Merge remote-tracking branch 'upstream/master' into issue-57__operator

.coveragerc

@@ -10,8 +10,11 @@ omit =
     odl/diagnostics/*
     odl/util/*
 
-    # Omit untill coveralls supports cuda.
+    # Omit until coveralls supports cuda.
     odl/space/cu_ntuples.py
+
+    # Omit until coveralls supports pywt.
+    odl/trafos/wavelet.py
 
 [report]
 # Regexes for lines to exclude from consideration

conftest.py

@@ -21,8 +21,12 @@
 from future import standard_library
 standard_library.install_aliases()
 
-from odl import CUDA_AVAILABLE
+from odl.space.cu_ntuples import CUDA_AVAILABLE
+from odl.trafos.wavelet import PYWAVELETS_AVAILABLE
+
 collect_ignore = ['setup.py', 'run_tests.py']
+
 if not CUDA_AVAILABLE:
     collect_ignore.append('odl/space/cu_ntuples.py')
-    #collect_ignore.append('test/space/cu_ntuples_test.py')
+if not PYWAVELETS_AVAILABLE:
+    collect_ignore.append('odl/trafos/wavelet.py')

doc/source/generate_doc.py

@@ -1,21 +1,21 @@
-import pkgutil
 import odl
 import inspect
 import importlib
-import sys
+
 
 __all__ = ('make_interface',)
 
 module_string = """
+.. rubric:: Modules
+
 .. toctree::
    :maxdepth: 2
 
    {}
 """
 
 fun_string = """
-Functions
----------
+.. rubric:: Functions
 
 .. autosummary::
    :toctree: generated/
@@ -24,8 +24,7 @@
 """
 
 class_string = """
-Classes
--------
+.. rubric:: Classes
 
 .. autosummary::
    :toctree: generated/
@@ -46,18 +45,41 @@
 """
 
 
-def make_interface():
+def import_submodules(package, name=None, recursive=True):
+    """ Import all submodules of a module, recursively, including subpackages
+    """
+    if isinstance(package, str):
+        package = importlib.import_module(package)
+
+    if name is None:
+        name = package.__name__
 
-    sys.path.append(odl.__path__)
+    submodules = [m[0] for m in inspect.getmembers(
+        package, inspect.ismodule) if m[1].__name__.startswith('odl')]
 
-    modnames = [modname for _, modname, _ in pkgutil.walk_packages(
-        path=odl.__path__, prefix=odl.__name__ + '.', onerror=lambda x: None)]
+    results = {}
+    for pkgname in submodules:
+        full_name = name + '.' + pkgname
+        try:
+            results[full_name] = importlib.import_module(full_name)
+            if recursive:
+                results.update(import_submodules(full_name, full_name))
+        except ImportError:
+            pass
+    return results
+
+
+def make_interface():
+    modnames = [modname for modname in import_submodules(odl)]
 
     modnames += ['odl']
 
     for modname in modnames:
+        if not modname.startswith('odl'):
+            modname = 'odl.' + modname
+
         shortmodname = modname.split('.')[-1]
-        print('generated: ' + modname + '.rst')
+        print('{: <16} : generated {}.rst'.format(shortmodname, modname))
 
         line = '=' * len(shortmodname)
 

doc/source/guide/introduction/installing.rst

@@ -13,11 +13,11 @@ If you have done any step before, you can ofc skip it.
 
 Install Python
 ==============
-To begin with, you need a python distribution. If you are an experienced user, you can use any distribution you'd like. If you are a python novice, we recommend that you install a full package such as Anaconda. 
+To begin with, you need a python distribution. If you are an experienced user, you can use any distribution you'd like.
 
 Anaconda
 --------
-To install Anaconda
+If you are a python novice using Windows, we recommend that you install a full package such as Anaconda. To install Anaconda
 
 1. Download Anaconda from `anaconda's webpage <https://www.continuum.io/downloads>`_
 2. Once installed run in a console
@@ -28,7 +28,6 @@ To install Anaconda
 
 Install Git
 ===========
-
 You also need to install Git to be able to download odl.
 
 Overview
@@ -46,7 +45,6 @@ OS X             Use the git-osx-installer_
 
 In detail
 ---------
-
 See the git page for the most recent information.
 
 Have a look at the github install help pages available from `github help`_
@@ -57,7 +55,6 @@ There are good instructions here: http://book.git-scm.com/2_installing_git.html
 
 Install ODL
 ===========
-
 You are now ready to install ODL! To do that, run the following where you want to install it
 
 	``git clone https://github.com/odlgroup/odl``
@@ -67,11 +64,11 @@ You are now ready to install ODL! To do that, run the following where you want t
 
 For installation in a local user folder run
 
-	``user$ pip install --user .``
+	``user$ pip install --user -e .``
 
 For system-wide installation, run (as root, e.g. using ``sudo`` or equivalent)
 
-	``root# pip install .``
+	``root# pip install -e .``
 
 (Optional) Install ODLpp
 ========================

odl/__init__.py

@@ -52,8 +52,5 @@
 __all__ += space.__all__
 
 from . import trafos
-from .trafos import *
-__all__ += trafos.__all__
-
 from . import solvers
 from . import tomo

odl/diagnostics/examples.py

@@ -15,6 +15,8 @@
 # You should have received a copy of the GNU General Public License
 # along with ODL.  If not, see <http://www.gnu.org/licenses/>.
 
+"""Functions for generating standardized examples in spaces."""
+
 # Imports for common Python 2/3 codebase
 from __future__ import print_function, division, absolute_import
 from future import standard_library

odl/diagnostics/operator.py

@@ -15,6 +15,8 @@
 # You should have received a copy of the GNU General Public License
 # along with ODL.  If not, see <http://www.gnu.org/licenses/>.
 
+"""Standardized tests for `Operator`'s."""
+
 # Imports for common Python 2/3 codebase
 from __future__ import print_function, division, absolute_import
 from future import standard_library

odl/diagnostics/space.py

@@ -15,6 +15,8 @@
 # You should have received a copy of the GNU General Public License
 # along with ODL.  If not, see <http://www.gnu.org/licenses/>.
 
+"""Standardized tests for `LinearSpace`'s."""
+
 # Imports for common Python 2/3 codebase
 from __future__ import print_function, division, absolute_import
 from future import standard_library