Updated docs

docs/requirements.txt

@@ -1 +1,2 @@
-sphinxcontrib.httpdomain
+sphinxcontrib.httpdomain
+sphinx_rtd_theme

docs/source/apirequests.rst

@@ -42,21 +42,23 @@ CURL
 .. code-block:: none
 
    curl -X POST -H "Content-Type: application/json" -d \\
-   '{"picamera_settings": {"shutter_speed": 2000}, "jpeg_quality": 90}' http://192.168.1.126:5000/api/v1/config
+   '{"camera_settings": {"picamera_settings": {"shutter_speed": 2000}, "jpeg_quality": 90}}' http://192.168.1.126:5000/api/v1/config
 
 HTTPie
 ++++++
 .. code-block:: none
 
-   http POST http://192.168.1.126:5000/api/v1/config jpeg_quality:=90 picamera_settings:='{"shutter_speed": 2000}'
+   http POST http://192.168.1.126:5000/api/v1/config camera_settings:='{"jpeg_quality": 90, "picamera_settings": {"shutter_speed": 2000}}' 
 
 Python Requests
 +++++++++++++++
 .. code-block:: python
 
    json_payload = {
-        "jpeg_quality": 90,
-        "picamera_settings": {"shutter_speed": 2000}
+       camera_settings: {
+            "jpeg_quality": 90,
+            "picamera_settings": {"shutter_speed": 2000}
+        }
    }
    requests.post('http://192.168.1.126:5000/api/v1/config', json=json_payload)
 

docs/source/config.rst

@@ -1,5 +1,5 @@
 Microscope configuration
-=======================================================
+========================
 
 .. toctree::
    :maxdepth: 2
@@ -18,7 +18,7 @@ in separate "auxillary" config files, and are linked together by adding the conf
 microscope RC file. This is set up by default, as shown below:
 
 Default microscope_settings.yaml
-+++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++
 .. code-block:: yaml
 
     # Resolutions for streaming and capture
@@ -58,7 +58,7 @@ Example picamera_settings.yaml
 
 
 Loading the runtime-config
-+++++++
+++++++++++++++++++++++++++
 
 By default, a microscope object will load the a runtime-config from the default location.
 This RC can then be passed to any hardware attached to the microscope. This can be particularly

docs/source/plugins/class.rst

@@ -22,12 +22,17 @@ Lock module
 Default plugins
 ---------------
 
-Microscope plugin
-+++++++++++++++++
-.. automodule:: openflexure_microscope.plugins.default.plugin
+Autofocus
++++++++++
+.. automodule:: openflexure_microscope.plugins.default.autofocus
     :members:
 
-Web API plugin
-++++++++++++++
-.. automodule:: openflexure_microscope.plugins.default.api
+Camera calibration
+++++++++++++++++++
+.. automodule:: openflexure_microscope.plugins.default.camera_calibration
     :members:
+
+Scan and Stack
+++++++++++++++
+.. automodule:: openflexure_microscope.plugins.default.scan
+    :members:

docs/source/plugins/introduction.rst

@@ -26,7 +26,7 @@ Generally, for adding anything other than very simple functionality, plugins sho
 The main restriction is that the plugin package must be importable using an absolute import from within the Python environment being used to load your microscope. 
 
 Loading plugins with microscope_settings.yaml
---------------------------------------
+---------------------------------------------
 Both types of plugin are loaded by specifying the plugin class in your :ref:`MicroscopeRC`. In the case of a single-file plugin, specify the path to the plugin file, followed by the name of your :py:class:`openflexure_microscope.plugins.MicroscopePlugin` child class, separated by a colon. For packaged plugins, specify the absolute module name in place of the path.
 
 For example, the plugins section of your microscope_settings.yaml file may look like: