diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 00000000..ebad7585
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,194 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+BASENAME      = $(subst .,,$(subst $() $(),,diffpy.pdfgui))
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+# Manual publishing to the gh-pages branch
+
+GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir)
+GITREMOTE = origin
+GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url)
+GITLASTCOMMIT = $(shell git rev-parse --short HEAD)
+
+publish:
+	@test -d build/html || \
+	    ( echo >&2 "Run 'make html' first!"; false )
+	git show-ref --verify --quiet refs/heads/gh-pages || \
+	    git branch --track gh-pages $(GITREMOTE)/gh-pages
+	test -d build/gh-pages || \
+	    git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages
+	cd build/gh-pages && \
+	    git pull $(GITREMOTEURL) gh-pages
+	rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \
+	    --exclude-from=build/gh-pages/.rsync-exclude \
+	    --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/
+	cd build/gh-pages && \
+	    git add --all . && \
+	    git diff --cached --quiet || \
+	    git commit -m "Sync with the source at $(GITLASTCOMMIT)."
+	cd build/gh-pages && \
+	    git push origin gh-pages
diff --git a/doc/TUTORIAL.rst b/doc/TUTORIAL.rst
new file mode 100644
index 00000000..2cb5b5ce
--- /dev/null
+++ b/doc/TUTORIAL.rst
@@ -0,0 +1,148 @@
+===============================================================================
+                        Welcome to the PDFgui tutorial                       
+===============================================================================
+
+The latest version of this document is available online at
+
+`http://danse.us/trac/diffraction/browser/diffraction/diffpy/diffpy/pdfgui/doc`_
+
+Please, have your co-workers or students try it out and let us know if you
+have any comments.  We want to make it really easy for the new users to get
+started with PDFgui.
+
+-------------------------------------------------------------------------------
+
+Lesson 1: Creating simple fit of Ni PDF
+----------------------------------------
+
+Input files:
+
+* `<tutorial/Ni-xray.gr>`_ - experimental X-ray PDF data
+* `<tutorial/Ni.stru>`_ - Ni f.c.c. structure in PDFfit format
+
+Procedure:
+
+1. Open a terminal and type ``pdfgui`` to start the program.
+
+2. Create a new Fit:
+    1. Select "FITTING" in the left-most vertical tab.
+    2. Click right mouse button in the left panel and choose "New Fit" in the pop-up menu.
+
+3. Load structure model:
+    1. Place the cursor of the mouse onto the title of the Fit, click the right button and choose "Insert Phase" in the pop-up menu.
+    2. Click the "Open" button and load the `Ni.stru` file.
+
+   The right panel has 3 tabs for the initial configuration, constraints panel for expressing structure properties as functions of tunable parameters, and Results panel for refined structure.
+
+4. Load experimental PDF data:
+    1. Select the title of "Fit 1", click the right button and choose "Insert Data Set" in the pop-up menu.
+    2. Load the `Ni-xray.gr` file.
+
+   Again, the right panel shows 3 tabs for properties of this dataset.
+
+5. Define what is refined:
+    1. Click on the `Ni-xray.gr` data and select the "Constraints" tab.
+    2. Type ``@1`` into "Scale Factor" edit box.
+    3. Select the `Ni.stru` phase and its "Constraints" tab.
+    4. Fill "a", "b", "c" boxes with ``@5``.
+
+   A refined variable can be expressed as a math expression:
+   ``f(@n1, @n2, @n3, ...)`` where
+   ``@n1`` stands for fitted parameter and
+   ``n1, n2, ...`` are arbitrary positive integers.
+   This allows simple linking of related variables - for example, since
+   cell lengths a, b, c are all expressed as ``@5``, the refined structure will remain cubic.
+
+6. Start the refinement:
+    1. Select "Fit 1" in the left panel.  The parameters panel shows a list of used parameters and their initial values.
+    2. Click the "gear" icon on the toolbar and watch the fit progress in the terminal window.
+
+7. Plot the results:
+    1. Select "PLOTTING" in the left-most vertical tab.
+    2. Select the `Ni-xray.gr` dataset.
+    3. Select "r" as the X plotting variable.
+    4. Hold down shift and select "Gcalc" and "Gtrunc" as the Y plotting variables.
+    5. Click "Plot" button.
+
+   A new window pops up with plots.  You can try out the buttons in the toolbar below.
+
+8. Save your project for later use.
