Merge pull request #251 from NeurodataWithoutBorders/docutils/update

Docutils/update

Author: oruebel

core/nwb.namespace.yaml

@@ -14,14 +14,36 @@ namespaces:
   full_name: NWB core
   schema:
   - source: nwb.base.yaml
+    title: Base data types
+    doc: This source module contains base data types used throughout the NWB:N data format.
   - source: nwb.epoch.yaml
+    title: Epochs
+    doc: This source module contains neurodata_types for epoch data.
   - source: nwb.image.yaml
+    title: Image data
+    doc: This source module contains neurodata_types for image data.
   - source: nwb.file.yaml
+    title: NWB:N file
+    doc: Main NWB:N file specification.
   - source: nwb.misc.yaml
+    title: Miscellaneous neurodata_types.
+    doc: Miscellaneous types.
   - source: nwb.behavior.yaml
+    title: Behavior
+    doc: This source module contains neurodata_types for behavior data.
   - source: nwb.ecephys.yaml
+    title: Extracellular electrophysiology
+    doc: This source module contains neurodata_types for extracellular electrophysiology data.
   - source: nwb.icephys.yaml
+    title: Intracellular electrophysiology
+    doc: This source module contains neurodata_types for intracellular electrophysiology data.
   - source: nwb.ogen.yaml
+    title: Optogenetics
+    doc: This source module contains neurodata_types for opto-genetics data.
   - source: nwb.ophys.yaml
+    title: Optical physiology
+    doc: This source module contains neurodata_types for optical physiology data.
   - source: nwb.retinotopy.yaml
-  version: 2.0.0
+    title: Retinotopy
+    doc: This source module contains neurodata_type for retinotopy data.
+  version: 2.0.1

docs/format/source/conf_doc_autogen.py

@@ -47,13 +47,10 @@
 # Should the YAML sources be included for the different modules
 spec_show_yaml_src = True
 
-# Should the JSON sources be included for the different modules
-spec_show_json_src = False
-
 # Show figure of the hierarchy of objects defined by the spec
 spec_show_hierarchy_plots = True
 
-# Should the sources of the neurodata_types (JSON/YAML) be rendered in a separate section (True) or
+# Should the sources of the neurodata_types (YAML) be rendered in a separate section (True) or
 # in the same location as the base documentation
 spec_generate_src_file = True
 
@@ -82,3 +79,15 @@
 # Resolve includes to always show the full list of objects that are part of a type (True)
 # or to show only the parts that are actually new to a current type while only linking to base types
 spec_resolve_type_inc = False
+
+# Default type map to be used. This is the type map where dependent namespaces are stored. In the case of
+# NWB this is spec_default_type_map = pynwb.get_type_map()
+import pynwb
+spec_default_type_map = pynwb.get_type_map()
+
+# Default specification classes for groups datasets and namespaces. In the case of NWB these are the NWB-specfic
+# spec classes. In the general cases these are the spec classes from HDMF
+spec_group_spec_cls = pynwb.spec.NWBGroupSpec
+spec_dataset_spec_cls = pynwb.spec.NWBDatasetSpec
+spec_namespace_spec_cls = pynwb.spec.NWBNamespace
+

docs/format/source/format_description.rst

@@ -154,8 +154,6 @@ processing modules, a default name (usually the same as the neurodata_type) is
 commonly specified to further ease identification of the data in a file. However, to
 support storage of multiple instances of the same subtype in the
 same processing module, NWB:N allows users to optionally define custom names as well.
-A detailed overview of the main data processing containers is available in
-:numref:`Data_Processing`.
 
 
 .. _sec-extending-the-format:
@@ -197,8 +195,8 @@ electrical versus optical physiology) as well as new modalities (e.g.,
 video tracking of whisker positions). When a neurodata_type inherits from *TimeSeries*,
 new data objects (i.e., datasets, attributes, groups, and links)
 can be added while all objects of the parent *TimeSeries* type are
-inherited and, hence, part of the new neurodata_type. Section :numref:`TimeSeries_Types`
-provides detailed definitions for all core *TimeSeries* types.
+inherited and, hence, part of the new neurodata_type. Section :numref:`sec-TimeSeries`
+includes a list of all *TimeSeries* types.
 
 Extending *NWBContainer* works in the same way, e.g., to create more specific types for
 data processing.

docs/format/source/format_release_notes.rst

@@ -1,12 +1,24 @@
 Release Notes
 =============
 
-2.0.0 Beta (2017/18)
---------------------
+2.0.1 (March 2019)
+------------------
 
-**First release:** November 2017
+**Change:** Added ``doc`` and ``title`` descriptions for the individual source files included in the main namespace.
+
+**Reason:** Enhance documentation of the namespace and facilitate presentation of types in autogenerated docs by
+making it easier to sort ``neurodata_types`` into meaningful categories (i.e., sections) with approbriate tiles and
+descriptions.
+
+**Backwards compatibility:** No changes to the actual specification fo the format are made. 2.0.1 is fully compatible
+with 2.0.0.
+
+
+2.0.0 (January 2019)
+---------------------
+
+**Main release:** November 2017 (Beta), November 2018 (RC), January 2019 (final)
 
-**Subsequent releases:** The schema was improved and updated throughout the beta phase with full release planed for fall 2018.
 
 Added new base data types: ``NWBContainer``, ``NWBData``, ``NWBDataInterface``
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^