Added docs inc. autodocs

Basic structure of documentation. Autodocs cannot find some of the modules in ampscan - its unclear why. Altering the docstrings may help.

docs/source/AmpScan.rst

+AmpScan package
+===============
+
+Submodules
+----------
+
+AmpScan.AmpScanGUI module
+-------------------------
+
+.. automodule:: AmpScan.AmpScanGUI
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.align module
+--------------------
+
+.. automodule:: AmpScan.align
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.ampVis module
+---------------------
+
+.. automodule:: AmpScan.ampVis
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.analyse module
+----------------------
+
+.. automodule:: AmpScan.analyse
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.core module
+-------------------
+
+.. automodule:: AmpScan.core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.cython\_ext module
+--------------------------
+
+.. automodule:: AmpScan.cython_ext
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.fe module
+-----------------
+
+.. automodule:: AmpScan.fe
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.pressSens module
+------------------------
+
+.. automodule:: AmpScan.pressSens
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.registration module
+---------------------------
+
+.. automodule:: AmpScan.registration
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.runAmpScanGUI module
+----------------------------
+
+.. automodule:: AmpScan.runAmpScanGUI
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.setup module
+--------------------
+
+.. automodule:: AmpScan.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.smooth module
+---------------------
+
+.. automodule:: AmpScan.smooth
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.socketDesignGUI module
+------------------------------
+
+.. automodule:: AmpScan.socketDesignGUI
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.surrogateModelGUI module
+--------------------------------
+
+.. automodule:: AmpScan.surrogateModelGUI
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.surrogateModelGUI\_2 module
+-----------------------------------
+
+.. automodule:: AmpScan.surrogateModelGUI_2
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.trim module
+-------------------
+
+.. automodule:: AmpScan.trim
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+AmpScan.tsbSocketDesign module
+------------------------------
+
+.. automodule:: AmpScan.tsbSocketDesign
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: AmpScan
+    :members:
+    :undoc-members:
+    :show-inheritance: