Merge branch 'doc/apidoc' into 'master'

Doc/apidoc

See merge request fsl/fslpy!123

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)
 

doc/fsl.scripts.resample_image.rst

+``fsl.scripts.resample_image``
+==============================
+
+.. automodule:: fsl.scripts.resample_image
+    :members:
+    :undoc-members:
+    :show-inheritance:

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:

doc/fsl.utils.image.resample.rst

+``fsl.utils.image.resample``
+============================
+
+.. automodule:: fsl.utils.image.resample
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.image.rst

+``fsl.utils.image``
+===================
+
+.. toctree::
+   :hidden:
+
+   fsl.utils.image.resample
+
+.. automodule:: fsl.utils.image
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.parse_data.rst

+``fsl.utils.parse_data``
+========================
+
+.. automodule:: fsl.utils.parse_data
+    :members:
+    :undoc-members:
+    :show-inheritance:

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

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:

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

requirements-dev.txt

-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

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]