector.input_spec()
 
     for key, metadata in list(input_map.items()):

diff --git a/nipype/external/cloghandler.py b/nipype/external/cloghandler.py
@@ -36,10 +36,6 @@
 testing, performance was more than adequate, but if you need a high-volume or
 low-latency solution, I suggest you look elsewhere.
 
-This module currently only support the 'nt' and 'posix' platforms due to the
-usage of the portalocker module.  I do not have access to any other platforms
-for testing, patches are welcome.
-
 See the README file for an example usage of this module.
 
 """
@@ -63,13 +59,7 @@
 except ImportError:
     codecs = None
 
-# Question/TODO: Should we have a fallback mode if we can't load portalocker /
-# we should still be better off than with the standard RotattingFileHandler
-# class, right? We do some rename checking... that should prevent some file
-# clobbering that the builtin class allows.
-
-# sibling  module than handles all the ugly platform-specific details of file locking
-from .portalocker import lock, unlock, LOCK_EX, LOCK_NB, LockException
+from filelock import SoftFileLock
 
 # A client can set this to true to automatically convert relative paths to
 # absolute paths (which will also hide the absolute path warnings)
@@ -168,11 +158,8 @@ def __init__(self,
         self.maxBytes = maxBytes
         self.backupCount = backupCount
         # Prevent multiple extensions on the lock file (Only handles the normal "*.log" case.)
-        if filename.endswith(".log"):
-            lock_file = filename[:-4]
-        else:
-            lock_file = filename
-        self.stream_lock = open(lock_file + ".lock", "w")
+        self.lock_file = '%s.lock' % filename
+        self.stream_lock = SoftFileLock(self.lock_file)
 
         # For debug mode, swap out the "_degrade()" method with a more a verbose one.
         if debug:
@@ -189,7 +176,7 @@ def acquire(self):
         in 'degraded' mode. """
         # handle thread lock
         Handler.acquire(self)
-        lock(self.stream_lock, LOCK_EX)
+        self.stream_lock.acquire()
         if self.stream.closed:
             self._openFile(self.mode)
 
@@ -206,7 +193,7 @@ def release(self):
                 self.stream.close()
         finally:
             try:
-                unlock(self.stream_lock)
+                self.stream_lock.release()
             finally:
                 # release thread lock
                 Handler.release(self)