Merge branch 'mnt/doc' into 'master'

Mnt/doc

See merge request fsl/fslpy!239

CHANGELOG.rst

@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+
+3.2.1 (Tuesday 23rd June 2020)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Minor updates to documentation.
+
+
 3.2.0 (Thursday 11th June 2020)
 -------------------------------
 

doc/conf.py

@@ -361,26 +361,12 @@ epub_exclude_files = ['search.html']
 # special-members flag)
 autoclass_content = 'class'
 
-# Document private members and special members (e.g. __init__)
-autodoc_default_flags = ['private-members', 'special-members']
 
-# Documentation for python modules is in the same order
-# as the source code.
-autodoc_member_order = 'bysource'
-
-def autodoc_skip_member(app, what, name, obj, skip, options):
-
-    # Do not document the _sync_* properties
-    # that are added by the props package to
-    # all SyncableHasProperties classes.
-    if what == 'class':
-        attName = name.split('.')[-1]
-        return skip or attName.startswith('_sync_')
-
-    return skip or False
-
-
-def setup(app):
-    app.connect('autodoc-skip-member', autodoc_skip_member)
+autodoc_default_options = {
+    'special-members' : True,
+    'private-members' : True,
+    'undoc-members'   : True,
+    'member-order'    : 'bysource',
+}
 
 graphviz_output_format = 'svg'

fsl/data/gifti.py

@@ -314,6 +314,7 @@ def relatedFiles(fname, ftypes=None):
 
     This function assumes that the GIFTI files are named according to a
     standard convention - the following conventions are supported:
+
      - HCP-style, i.e.: ``<subject>.<hemi>.<type>.<space>.<ftype>.gii``
      - BIDS-style, i.e.:
        ``<source_prefix>_hemi-<hemi>[_space-<space>]*_<suffix>.<ftype>.gii``

fsl/data/image.py

@@ -1005,7 +1005,7 @@ class Image(Nifti):
 
         :arg image:      A string containing the name of an image file to load,
                          or a :mod:`numpy` array, or a :mod:`nibabel` image
-                         object, or an ``Image``object.
+                         object, or an ``Image`` object.
 
         :arg name:       A name for the image.
 

fsl/transform/fnirt.py

@@ -82,6 +82,12 @@ the reference image, and may contain:
    the source image coordinates which correspond to those reference image
    coordinates.
 
+.. note:: FNIRT deformation field files give no indication as to whether they
+          contain relative displacements or absolute coordinates, so heuristics
+          must be used to infer what is stored in a a particular file. The
+          :func:`.nonlinear.detectDeformationType` function can be used to
+          determine whether a file contains relative displacements or absolute
+          coordinates.
 
 If an initial linear registration was used as the starting point for FNIRT,
 this is encoded into the displacements/coordinates themselves, so they can be

fsl/utils/fslsub.py

@@ -63,7 +63,7 @@ class SubmitParams(object):
 
     Any command line script can be submitted by the parameters by calling the `SubmitParams` object:
 
-    .. codeblock:: python
+    .. code-block:: python
 
         submit = SubmitParams(minutes=1, logdir='log', wait_for=['108023', '108019'])
         submit('echo finished')
@@ -71,14 +71,14 @@ class SubmitParams(object):
     This will run "echo finished" with a maximum runtime of 1 minute after the jobs with IDs 108023 and 108019 are finished.
     It is the equivalent of
 
-    .. codeblock:: bash
+    .. code-block:: bash
 
         fsl_sub -T 1 -l log -j 108023,108019 "echo finished"
 
     For python scripts that submit themselves to the cluster, it might be useful to give the user some control
     over at least some of the submission parameters. This can be done using:
 
-    .. codeblock:: python
+    .. code-block:: python
 
         import argparse
         parser = argparse.ArgumentParser("my script doing awesome stuff")

fsl/wrappers/wrapperutils.py

@@ -606,6 +606,7 @@ class FileOrThing(object):
         :arg load:      Function which is called to load items for arguments
                         that were set to :data:`LOAD`. Must accept the
                         following arguments:
+
                          - the name of the argument
                          - path to the file to be loaded