+
+-------------------------------------------------------------------------------
+
+Lesson 2: Build structure model using crystal symmetry
+------------------------------------------------------
+
+In the previous example the initial structure was defined by an existing file. However, PDFgui makes it very easy to build a structure model from scratch and constrain it with arbitrary crystal symmetry.
+
+1. Create a blank structure:
+    1. Click the FITTING tab.
+    2. Repeat steps 1-3a from Lesson 1, but choose the "New" button. Rename "New Phase" to "Ni fcc".
+
+2. Define asymmetric unit:
+    1. Right click the header of the empty atoms grid in the "Configure" page.
+    2. Insert 1 atom using the popup menu.
+    3. Change the elem cell to "Ni".
+    4. Select the u11-u33 cells and type "0.004" and press Enter.
+
+3. Expand to all equivalent positions:
+    1. Right click the first Ni atom and select "Expand space group". A "Space Group Expansion" dialog should open.
+    2. In the dialog, select Fm-3m or just type 225 in the "Space Group" box and hit "OK".
+
+   You should now have four atoms in the atoms grid.
+
+4. Generate symmetry constraints:
+    1. Select the "Constraints" tab.
+    2. Select all atoms. This can be done by dragging the mouse over the atom names or by clicking on the "elem" header.
+    3. Right click in a selected cell and select "Symmetry constraints." A "Space Group Constraints" dialog should open.
+    4. "Fm-3m" should already appear in the "Space Group" box. If it does not, select it as you did in step 3 and hit "OK".
+
+   The u11-u33 cells should all read the same value. The "x", "y" and "z" cells should be all empty because Ni atoms are at special positions in Fm-3m. You may try to select lower-symmetry space and check what happens with the constraints. The space group constraints may be mixed by selecting different groups of atoms, for example, when only certain species show lowered symmetry.
+
+5. Continue the fit as in Lesson 1.
+
+-------------------------------------------------------------------------------
+
+Lesson 3: Multi-stage fitting
+-----------------------------
+
+Learn how to string together fits.
+
+1. Create a fit as in Lesson 1.
+
+2. Copy the fit:
+    1. Right click on the fit name "Fit 1" in the right panel (the fit tree).
+    2. Select "Copy" from the pop-up menu.
+
+3. Paste the fit:
+    1. Right click in the empty space between the first fit in the fit tree.
+    2. Select "Paste Fit." This will create "Fit 1_copy", a copy of "Fit 1" in the fit tree.
+
+4. Link the fits:
+    1. Click on "Fit 1_copy" in the fit tree.
+    2. In the "Parameters" panel, select the entire "Initial" column.
+    3. Type ``=Fit 1`` and then press Enter. The "Initial" values of the parameters should now read ``=Fit1:n``, where "n" is the index of the parameter.
+
+   This is the linking syntax: ``=name:index``.
+   "name" is the name of another fit.
+   "index" is the index of a parameter in that fit.
+   If you omit "index", it will default to the index of the parameter you are linking from. A linked parameter uses the refined value of the link as its initial value. This is useful when you are running several related fits.
+
+5. Add more fit parameters:
+    1. Select the "Constraints" tab of the `Ni.stru` phase below "Fit 1_copy".
+    2. Write ``@9`` in the "delta2" box.
+
+6. Run the fit and plot the results:
+    1. Run the fit as in Lesson 1.
+    2. Plot the fit as in Lesson 1, but this time hold down Control and select the data sets from "Fit 1" and "Fit 1_copy". You can change the "offset" in the plotting window to 0 to place the plots on top of each other.
