doc/fsl.wrappers.fslmaths.rst

+``fsl.wrappers.fslmaths``
+=========================
+
+.. automodule:: fsl.wrappers.fslmaths
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.fslstats.rst

+``fsl.wrappers.fslstats``
+=========================
+
+.. automodule:: fsl.wrappers.fslstats
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.fugue.rst

+``fsl.wrappers.fugue``
+======================
+
+.. automodule:: fsl.wrappers.fugue
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.melodic.rst

+``fsl.wrappers.melodic``
+========================
+
+.. automodule:: fsl.wrappers.melodic
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.misc.rst

+``fsl.wrappers.misc``
+=====================
+
+.. automodule:: fsl.wrappers.misc
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.oxford_asl.rst

+``fsl.wrappers.oxford_asl``
+===========================
+
+.. automodule:: fsl.wrappers.oxford_asl
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.randomise.rst

+``fsl.wrappers.randomise``
+==========================
+
+.. automodule:: fsl.wrappers.randomise
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.rst

+``fsl.wrappers``
+================
+
+.. toctree::
+   :hidden:
+
+   fsl.wrappers.avwutils
+   fsl.wrappers.bedpostx
+   fsl.wrappers.bet
+   fsl.wrappers.bianca
+   fsl.wrappers.cluster_commands
+   fsl.wrappers.dtifit
+   fsl.wrappers.eddy
+   fsl.wrappers.epi_reg
+   fsl.wrappers.fast
+   fsl.wrappers.feat
+   fsl.wrappers.first
+   fsl.wrappers.flirt
+   fsl.wrappers.fnirt
+   fsl.wrappers.fsl_anat
+   fsl.wrappers.fsl_sub
+   fsl.wrappers.fslmaths
+   fsl.wrappers.fslstats
+   fsl.wrappers.fugue
+   fsl.wrappers.melodic
+   fsl.wrappers.misc
+   fsl.wrappers.oxford_asl
+   fsl.wrappers.randomise
+   fsl.wrappers.tbss
+   fsl.wrappers.wrapperutils
+
+.. automodule:: fsl.wrappers
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.tbss.rst

+``fsl.wrappers.tbss``
+=====================
+
+.. automodule:: fsl.wrappers.tbss
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.wrapperutils.rst

+``fsl.wrappers.wrapperutils``
+=============================
+
+.. automodule:: fsl.wrappers.wrapperutils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/index.rst

@@ -4,12 +4,57 @@
 
 
 The ``fslpy`` package is a collection of utilities and data abstractions used
-by |fsleyes_apidoc|_.
+within `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki>`_ and by
+|fsleyes_apidoc|_.
+
+
+The top-level Python package for ``fslpy`` is called :mod:`fsl`.  It is
+broadly split into the following sub-packages:
+
++----------------------+-----------------------------------------------------+
+| :mod:`fsl.data`      | contains data abstractions and I/O routines for a   |
+|                      | range of FSL and neuroimaging file types. Most I/O  |
+|                      | routines use `nibabel <https://nipy.org/nibabel/>`_ |
+|                      | extensively.                                        |
++----------------------+-----------------------------------------------------+
+| :mod:`fsl.utils`     | contains a range of miscellaneous utilities,        |
+|                      | including :mod:`fsl.utils.path`,                    |
+|                      | :mod:`fsl.utils.run`, and :mod:`fsl.utils.bids`     |
++----------------------+-----------------------------------------------------+
+| :mod:`fsl.scripts`   | contains a range of scripts which are installed as  |
+|                      | FSL commands.                                       |
++----------------------+-----------------------------------------------------+
+| :mod:`fsl.transform` | contains functions and classes for working with     |
+|                      | FSL-style linear and non-linear transformations.    |
++----------------------+-----------------------------------------------------+
+| :mod:`fsl.version`   | simply contains the ``fslpy`` version number.       |
++----------------------+-----------------------------------------------------+
+| :mod:`fsl.wrappers`  | contains Python functions which can be used to      |
+|                      | invoke FSL commands.                                |
++----------------------+-----------------------------------------------------+
+
+The :mod:`fsl` package provides the top-level Python package namespace for
+``fslpy``, and for other FSL python libaries. It is a `native namespace
+package <https://packaging.python.org/guides/packaging-namespace-packages/>`_,
+which means that there is no ``fsl/__init__.py`` file.
+
+
+Other libraries can use the ``fsl`` package namepace simply by also omitting a
+``fsl/__init__.py`` file, and by ensuring that there are no naming conflicts
+with any sub-packages of ``fslpy`` or any other projects which use the ``fsl``
+package namespace.
+
+
 
 .. toctree::
    :hidden:
 
    self
-   fsl
+   fsl.data
+   fsl.scripts
+   fsl.transform
+   fsl.utils
+   fsl.wrappers
+   fsl.version
    contributing
    changelog

doc/mock_modules.txt

 deprecation
+dill
+h5py
 nibabel
+nibabel.cifti2
 nibabel.fileslice
+nibabel.freesurfer
 numpy
 numpy.linalg
 scipy
 scipy.ndimage
+scipy.ndimage.interpolation
+six

fsl/__init__.py

-#!/usr/bin/env python
-#
-# __init__.py - The fslpy library.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-"""The :mod:`fsl` package is a library which contains convenience classes
-and functions for use by FSL python tools. It is broadly split into the
-following sub-packages:
-
-.. autosummary::
-
-   fsl.data
-   fsl.utils
-   fsl.scripts
-   fsl.version
-
-.. note:: The ``fsl`` namespace is a ``pkgutil``-style *namespace package* -
-          it can be used across different projects - see
-          https://packaging.python.org/guides/packaging-namespace-packages/
-          for details.
-"""
-
-__path__ = __import__('pkgutil').extend_path(__path__, __name__)

fsl/data/__init__.py

@@ -7,3 +7,7 @@
 """This module contains various data types and associated I/O routines,
 models, constants, and other data-like things used throughout ``fslpy``.
 """
+
+
+from .utils import (guessType,  # noqa
+                    makeWriteable)