diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 1088480c33d93f9196a17c4fadfa2c7735108f11..7089e91b85792f7a94adde3dbd1dce993be5e56d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -34,7 +34,7 @@ Fixed
^^^^^
-* Minor fixes to some :mod:`.filetree` tree definitions.
+* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Deprecated
@@ -477,7 +477,7 @@ Changed
* :meth:`.MGHImage` objects now have a :meth:`.MGHImage.save` method.
* Adjustments to the ``conda`` package build and deployment process.
* The :func:`.ImageWrapper.canonicalShape` function has been moved
- to the :mod:`.image` class.
+ to the :mod:`.data.image` class.
* The :func:`.ImageWrapper.naninfrange` function has been moved
into its own :mod:`.naninfrange` module.
@@ -493,7 +493,7 @@ Deprecated
^^^^^^^^^^
-* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.image` module)
+* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
module)
diff --git a/doc/fsl.scripts.resample_image.rst b/doc/fsl.scripts.resample_image.rst
new file mode 100644
index 0000000000000000000000000000000000000000..cf19d5d835bb4e7d2554c7468b7467d7d759b66d
--- /dev/null
+++ b/doc/fsl.scripts.resample_image.rst
@@ -0,0 +1,7 @@
+``fsl.scripts.resample_image``
+==============================
+
+.. automodule:: fsl.scripts.resample_image
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.scripts.rst b/doc/fsl.scripts.rst
index 2d18375d7aba2f04189ed4347cdac76c94c5358d..ece0e2b6e0731daa11612a583244a955bfcf0f99 100644
--- a/doc/fsl.scripts.rst
+++ b/doc/fsl.scripts.rst
@@ -9,6 +9,7 @@
fsl.scripts.imcp
fsl.scripts.imglob
fsl.scripts.immv
+ fsl.scripts.resample_image
.. automodule:: fsl.scripts
:members:
diff --git a/doc/fsl.utils.image.resample.rst b/doc/fsl.utils.image.resample.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d994581a0aa087717976646697d020d14dbd027d
--- /dev/null
+++ b/doc/fsl.utils.image.resample.rst
@@ -0,0 +1,7 @@
+``fsl.utils.image.resample``
+============================
+
+.. automodule:: fsl.utils.image.resample
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.image.rst b/doc/fsl.utils.image.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7b0ef37d91cb0bfbd100943b08d4d52c6a864275
--- /dev/null
+++ b/doc/fsl.utils.image.rst
@@ -0,0 +1,12 @@
+``fsl.utils.image``
+===================
+
+.. toctree::
+ :hidden:
+
+ fsl.utils.image.resample
+
+.. automodule:: fsl.utils.image
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.parse_data.rst b/doc/fsl.utils.parse_data.rst
new file mode 100644
index 0000000000000000000000000000000000000000..741dfff1ebb22422e0f6ffe9c05661c70ba2b732
--- /dev/null
+++ b/doc/fsl.utils.parse_data.rst
@@ -0,0 +1,7 @@
+``fsl.utils.parse_data``
+========================
+
+.. automodule:: fsl.utils.parse_data
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.rst b/doc/fsl.utils.rst
index 76631a31b4156a09fee7ca689bf964d8da6f9d02..5722c7eb4f726f3b17c1ce32f7edee2f85779e4a 100644
--- a/doc/fsl.utils.rst
+++ b/doc/fsl.utils.rst
@@ -12,11 +12,13 @@
fsl.utils.fslsub
fsl.utils.idle
fsl.utils.imcp
+ fsl.utils.image
fsl.utils.memoize
fsl.utils.meta
fsl.utils.naninfrange
fsl.utils.notifier
fsl.utils.path
+ fsl.utils.parse_data
fsl.utils.platform
fsl.utils.run
fsl.utils.settings
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index b1f1f46eddb6d007ab366852a4328df97a84547c..e54968515d7e3e061370ce263f8afedc39d3e25a 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -41,8 +41,8 @@ class FileTreeQuery(object):
a directory for files which match a specific query.
A ``FileTreeQuery`` scans the contents of a directory which is described
- by a :class:`.FileTree`, and identifies all file types (a.k.a. _templates_
- or _short names_) that are present, and the values of variables within each
+ by a :class:`.FileTree`, and identifies all file types (a.k.a. *templates*
+ or *short names*) that are present, and the values of variables within each
short name that are present. The :meth:`query` method can be used to
retrieve files which match a specific short name, and variable values.
@@ -327,7 +327,7 @@ def allVariables(
"""Identifies the ``FileTree`` variables which are actually represented
in files in the directory.
- :arg filetree: The ``FileTree``object
+ :arg filetree: The ``FileTree`` object
:arg matches: list of ``Match`` objects (e.g. as returned by :func:`scan`)
:returns: a tuple containing two dicts:
diff --git a/fsl/utils/image/__init__.py b/fsl/utils/image/__init__.py
index 8e22533648b6ff1c4125b31e0375b594f937164b..36bde925ddd642203560caf5ac58ff99a364d386 100644
--- a/fsl/utils/image/__init__.py
+++ b/fsl/utils/image/__init__.py
@@ -9,7 +9,7 @@ manipulating and working with :class:`.Image` objects.
The following modules are available:
-.. autosumary::
+.. autosummary::
:nosignature
.image.resample
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 4b113427907f852c9e4b7c7813eb528e97cbbf43..d559b9585f52e10bcb9cb8c28048f75fb9466974 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,6 +1,6 @@
-sphinx==1.6.*
-sphinx_rtd_theme==0.*
-mock==2.*
-coverage==4.*
-pytest==3.*
-pytest-cov==2.*
+sphinx
+sphinx_rtd_theme
+mock
+coverage
+pytest
+pytest-cov
diff --git a/setup.py b/setup.py
index 0873bffe228abb22dc7a04647fe6a7b4ff93b5bc..4bb48c2323f30ea2b05be4aff6b7c964ebdefa79 100644
--- a/setup.py
+++ b/setup.py
@@ -67,7 +67,7 @@ class doc(Command):
print('Building documentation [{}]'.format(destdir))
- import sphinx
+ import sphinx.cmd.build as sphinx_build
try:
import unittest.mock as mock
@@ -83,7 +83,7 @@ class doc(Command):
patches = [mock.patch.dict('sys.modules', **mockedModules)]
[p.start() for p in patches]
- sphinx.main(['sphinx-build', docdir, destdir])
+ sphinx_build.main([docdir, destdir])
[p.stop() for p in patches]