nipy · matteomancini · Nov 14, 2017 · Nov 15, 2017 · Nov 15, 2017 · Nov 15, 2017
diff --git a/.zenodo.json b/.zenodo.json
diff --git a/CHANGES b/CHANGES
@@ -1,12 +1,13 @@
-Upcoming release
+Upcoming release (0.14.1)
 ================
 
 
-0.14.0 (<TBD>)
-==============
+0.14.0 (November 29, 2017)
+==========================
 
 ###### [Full changelog](https://github.com/nipy/nipype/milestone/13)
 
+* FIX+MAINT: Revision of the resource monitor (https://github.com/nipy/nipype/pull/2285)
 * FIX: MultiProc mishandling crashes (https://github.com/nipy/nipype/pull/2301)
 * MAINT: Revise use of `subprocess.Popen` (https://github.com/nipy/nipype/pull/2289)
 * ENH: Memorize version checks (https://github.com/nipy/nipype/pull/2274, https://github.com/nipy/nipype/pull/2295)

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 = "0.14.0-rc1"
+release = "0.14.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst
@@ -74,11 +74,11 @@ Execution
 
 *display_variable*
 	Override the ``$DISPLAY`` environment variable for interfaces that require
-    an X server. This option is useful if there is a running X server, but
-    ``$DISPLAY`` was not defined in nipype's environment. For example, if an X
+    an X server. This option is useful if there is a running X server, but 
+    ``$DISPLAY`` was not defined in nipype's environment. For example, if an X 
     server is listening on the default port of 6000, set ``display_variable = :0``
-    to enable nipype interfaces to use it. It may also point to displays provided
-    by VNC, `xnest <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html>`_
+    to enable nipype interfaces to use it. It may also point to displays provided 
+    by VNC, `xnest <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html>`_ 
     or `Xvfb <http://www.x.org/archive/X11R6.8.1/doc/Xvfb.1.html>`_.
     If neither ``display_variable`` nor the ``$DISPLAY`` environment variable are
     set, nipype will try to configure a new virtual server using Xvfb.
@@ -153,14 +153,29 @@ Execution
     crashfiles allow portability across machines and shorter load time.
     (possible values: ``pklz`` and ``txt``; default value: ``pklz``)
 
-*resource_monitor*
+
+Resource Monitor
+~~~~~~~~~~~~~~~~
+
+*enabled*
     Enables monitoring the resources occupation (possible values: ``true`` and
-    ``false``; default value: ``false``)
+    ``false``; default value: ``false``). All the following options will be
+    dismissed if the resource monitor is not enabled.
 
-*resource_monitor_frequency*
+*sample_frequency*
     Sampling period (in seconds) between measurements of resources (memory, cpus)
-    being used by an interface. Requires ``resource_monitor`` to be ``true``.
-    (default value: ``1``)
+    being used by an interface (default value: ``1``)
+
+*summary_file*
+    Indicates where the summary file collecting all profiling information from the
+    resource monitor should be stored after execution of a workflow.
+    The ``summary_file`` does not apply to interfaces run independently.
+    (unset by default, in which case the summary file will be written out to 
+    ``<base_dir>/resource_monitor.json`` of the top-level workflow).
+
+*summary_append*
+    Append to an existing summary file (only applies to workflows).
+    (default value: ``true``, possible values: ``true`` or ``false``).
 
 Example
 ~~~~~~~
@@ -175,6 +190,10 @@ Example
     hash_method = timestamp
     display_variable = :1
 
+    [monitoring]
+    enabled = false
+
+
 Workflow.config property has a form of a nested dictionary reflecting the
 structure of the .cfg file.
 

diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
@@ -20,8 +20,9 @@ echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
 echo 'crashfile_format = txt' >> ${HOME}/.nipype/nipype.cfg
 
 if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
-    echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg
-    echo 'resource_monitor_frequency = 3' >> ${HOME}/.nipype/nipype.cfg
+    echo '[monitoring]' >> ${HOME}/.nipype/nipype.cfg
+    echo 'enabled = true' >> ${HOME}/.nipype/nipype.cfg
+    echo 'sample_frequency = 3' >> ${HOME}/.nipype/nipype.cfg
 fi
 
 # Set up coverage

diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py
@@ -9,7 +9,8 @@ def test_ACompCor_inputs():
     header_prefix=dict(),
     high_pass_cutoff=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     ignore_initial_volumes=dict(usedefault=True,

diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py
@@ -6,7 +6,8 @@
 def test_AddCSVRow_inputs():
     input_map = dict(_outputs=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py
@@ -8,7 +8,8 @@ def test_ArtifactDetect_inputs():
     ),
     global_threshold=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     intersect_mask=dict(),

diff --git a/nipype/algorithms/tests/test_auto_CalculateMedian.py b/nipype/algorithms/tests/test_auto_CalculateMedian.py
@@ -4,7 +4,8 @@
 
 
 def test_CalculateMedian_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_files=dict(),

diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py
@@ -10,7 +10,8 @@ def test_ComputeDVARS_inputs():
     ),
     figsize=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py
@@ -4,7 +4,8 @@
 
 
 def test_ComputeMeshWarp_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     metric=dict(usedefault=True,

diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py
@@ -9,7 +9,8 @@ def test_CreateNifti_inputs():
     ),
     header_file=dict(mandatory=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     )

diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py
@@ -4,7 +4,8 @@
 
 
 def test_Distance_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     mask_volume=dict(),

diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py
@@ -8,7 +8,8 @@ def test_FramewiseDisplacement_inputs():
     ),
     figsize=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py
@@ -4,7 +4,8 @@
 
 
 def test_FuzzyOverlap_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_ref=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py
@@ -4,7 +4,8 @@
 
 
 def test_Gunzip_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py
@@ -4,7 +4,8 @@
 
 
 def test_ICC_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     mask=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py
@@ -5,7 +5,8 @@
 
 def test_MeshWarpMaths_inputs():
     input_map = dict(float_trait=dict(),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_surf=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py
@@ -4,7 +4,8 @@
 
 
 def test_ModifyAffine_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     transformation_matrix=dict(usedefault=True,

diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py
@@ -4,7 +4,8 @@
 
 
 def test_NonSteadyStateDetector_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py
@@ -4,7 +4,8 @@
 
 
 def test_P2PDistance_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     metric=dict(usedefault=True,

diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py
@@ -10,7 +10,8 @@ def test_PickAtlas_inputs():
     ),
     hemi=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     labels=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py
@@ -4,7 +4,8 @@
 
 
 def test_Similarity_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     mask1=dict(),

diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py
@@ -4,7 +4,8 @@
 
 
 def test_SimpleThreshold_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     threshold=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py
@@ -12,7 +12,8 @@ def test_SpecifyModel_inputs():
     ),
     high_pass_filter_cutoff=dict(mandatory=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     input_units=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py
@@ -14,7 +14,8 @@ def test_SpecifySPMModel_inputs():
     ),
     high_pass_filter_cutoff=dict(mandatory=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     input_units=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py
@@ -12,7 +12,8 @@ def test_SpecifySparseModel_inputs():
     ),
     high_pass_filter_cutoff=dict(mandatory=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     input_units=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py
@@ -6,7 +6,8 @@
 def test_StimulusCorrelation_inputs():
     input_map = dict(concatenated_design=dict(mandatory=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     intensity_values=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py
@@ -9,7 +9,8 @@ def test_TCompCor_inputs():
     header_prefix=dict(),
     high_pass_cutoff=dict(usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     ignore_initial_volumes=dict(usedefault=True,

diff --git a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py
@@ -4,7 +4,8 @@
 
 
 def test_TVTKBaseInterface_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     )

diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py
@@ -4,7 +4,8 @@
 
 
 def test_WarpPoints_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     interp=dict(mandatory=True,

diff --git a/nipype/algorithms/tests/test_mesh_ops.py b/nipype/algorithms/tests/test_mesh_ops.py
@@ -15,7 +15,7 @@
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_ident_distances(tmpdir):
-    tmpdir.chdir()
+    tmpdir.chdir() 
 
     in_surf = example_data('surf01.vtk')
     dist_ident = m.ComputeMeshWarp()

diff --git a/nipype/info.py b/nipype/info.py
@@ -10,7 +10,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '0.14.0-rc1'
+__version__ = '0.14.1-dev'
 
 
 def get_nipype_gitversion():

diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py
@@ -9,7 +9,8 @@ def test_ABoverlap_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     in_file_a=dict(argstr='%s',

diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py
@@ -9,7 +9,8 @@ def test_AFNICommand_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
-    ignore_exception=dict(nohash=True,
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
     usedefault=True,
     ),
     num_threads=dict(nohash=True,