incorporate manual into deploying docs (#198)

doc/manual/extractEquations.py

@@ -11,7 +11,7 @@
 # constants
 
 rc = {
-    "directory": "images",  # output directory
+    "directory": "../source/images",  # output directory
     "resolution": 72,  # equation images resolution
     "eqns": [],  # list of raw equation codes
     "tmpdir": None,  # temporary directory

doc/manual/fixHTMLCode.py

@@ -12,7 +12,7 @@
 # constants
 
 rc = {
-    "directory": "images",  # directory with equation images
+    "directory": "../source/images",  # directory with equation images
 }
 
 eqmark = "<!-- EquationMark -->"

doc/manual/html/readme.txt

@@ -0,0 +1,2 @@
+This directory need to be relativly the same as doc/build/html/manual from
+doc/source/_static/images

doc/source/index.rst

@@ -17,8 +17,8 @@ or neutron diffraction data and comes with built in graphical and structure
 visualization capabilities.
 
 PDFgui is a friendly interface to the PDFfit2 refinement engine, with many
-powerful extensions. To get started, please open the manual (:download:`html <../manual/pdfgui.html>`
-/:download:`pdf <../manual/pdfgui.pdf>`) from the help menu or follow the :ref:`quick_start`.
+powerful extensions. To get started, please open the :ref:`manual`
+(:download:`pdf <../manual/pdfgui.pdf>`) from the help menu or follow the :ref:`tutorial`.
 
 =======
 Authors
@@ -89,6 +89,7 @@ Table of contents
 
    license
    release
+   manual
    Package API <api/diffpy.pdfgui>
 
 =======

doc/source/manual.rst

@@ -0,0 +1,16 @@
+.. _manual:
+
+Manual
+======
+
+Resources used
+--------------
+
+- :download:`Ni data <manual_resources/Ni data.zip>`
+- :download:`Temperature data series <manual_resources/Temperature data series.zip>`
+- :download:`Doping data series <manual_resources/Doping data series.zip>`
+- :download:`tui Mn-O script <manual_resources/tui_mno_bond_lengths.py>`
+- :download:`Nanoparticle structure <manual_resources/Nanoparticle structure.zip>`
+
+.. raw:: html
+    :file: ../manual/html/pdfgui.html

doc/source/tutorial.rst

@@ -1,4 +1,4 @@
-.. _quick_start:
+.. _tutorial:
 
 Tutorial
 ########
@@ -13,8 +13,9 @@ Lesson 1: Creating simple fit of Ni PDF
 
 Input files:
 
-* :download:`Ni-xray.gr <../tutorial/Ni-xray.gr>` - experimental X-ray PDF data
-* :download:`Ni.stru <../tutorial/Ni.stru>` - Ni f.c.c. structure in PDFfit format
+- :download:`Ni data <manual_resources/Ni data.zip>` containing:
+    1. Ni-xray.gr - experimental X-ray PDF data
+    2. Ni.stru - Ni f.c.c. structure in PDFfit format
 
 Procedure: