Merge branch 'sphinx-docs' into dev

docs/conf.py

@@ -34,6 +34,7 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
     'numpydoc',
     'sphinx.ext.intersphinx',

microdrop/plugin_manager.py

@@ -16,27 +16,26 @@
 You should have received a copy of the GNU General Public License
 along with Microdrop.  If not, see <http://www.gnu.org/licenses/>.
 """
-
-import traceback
-import sys
 from StringIO import StringIO
-from contextlib import closing
 from collections import namedtuple
+from contextlib import closing
 import logging
-import re
 import os
 import platform
+import re
 import subprocess
+import sys
+import traceback
 
 from path_helpers import path
-import task_scheduler
-from run_exe import run_exe
-
 from pyutilib.component.core import ExtensionPoint, PluginGlobals
 # TODO Update plugins to import from `pyutilib.component.core` directly
 # instead of importing from here.
 from pyutilib.component.core import Plugin, SingletonPlugin, implements
-from interfaces import IPlugin, IWaveformGenerator, ILoggingPlugin
+from run_exe import run_exe
+import task_scheduler
+
+from .interfaces import IPlugin, IWaveformGenerator, ILoggingPlugin
 
 
 ScheduleRequest = namedtuple('ScheduleRequest', 'before after')

microdrop/protocol.py

@@ -136,12 +136,17 @@ def load(cls, filename):
         """
         Load a Protocol from a file.
 
-        Args:
-            filename: path to file.
-        Raises:
-            TypeError: file is not a Protocol.
-            FutureVersionError: file was written by a future version of the
-                software.
+        Parameters
+        ----------
+        filename : str
+            Path to file.
+
+        Raises
+        ------
+        TypeError
+            If file is not a :class:`Protocol`.
+        FutureVersionError
+            If file was written by a future version of the software.
         """
         logger.debug("[Protocol].load(\"%s\")" % filename)
         logger.info("Loading Protocol from %s" % filename)
@@ -393,13 +398,14 @@ def to_json(self):
         Returns
         -------
         str
-            json-encoded dictionary, with two top-level keys:
+            JSON-encoded dictionary, with two top-level keys:
              - ``keys``:
                    * Each key is a list containing a plugin name and a
                      corresponding step field name.
              - ``values``:
                    * Maps to list of records (i.e., lists), one per protocol
                      step.
+
             Each record in the ``values`` list may be *zipped together* with
             ``keys`` to yield a plugin field name to value mapping for a single
             protocol step.

requirements-sphinx.txt

@@ -1,20 +1,34 @@
-application_repository
+application_repository>=0.5
 blinker
 configobj
+droplet-planning>=0.2
 flatland-fork
 geo-util
 ipython
-ipython-helpers
-microdrop_utility
+ipython-helpers>=0.4
+jinja2
+matplotlib>=1.5.0
+microdrop-device-converter>=0.1.post5
+microdrop_utility>=0.4.post2
+networkx
 numpydoc
-opencv-helpers
-path-helpers
-pygst-utils
+openpyxl
+pandas>=0.17.1
+path-helpers>=0.2.post3
+paver>=1.2.4
+pip-helpers>=0.6
 pygtk_textbuffer_with_undo
 pyparsing
-pyutilib==3.9.2706
+pyutilib.component.core>=4.4.1
+pyutilib.component.loader>=3.3.1
 pyyaml
 pyzmq
-svg_model
+run-exe>=0.5
+si-prefix>=0.4.post10
+scipy
+svgwrite
+svg-model>=0.6
 task_scheduler
-wheeler.pygtkhelpers
+tornado
+wheeler.pygtkhelpers>=0.13.post17
+zmq-plugin>=0.2.post2

requirements.txt

@@ -1,19 +1,34 @@
-application_repository
+application_repository>=0.5
 blinker
 configobj
+droplet-planning>=0.2
 flatland-fork
 geo-util
 ipython
-ipython-helpers
-microdrop_utility
-opencv-helpers
-path-helpers
-pygst-utils
+ipython-helpers>=0.4
+jinja2
+matplotlib>=1.5.0
+microdrop-device-converter>=0.1.post5
+microdrop-plugin-template>=1.1.post30
+microdrop_utility>=0.4.post2
+networkx
+openpyxl
+pandas>=0.17.1
+path-helpers>=0.2.post3
+paver>=1.2.4
+pip-helpers>=0.6
 pygtk_textbuffer_with_undo
 pyparsing
-pyutilib==3.9.2706
+pyutilib.component.core>=4.4.1
+pyutilib.component.loader>=3.3.1
 pyyaml
 pyzmq
-svg_model
+run-exe>=0.5
+si-prefix>=0.4.post10
+scipy
+svgwrite
+svg-model>=0.6
 task_scheduler
-wheeler.pygtkhelpers
+tornado
+wheeler.pygtkhelpers>=0.13.post17
+zmq-plugin>=0.2.post2