Polish and document API

Many, many formerly public classes and functions are now private. This is done to minimize the number of public classes/functions, which after release should be treated as stable APIs that are ideally modified only in backwards compatible ways. Of those that remain public, some were renamed: * ``LoadAndPrepareData`` --> ``load_dataset`` * ``setup`` --> ``setup_ftpauth`` * ``MyWritableEpochSource`` --> ``NeuroticWritableEpochSource`` * ``DataExplorer`` --> ``MainWindow``
jpgill86 · Jul 27, 2019 · bc1f7d0 · bc1f7d0
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diff --git a/docs/api.rst b/docs/api.rst
@@ -0,0 +1,38 @@
+.. _api:
+
+API Reference
+=============
+
+In addition to using **neurotic** as a standalone app, you can also leverage
+its API in your own code.
+
+The core of the API consists of two classes and one function:
+
+* :class:`neurotic.datasets.metadata.MetadataSelector`: Read metadata files, download datasets
+* :func:`neurotic.datasets.data.load_dataset`: Read datasets, apply filters and spike detection
+* :class:`neurotic.gui.config.EphyviewerConfigurator`: Launch ephyviewer
+
+All public package contents are automatically imported directly into the
+``neurotic`` namespace. This means that a class like
+``neurotic.datasets.metadata.MetadataSelector`` can be accessed more compactly
+as ``neurotic.MetadataSelector``.
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Datasets
+
+   api/data
+   api/download
+   api/ftpauth
+   api/metadata
+
+
+.. toctree::
+  :maxdepth: 1
+  :caption: GUI
+
+  api/config
+  api/epochencoder
+  api/notebook
+  api/standalone
diff --git a/docs/api/config.rst b/docs/api/config.rst
@@ -0,0 +1,6 @@
+.. _api-config:
+
+``neurotic.gui.config``
+=======================
+
+.. automodule:: neurotic.gui.config
diff --git a/docs/api/data.rst b/docs/api/data.rst
@@ -0,0 +1,6 @@
+.. _api-data:
+
+``neurotic.datasets.data``
+==========================
+
+.. automodule:: neurotic.datasets.data
diff --git a/docs/api/download.rst b/docs/api/download.rst
@@ -0,0 +1,6 @@
+.. _api-download:
+
+``neurotic.datasets.download``
+==============================
+
+.. automodule:: neurotic.datasets.download
diff --git a/docs/api/epochencoder.rst b/docs/api/epochencoder.rst
@@ -0,0 +1,6 @@
+.. _api-epochencoder:
+
+``neurotic.gui.epochencoder``
+=============================
+
+.. automodule:: neurotic.gui.epochencoder
diff --git a/docs/api/ftpauth.rst b/docs/api/ftpauth.rst
@@ -0,0 +1,6 @@
+.. _api-ftpauth:
+
+``neurotic.datasets.ftpauth``
+=============================
+
+.. automodule:: neurotic.datasets.ftpauth
diff --git a/docs/api/metadata.rst b/docs/api/metadata.rst
@@ -0,0 +1,6 @@
+.. _api-metadata:
+
+``neurotic.datasets.metadata``
+==============================
+
+.. automodule:: neurotic.datasets.metadata
diff --git a/docs/api/notebook.rst b/docs/api/notebook.rst
@@ -0,0 +1,6 @@
+.. _api-notebook:
+
+``neurotic.gui.notebook``
+=========================
+
+.. automodule:: neurotic.gui.notebook
diff --git a/docs/api/standalone.rst b/docs/api/standalone.rst
@@ -0,0 +1,6 @@
+.. _api-standalone:
+
+``neurotic.gui.standalone``
+===========================
+
+.. automodule:: neurotic.gui.standalone
diff --git a/docs/conf.py b/docs/conf.py
@@ -201,8 +201,12 @@
 
 # -- Options for intersphinx extension ---------------------------------------
 
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {
+    'python':       ('https://docs.python.org/3', None),
+    'neo':          ('https://neo.readthedocs.io/en/latest', None),
+    'ephyviewer':   ('https://ephyviewer.readthedocs.io/en/latest', None),
+    'elephant':     ('https://elephant.readthedocs.io/en/latest', None),
+}
 
 # -- Options for todo extension ----------------------------------------------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -24,6 +24,7 @@ colleagues and they too will quickly be looking at the same datasets!
    install
    gettingstarted
    metadata
+   api
    releasenotes
 
 

diff --git a/docs/metadata.rst b/docs/metadata.rst
@@ -173,8 +173,8 @@ to the metadata file. In the example above, if the metadata file is located in
 
 .. _congig-metadata-globals:
 
-Global Configuration Settings:
-------------------------------
+Global Configuration Settings
+-----------------------------
 
 The top-level name ``neurotic_config`` is reserved for configuration settings
 that apply to all datasets or to the app itself. Presently, only one

diff --git a/docs/releasenotes.rst b/docs/releasenotes.rst
@@ -6,14 +6,14 @@ Release Notes
 .. toctree::
     :maxdepth: 1
 
-    releases/0.7.0.rst
-    releases/0.6.0.rst
-    releases/0.5.1.rst
-    releases/0.5.0.rst
-    releases/0.4.2.rst
-    releases/0.4.1.rst
-    releases/0.4.0.rst
-    releases/0.3.0.rst
-    releases/0.2.0.rst
-    releases/0.1.1.rst
-    releases/0.1.0.rst
+    releases/0.7.0
+    releases/0.6.0
+    releases/0.5.1
+    releases/0.5.0
+    releases/0.4.2
+    releases/0.4.1
+    releases/0.4.0
+    releases/0.3.0
+    releases/0.2.0
+    releases/0.1.1
+    releases/0.1.0