+
+-------------------------------------------------------------------------------
+
+References:
+-----------
+
+1. `(pdf) <manual/Proffen-jac-1999.pdf>`_,
+   Th. Proffen and S. J. L. Billinge, PDFFIT a program for full profile structural refinement of the atomic pair distribution function, J. Appl. Crystallogr. 32, 572-575 (1999)
+
+2. `(pdf) <manual/Farrow-jpcm-2007.pdf>`_,
+   C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and PDFgui: Computer programs for studying nanostructure in crystals, J. Phys.: Condens. Matter 19, 335219 (2007)
diff --git a/src/diffpy/pdfgui/doc/epydoc/Makefile b/doc/epydoc/Makefile
similarity index 100%
rename from src/diffpy/pdfgui/doc/epydoc/Makefile
rename to doc/epydoc/Makefile
diff --git a/src/diffpy/pdfgui/doc/epydoc/epydoc.cfg b/doc/epydoc/epydoc.cfg
similarity index 100%
rename from src/diffpy/pdfgui/doc/epydoc/epydoc.cfg
rename to doc/epydoc/epydoc.cfg
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 00000000..2be83069
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd
diff --git a/src/diffpy/pdfgui/doc/manual/.gitignore b/doc/manual/.gitignore
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/.gitignore
rename to doc/manual/.gitignore
diff --git a/src/diffpy/pdfgui/doc/Farrow-jpcm-2007.pdf b/doc/manual/Farrow-jpcm-2007.pdf
similarity index 100%
rename from src/diffpy/pdfgui/doc/Farrow-jpcm-2007.pdf
rename to doc/manual/Farrow-jpcm-2007.pdf
diff --git a/src/diffpy/pdfgui/doc/Proffen-jac-1999.pdf b/doc/manual/Proffen-jac-1999.pdf
similarity index 100%
rename from src/diffpy/pdfgui/doc/Proffen-jac-1999.pdf
rename to doc/manual/Proffen-jac-1999.pdf
diff --git a/src/diffpy/pdfgui/doc/manual/acknowledgements.texinfo b/doc/manual/acknowledgements.texinfo
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/acknowledgements.texinfo
rename to doc/manual/acknowledgements.texinfo
diff --git a/src/diffpy/pdfgui/doc/manual/disclaimer.texinfo b/doc/manual/disclaimer.texinfo
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/disclaimer.texinfo
rename to doc/manual/disclaimer.texinfo
diff --git a/src/diffpy/pdfgui/doc/manual/extractEquations.py b/doc/manual/extractEquations.py
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/extractEquations.py
rename to doc/manual/extractEquations.py
diff --git a/src/diffpy/pdfgui/doc/manual/fixHTMLCode.py b/doc/manual/fixHTMLCode.py
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/fixHTMLCode.py
rename to doc/manual/fixHTMLCode.py
diff --git a/src/diffpy/pdfgui/doc/manual/images/Makefile b/doc/manual/images/Makefile
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/Makefile
rename to doc/manual/images/Makefile
diff --git a/src/diffpy/pdfgui/doc/manual/images/eq-01.png b/doc/manual/images/eq-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/eq-01.png
rename to doc/manual/images/eq-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/eq-02.png b/doc/manual/images/eq-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/eq-02.png
rename to doc/manual/images/eq-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-01.png b/doc/manual/images/fig2-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-01.png
rename to doc/manual/images/fig2-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-02.png b/doc/manual/images/fig2-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-02.png
rename to doc/manual/images/fig2-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-03.png b/doc/manual/images/fig2-03.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-03.png
rename to doc/manual/images/fig2-03.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-04.png b/doc/manual/images/fig2-04.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-04.png
rename to doc/manual/images/fig2-04.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-05.png b/doc/manual/images/fig2-05.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-05.png
rename to doc/manual/images/fig2-05.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-06.png b/doc/manual/images/fig2-06.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-06.png
rename to doc/manual/images/fig2-06.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-07.png b/doc/manual/images/fig2-07.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-07.png
rename to doc/manual/images/fig2-07.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-08.png b/doc/manual/images/fig2-08.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-08.png
rename to doc/manual/images/fig2-08.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-09.png b/doc/manual/images/fig2-09.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-09.png
rename to doc/manual/images/fig2-09.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-10.png b/doc/manual/images/fig2-10.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-10.png
rename to doc/manual/images/fig2-10.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig2-11.png b/doc/manual/images/fig2-11.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig2-11.png
rename to doc/manual/images/fig2-11.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-01.png b/doc/manual/images/fig3-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-01.png
rename to doc/manual/images/fig3-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-02.png b/doc/manual/images/fig3-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-02.png
rename to doc/manual/images/fig3-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-03.png b/doc/manual/images/fig3-03.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-03.png
rename to doc/manual/images/fig3-03.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-04.png b/doc/manual/images/fig3-04.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-04.png
rename to doc/manual/images/fig3-04.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-05.png b/doc/manual/images/fig3-05.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-05.png
rename to doc/manual/images/fig3-05.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-06.png b/doc/manual/images/fig3-06.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-06.png
rename to doc/manual/images/fig3-06.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-07.png b/doc/manual/images/fig3-07.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-07.png
rename to doc/manual/images/fig3-07.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-08.png b/doc/manual/images/fig3-08.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-08.png
rename to doc/manual/images/fig3-08.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-09.png b/doc/manual/images/fig3-09.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-09.png
rename to doc/manual/images/fig3-09.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig3-10.png b/doc/manual/images/fig3-10.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig3-10.png
rename to doc/manual/images/fig3-10.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig4-01.png b/doc/manual/images/fig4-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig4-01.png
rename to doc/manual/images/fig4-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/fig4-02.png b/doc/manual/images/fig4-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/fig4-02.png
rename to doc/manual/images/fig4-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-01.png b/doc/manual/images/originals/fig2-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-01.png
rename to doc/manual/images/originals/fig2-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-01.xcf b/doc/manual/images/originals/fig2-01.xcf
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-01.xcf
rename to doc/manual/images/originals/fig2-01.xcf
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-02.png b/doc/manual/images/originals/fig2-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-02.png
rename to doc/manual/images/originals/fig2-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-03.png b/doc/manual/images/originals/fig2-03.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-03.png
rename to doc/manual/images/originals/fig2-03.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-04.png b/doc/manual/images/originals/fig2-04.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-04.png
rename to doc/manual/images/originals/fig2-04.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-05.png b/doc/manual/images/originals/fig2-05.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-05.png
rename to doc/manual/images/originals/fig2-05.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-06.png b/doc/manual/images/originals/fig2-06.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-06.png
rename to doc/manual/images/originals/fig2-06.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-07.png b/doc/manual/images/originals/fig2-07.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-07.png
rename to doc/manual/images/originals/fig2-07.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-08.png b/doc/manual/images/originals/fig2-08.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-08.png
rename to doc/manual/images/originals/fig2-08.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-09.png b/doc/manual/images/originals/fig2-09.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-09.png
rename to doc/manual/images/originals/fig2-09.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-10.png b/doc/manual/images/originals/fig2-10.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-10.png
rename to doc/manual/images/originals/fig2-10.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig2-11.png b/doc/manual/images/originals/fig2-11.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig2-11.png
rename to doc/manual/images/originals/fig2-11.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-01.png b/doc/manual/images/originals/fig3-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-01.png
rename to doc/manual/images/originals/fig3-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-02.png b/doc/manual/images/originals/fig3-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-02.png
rename to doc/manual/images/originals/fig3-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-03.png b/doc/manual/images/originals/fig3-03.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-03.png
rename to doc/manual/images/originals/fig3-03.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-04.png b/doc/manual/images/originals/fig3-04.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-04.png
rename to doc/manual/images/originals/fig3-04.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-05.png b/doc/manual/images/originals/fig3-05.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-05.png
rename to doc/manual/images/originals/fig3-05.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-06.png b/doc/manual/images/originals/fig3-06.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-06.png
rename to doc/manual/images/originals/fig3-06.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-07.png b/doc/manual/images/originals/fig3-07.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-07.png
rename to doc/manual/images/originals/fig3-07.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-08.png b/doc/manual/images/originals/fig3-08.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-08.png
rename to doc/manual/images/originals/fig3-08.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-09.png b/doc/manual/images/originals/fig3-09.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-09.png
rename to doc/manual/images/originals/fig3-09.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig3-10.png b/doc/manual/images/originals/fig3-10.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig3-10.png
rename to doc/manual/images/originals/fig3-10.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig4-01.png b/doc/manual/images/originals/fig4-01.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig4-01.png
rename to doc/manual/images/originals/fig4-01.png
diff --git a/src/diffpy/pdfgui/doc/manual/images/originals/fig4-02.png b/doc/manual/images/originals/fig4-02.png
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/images/originals/fig4-02.png
rename to doc/manual/images/originals/fig4-02.png
diff --git a/src/diffpy/pdfgui/doc/manual/pdfgui.html b/doc/manual/pdfgui.html
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/pdfgui.html
rename to doc/manual/pdfgui.html
diff --git a/src/diffpy/pdfgui/doc/manual/pdfgui.pdf b/doc/manual/pdfgui.pdf
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/pdfgui.pdf
rename to doc/manual/pdfgui.pdf
diff --git a/src/diffpy/pdfgui/doc/manual/pdfgui.texinfo b/doc/manual/pdfgui.texinfo
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/pdfgui.texinfo
rename to doc/manual/pdfgui.texinfo
diff --git a/src/diffpy/pdfgui/doc/manual/redistribution.texinfo b/doc/manual/redistribution.texinfo
similarity index 100%
rename from src/diffpy/pdfgui/doc/manual/redistribution.texinfo
rename to doc/manual/redistribution.texinfo
diff --git a/doc/source/_static/.placeholder b/doc/source/_static/.placeholder
new file mode 100644
index 00000000..e69de29b
diff --git a/doc/source/api/diffpy.pdfgui.example_package.rst b/doc/source/api/diffpy.pdfgui.example_package.rst
new file mode 100644
index 00000000..0390b965
--- /dev/null
+++ b/doc/source/api/diffpy.pdfgui.example_package.rst
@@ -0,0 +1,31 @@
+.. _example_package documentation:
+
+|title|
+=======
+
+.. |title| replace:: diffpy.pdfgui.example_package package
+
+.. automodule:: diffpy.pdfgui.example_package
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+|foo|
+-----
+
+.. |foo| replace:: diffpy.pdfgui.example_package.foo module
+
+.. automodule::  diffpy.pdfgui.example_package.foo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+|bar|
+-----
+
+.. |bar| replace:: diffpy.pdfgui.example_package.bar module
+
+.. automodule:: diffpy.pdfgui.example_package.foo
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/api/diffpy.pdfgui.rst b/doc/source/api/diffpy.pdfgui.rst
new file mode 100644
index 00000000..8166640e
--- /dev/null
+++ b/doc/source/api/diffpy.pdfgui.rst
@@ -0,0 +1,30 @@
+:tocdepth: -1
+
+|title|
+=======
+
+.. |title| replace:: diffpy.pdfgui package
+
+.. automodule:: diffpy.pdfgui
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   diffpy.pdfgui.example_package
+
+Submodules
+----------
+
+|module|
+--------
+
+.. |module| replace:: diffpy.pdfgui.example_submodule module
+
+.. automodule:: diffpy.pdfgui.example_submodule
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/conf.py b/doc/source/conf.py
new file mode 100644
index 00000000..cc57882a
--- /dev/null
+++ b/doc/source/conf.py
@@ -0,0 +1,289 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# diffpy.pdfgui documentation build configuration file, created by
+# sphinx-quickstart on Thu Jan 30 15:49:41 2014.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import time
+from importlib.metadata import version
+from pathlib import Path
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use Path().resolve() to make it absolute, like shown here.
+# sys.path.insert(0, str(Path(".").resolve()))
+sys.path.insert(0, str(Path("../..").resolve()))
+sys.path.insert(0, str(Path("../../src").resolve()))
+
+# abbreviations
+ab_authors = "Billinge Group members and community contributors"
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx_rtd_theme",
+    "m2r",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = [".rst", ".md"]
+
+# The encoding of source files.
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = "diffpy.pdfgui"
+copyright = "%Y, The Trustees of Columbia University in the City of New York"
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+
+fullversion = version(project)
+# The short X.Y version.
+version = "".join(fullversion.split(".post")[:1])
+# The full version, including alpha/beta/rc tags.
+release = fullversion
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+# language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+# today = ''
+today = time.strftime("%B %d, %Y", time.localtime())
+year = today.split()[-1]
+# Else, today_fmt is used as the format for a strftime call.
+# today_fmt = '%B %d, %Y'
+# substitute YEAR in the copyright string
+copyright = copyright.replace("%Y", year)
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ["build"]
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# A list of ignored prefixes for module index sorting.
+modindex_common_prefix = ["diffpy.pdfgui"]
+
+# Display all warnings for missing links.
+nitpicky = True
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+    "navigation_with_keys": "true",
+}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+# html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+# html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+# html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+# html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+# html_domain_indices = True
+
+# If false, no index is generated.
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Output file base name for HTML help builder.
+basename = "diffpy.pdfgui".replace(" ", "").replace(".", "")
+htmlhelp_basename = basename + "doc"
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    ("index", "diffpy.pdfgui.tex", "diffpy.pdfgui Documentation", ab_authors, "manual"),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+# latex_appendices = []
+
+# If false, no module index is generated.
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [("index", "diffpy.pdfgui", "diffpy.pdfgui Documentation", ab_authors, 1)]
+
+# If true, show URL addresses after external links.
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        "index",
+        "diffpy.pdfgui",
+        "diffpy.pdfgui Documentation",
+        ab_authors,
+        "diffpy.pdfgui",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+# intersphinx_mapping = {'http://docs.python.org/': None}
diff --git a/doc/source/index.rst b/doc/source/index.rst
new file mode 100644
index 00000000..7a8854ce
--- /dev/null
+++ b/doc/source/index.rst
@@ -0,0 +1,50 @@
+#######
+|title|
+#######
+
+.. |title| replace:: diffpy.pdfgui documentation
+
+diffpy.pdfgui - GUI for PDF simulation and structure refinement..
+
+| Software version |release|.
+| Last updated |today|.
+
+=======
+Authors
+=======
+
+diffpy.pdfgui is developed by Billinge Group
+and its community contributors.
+
+For a detailed list of contributors see
+https://github.com/diffpy/diffpy.pdfgui/graphs/contributors.
+
+============
+Installation
+============
+
+See the `README <https://github.com/diffpy/diffpy.pdfgui#installation>`_
+file included with the distribution.
+
+========
+Tutorial
+========
+
+A tutorial for this package can be found here: `<../TUTORIAL.rst>`
+
+=================
+Table of contents
+=================
+.. toctree::
+   :titlesonly:
+
+   license
+   release
+   Package API <api/diffpy.pdfgui>
+
+=======
+Indices
+=======
+
+* :ref:`genindex`
+* :ref:`search`
diff --git a/doc/source/license.rst b/doc/source/license.rst
new file mode 100644
index 00000000..cfab61c2
--- /dev/null
+++ b/doc/source/license.rst
@@ -0,0 +1,39 @@
+:tocdepth: -1
+
+.. index:: license
+
+License
+#######
+
+OPEN SOURCE LICENSE AGREEMENT
+=============================
+BSD 3-Clause License
+
+Copyright (c) 2024, The Trustees of Columbia University in 
+the City of New York.
+All Rights Reserved. 
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/doc/source/release.rst b/doc/source/release.rst
new file mode 100644
index 00000000..27cd0cc9
--- /dev/null
+++ b/doc/source/release.rst
@@ -0,0 +1,5 @@
+:tocdepth: -1
+
+.. index:: release notes
+
+.. include:: ../../CHANGELOG.rst
diff --git a/src/diffpy/pdfgui/doc/tutorial/1050K.gr b/doc/tutorial/1050K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/1050K.gr
rename to doc/tutorial/1050K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/1100K.gr b/doc/tutorial/1100K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/1100K.gr
rename to doc/tutorial/1100K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/1150K.gr b/doc/tutorial/1150K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/1150K.gr
rename to doc/tutorial/1150K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/300K.gr b/doc/tutorial/300K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/300K.gr
rename to doc/tutorial/300K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/550K.gr b/doc/tutorial/550K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/550K.gr
rename to doc/tutorial/550K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/650K.gr b/doc/tutorial/650K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/650K.gr
rename to doc/tutorial/650K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/700K.gr b/doc/tutorial/700K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/700K.gr
rename to doc/tutorial/700K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/720K.gr b/doc/tutorial/720K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/720K.gr
rename to doc/tutorial/720K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/730K.gr b/doc/tutorial/730K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/730K.gr
rename to doc/tutorial/730K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/740K.gr b/doc/tutorial/740K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/740K.gr
rename to doc/tutorial/740K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/750K.gr b/doc/tutorial/750K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/750K.gr
rename to doc/tutorial/750K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/800K.gr b/doc/tutorial/800K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/800K.gr
rename to doc/tutorial/800K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/880K.gr b/doc/tutorial/880K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/880K.gr
rename to doc/tutorial/880K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/980K.gr b/doc/tutorial/980K.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/980K.gr
rename to doc/tutorial/980K.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/CdSe-3nm.gr b/doc/tutorial/CdSe-3nm.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/CdSe-3nm.gr
rename to doc/tutorial/CdSe-3nm.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/CdSe-bulk.gr b/doc/tutorial/CdSe-bulk.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/CdSe-bulk.gr
