Fix the apidoc Note delimiter.

qipipe/interfaces/ants/utils.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft = python sts = 4 ts = 4 sw = 4 et:
 """ANTS Affine Initializer interface
-   
+
    Change directory to provide relative paths for doctests
    >>> import os
    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
@@ -21,22 +21,22 @@
 
 class AffineInitializerInputSpec(ANTSCommandInputSpec):
     """
-    :Note: The antsAffineInitializer command line options are positional
+    .. Note:: The antsAffineInitializer command line options are positional
         rather than keyword, e.g.::
-            
+
             antsAffineInitializer 3 fixed.nii.gz moving.nii.gz initial_xform.mat \
             10 0.3
-        
+
         rather than::
-            
+
             antsAffineInitializer 3 fixed.nii.gz moving.nii.gz initial_xform.mat \
             --search_factor 10 --radian_fraction 0.3
-        
+
         Therefore, each optional input field requires the prior input field,
         e.g. *radian_fraction* requires a *search_factor* input. Reasonable
         starting option values are shown in the :class:`AffineInitializer`
         example.
-        
+
         In particular, note that since an image mask is the last positional
         argument, if the *image_mask* input option is set, then all other
         options must be set as well.
@@ -79,7 +79,7 @@ class AffineInitializer(ANTSCommand):
     """
     Examples
     --------
-    
+
     >>> initalizer = AffineInitializer()
     >>> initalizer.inputs.dimension = 3
     >>> initalizer.inputs.fixed_image = 'NIFTI/volume003.nii.gz'
@@ -96,16 +96,16 @@ class AffineInitializer(ANTSCommand):
     _cmd = 'antsAffineInitializer'
     input_spec = AffineInitializerInputSpec
     output_spec = AffineInitializerOutputSpec
-    
-    
+
+
     def _format_arg(self, opt, spec, val):
         if opt == 'radian_fraction':
             # Suppress extraneous trailing zeros.
             # Cf. http://stackoverflow.com/questions/2440692/formatting-floats-in-python-without-superfluous-zeros
             return ('%f' % val).rstrip('0').rstrip('.')
         else:
             return super(AffineInitializer, self)._format_arg(opt, spec, val)
-    
+
     def _list_outputs(self):
         outputs = self._outputs().get()
         out_file = os.path.abspath(self.inputs.output_affine_transform)

qipipe/interfaces/fastfit.py

@@ -2,7 +2,7 @@
 OHSU - This module wraps the proprietary OHSU AIRC ``fastfit``
 software. ``fastfit`` optimizes the input pharmacokinetic model.
 
-:Note: this interface is adapted from the OHSU AIRC cluster file
+.. Note:: this interface is adapted from the OHSU AIRC cluster file
     ``/usr/global/scripts/fastfit_iface.py``.
 """
 

qipipe/interfaces/sticky_identity.py

@@ -43,7 +43,7 @@ class StickyIdentityInterface(IOBase):
         >> output_res.outputs.get()['a']  # bad!
         <undefined>
     
-    :Note: a better solution is to set a *preserve* flag on
+    .. Note:: a better solution is to set a *preserve* flag on
         IdentityInterface. If this solution is implemented by Nipype,
         then this :class:`StickyIdentityInterface` class will be
         deprecated.

qipipe/interfaces/xnat_download.py

@@ -45,7 +45,7 @@ class XNATDownload(BaseInterface):
     The ``XNATDownload`` Nipype interface wraps the
     :meth:`qixnat.facade.XNAT.download` method.
 
-    :Note: only one XNAT operation can run at a time.
+    .. Note:: only one XNAT operation can run at a time.
 
     Examples:
 

qipipe/interfaces/xnat_find.py

@@ -39,7 +39,7 @@ class XNATFind(BaseInterface):
     The ``XNATFind`` Nipype interface wraps the ``qixnat.facade.XNAT``
     ``find_one`` and ``find_or_create`` methods.
     
-    :Note: concurrent XNAT operations can fail. See the
+    .. Note:: concurrent XNAT operations can fail. See the
         :class:`qipipe.pipeline.staging.StagingWorkflow` note.
     """
 

qipipe/pipeline/modeling.py

@@ -145,7 +145,7 @@ class ModelingWorkflow(WorkflowBase):
 
     This workflow is adapted from the `AIRC DCE`_ implementation.
 
-    :Note: This workflow uses proprietary OHSU AIRC software, notably the
+    .. Note:: This workflow uses proprietary OHSU AIRC software, notably the
         OHSU implementation of the shutter speed model.
 
     .. reST substitutions:
@@ -443,7 +443,7 @@ def _create_airc_workflow(self, **opts):
         :class:`qipipe.pipeline.modeling.ModelingWorkflow` with the
         exception of XNAT upload.
 
-        :Note: This workflow is adapted from the AIRC workflow at
+        .. Note:: This workflow is adapted from the AIRC workflow at
         https://everett.ohsu.edu/hg/qin_dce. The AIRC workflow time
         series merge is removed and added as input to the workflow
         created by this method. The modeling optimization parameters

qipipe/pipeline/qipipeline.py

@@ -1151,14 +1151,14 @@ def _register(subject, session, scan, in_files, opts,
     A facade for the :meth:`qipipe.pipeline.registration.register
     method.
 
-    :Note: The *mask* and *reference_index* parameters are
+    .. Note:: The *mask* and *reference_index* parameters are
       registration options, but can't be included in the *opts*
       parameter, since they are potential upstream workflow node
       connection points. Since a mock registration technique
       does not connect these inputs, they have default values
       in the method signature as well.
 
-    :Note: contrary to Python convention, the *opts* method
+    .. Note:: contrary to Python convention, the *opts* method
       parameter is a required dictionary rather than a keyword
       double-splat argument (i.e., ``**opts``). The Nipype
       ``Function`` interface does not support double-splat
@@ -1186,7 +1186,7 @@ def register(subject, session, scan, reference_index, *in_files, **opts):
     """
     Runs the registration workflow on the given session scan images.
 
-    :Note: There is always a mask and resource argument. The mask
+    .. Note:: There is always a mask and resource argument. The mask
       file and resource name are either specified as an input or
       built by the workflow. The mask and resource are options in
       the registration run function. Therefore, we check that these
@@ -1341,7 +1341,7 @@ def roi(subject, session, scan, time_series, in_rois, opts):
     """
     Runs the ROI workflow on the given session scan images.
 
-    :Note: see the :meth:`register` note.
+    .. Note:: see the :meth:`register` note.
 
     :param subject: the subject name
     :param session: the session name

qipipe/pipeline/registration.py

@@ -111,7 +111,7 @@ class RegistrationWorkflow(WorkflowBase):
 
     - ``fsl.FNIRT``: the FSL `FNIRT interface`_ options
 
-    :Note: Since the XNAT *resource* name is unique, a
+    .. Note:: Since the XNAT *resource* name is unique, a
         :class:`qipipe.pipeline.registration.RegistrationWorkflow`
         instance can be used for only one registration workflow.
         Different registration inputs require different

qipipe/pipeline/staging.py

@@ -363,15 +363,17 @@ class VolumeStagingWorkflow(WorkflowBase):
 
     - *image*: the 3D volume stack NIfTI image file
 
-    :Note: Concurrent XNAT upload fails unpredictably due to one of
-        the causes described in the ``qixnat.facade.XNAT.find`` method
-        documentation.
+    .. Note:: Concurrent XNAT upload fails unpredictably due to one of
+    the causes described in the ``qixnat.facade.XNAT.find`` method
+    documentation.
 
         The errors are addressed by the following measures:
 
-        * setting an isolated pyxnat cache_dir for each execution node
+        * setting an isolated ``pyxnat`` *cache_dir* for each execution
+          node
 
-        * serializing the XNAT find-or-create access points with JoinNodes
+        * serializing the XNAT find-or-create access points with
+          ``JoinNode``s
 
         * increasing the SGE submission resource parameters as shown in
           the ``conf/staging.cfg [upload]`` section

qipipe/pipeline/workflow_base.py

@@ -349,7 +349,7 @@ def _configure_nodes(self, workflow):
         each WorkflowBase subclass after the workflow is built and
         prior to execution.
 
-        :Note: nested workflow nodes are not configured, e.g. if the
+        .. Note:: nested workflow nodes are not configured, e.g. if the
             ``registration`` workflow connects a `realign`` workflow
             node ``fnirt``, then the nested ``realign.fnirt`` node in
             ``registration`` is not configured by the parent workflow.

qipipe/staging/ohsu.py

@@ -133,12 +133,12 @@
 """
 The Sarcoma ROI .bqf ROI file match pattern.
 
-:Note: The Sarcoma ROI directories are inconsistently named, with several
+.. Note:: The Sarcoma ROI directories are inconsistently named, with several
     alternatives and duplicates.
 
     TODO - clarify which of the Sarcoma ROI naming variations should be used.
 
-:Note: There are no apparent lesion number indicators in the Sarcoma ROI
+.. Note:: There are no apparent lesion number indicators in the Sarcoma ROI
     input.
 
     TODO - confirm that there is no Sarcoma lesion indicator.

test/__init__.py

@@ -7,7 +7,7 @@
 """
 The test XNAT project name.
 
-:Note: this test project must be created in XNAT prior to running the
+.. Note:: this test project must be created in XNAT prior to running the
     tests.
 """
 

test/unit/pipeline/test_staging.py

@@ -19,38 +19,38 @@
 
 class TestStagingWorkflow(object):
     """Staging workflow unit tests."""
-    
+
     def setUp(self):
         shutil.rmtree(RESULTS, True)
-    
+
     def tearDown(self):
         shutil.rmtree(RESULTS, True)
-    
+
     def test_breast(self):
         self._test_collection('Breast')
-    
+
     def test_sarcoma(self):
         self._test_collection('Sarcoma')
-    
+
     def _test_collection(self, collection):
         """
-        Run the staging workflow on the given collection and verify that
-        the sessions are created in XNAT.
-        
-        :Note: This test does not verify the CTP staging area nor the
-        uploaded image file content. These features should be verified
-        manually.
-        
+        Run the staging workflow on the given collection and verify
+        that the sessions are created in XNAT.
+
+        .. Note:: This test does not verify the CTP staging area nor
+            the uploaded image file content. These features should be
+            verified manually.
+
         :param collection: the image collection name
         """
         fixture = os.path.join(FIXTURES, collection.lower())
         logger(__name__).debug("Testing the staging workflow on %s..." %
                                fixture)
-        
+
         # The staging destination and work area.
         dest = os.path.join(RESULTS, 'staged')
         work = os.path.join(RESULTS, 'work')
-        
+
         # The test {subject: directory} dictionary.
         sbj_dir_dict = subject_sources(collection, fixture)
         # The test subjects.
@@ -60,7 +60,7 @@ def _test_collection(self, collection):
         # The test input session directories.
         sess_dir_lists = (glob(d + '/*') for d in sbj_dirs)
         inputs = concat(*sess_dir_lists)
-        
+
         with qixnat.connect() as xnat:
             # Delete any existing test subjects.
             for sbj in subjects:
@@ -101,13 +101,13 @@ def _test_collection(self, collection):
                                 "The %s %s scan %s file %s was not created in XNAT" %
                                 (scan_input.subject, scan_input.session,
                                  scan_input.scan, base_name))
-            
+
             # Delete the test subjects.
             for sbj in subjects:
                 xnat.delete(PROJECT, sbj)
 
 
 if __name__ == "__main__":
     import nose
-    
+
     nose.main(defaultTest=__name__)

test/unit/qiprofile/__init__.py

@@ -1,7 +1,7 @@
 """
 The qiprofile update tests.
 
-:Note: most of the test cases require that the MongoDB and qiprofile REST
+.. Note:: most of the test cases require that the MongoDB and qiprofile REST
     servers are running on localhost.
 """