rename to doc/tutorial/CdSe-bulk.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/CdSe-nano.ddp3 b/doc/tutorial/CdSe-nano.ddp3
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/CdSe-nano.ddp3
rename to doc/tutorial/CdSe-nano.ddp3
diff --git a/src/diffpy/pdfgui/doc/tutorial/CdSe-wurtzite.stru b/doc/tutorial/CdSe-wurtzite.stru
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/CdSe-wurtzite.stru
rename to doc/tutorial/CdSe-wurtzite.stru
diff --git a/src/diffpy/pdfgui/doc/tutorial/Ni-neutron.gr b/doc/tutorial/Ni-neutron.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/Ni-neutron.gr
rename to doc/tutorial/Ni-neutron.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/Ni-xray.gr b/doc/tutorial/Ni-xray.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/Ni-xray.gr
rename to doc/tutorial/Ni-xray.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/Ni.stru b/doc/tutorial/Ni.stru
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/Ni.stru
rename to doc/tutorial/Ni.stru
diff --git a/src/diffpy/pdfgui/doc/tutorial/lcmo-template.ddp3 b/doc/tutorial/lcmo-template.ddp3
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/lcmo-template.ddp3
rename to doc/tutorial/lcmo-template.ddp3
diff --git a/src/diffpy/pdfgui/doc/tutorial/lmo-template.ddp3 b/doc/tutorial/lmo-template.ddp3
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/lmo-template.ddp3
rename to doc/tutorial/lmo-template.ddp3
diff --git a/src/diffpy/pdfgui/doc/tutorial/tui_mno_bond_lengths.py b/doc/tutorial/tui_mno_bond_lengths.py
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/tui_mno_bond_lengths.py
rename to doc/tutorial/tui_mno_bond_lengths.py
diff --git a/src/diffpy/pdfgui/doc/tutorial/x000t010q35.gr b/doc/tutorial/x000t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x000t010q35.gr
rename to doc/tutorial/x000t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/x004t010q35.gr b/doc/tutorial/x004t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x004t010q35.gr
rename to doc/tutorial/x004t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/x012t010q35.gr b/doc/tutorial/x012t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x012t010q35.gr
rename to doc/tutorial/x012t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/x016t010q35.gr b/doc/tutorial/x016t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x016t010q35.gr
rename to doc/tutorial/x016t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/x020t010q35.gr b/doc/tutorial/x020t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x020t010q35.gr
rename to doc/tutorial/x020t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/x024t010q35.gr b/doc/tutorial/x024t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x024t010q35.gr
rename to doc/tutorial/x024t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/tutorial/x028t010q35.gr b/doc/tutorial/x028t010q35.gr
similarity index 100%
rename from src/diffpy/pdfgui/doc/tutorial/x028t010q35.gr
rename to doc/tutorial/x028t010q35.gr
diff --git a/src/diffpy/pdfgui/doc/TUTORIAL.txt b/src/diffpy/pdfgui/doc/TUTORIAL.txt
deleted file mode 100644
index 283fc5bd..00000000
--- a/src/diffpy/pdfgui/doc/TUTORIAL.txt
+++ /dev/null
@@ -1,185 +0,0 @@
-==============================================================================
-=                       Welcome to the PDFgui tutorial                       =
-==============================================================================
-
-The latest version of this document is available online at
-
-http://danse.us/trac/diffraction/browser/diffraction/diffpy/diffpy/pdfgui/doc
-
-Please, have your co-workers or students try it out and let us know if you
-have any comments.  We want to make it really easy for the new users to get
-started with PDFgui.
-
-------------------------------------------------------------------------------
-
-Lesson 1:  Creating simple fit of Ni PDF
-
-  Input files:
-
-    tutorial/Ni-xray.gr     experimental X-ray PDF data
-    tutorial/Ni.stru        Ni f.c.c. structure in PDFfit format
-
-  Procedure:
-
-    1.  Open a terminal and type "pdfgui" to start the program.
-
-    2.  Create a new Fit:
-        (a) Select "FITTING" in the left-most vertical tab.
-        (b) Click right mouse button in the left panel and choose "New Fit"
-	    in the pop-up menu.
-
-    3.  Load structure model:
-
-        (a) Place the cursor of the mouse onto the title of the Fit, click
-            the right button and choose "Insert Phase" in the pop-up menu.
-        (b) Click the "Open" button and load the Ni.stru file.
-
-        The right panel has 3 tabs for the initial configuration, constraints
-        panel for expressing structure properties as functions of tunable
-        parameters, and Results panel for refined structure.
-
-    4.  Load experimental PDF data:
-        (a) Select the title of "Fit 1", click the right button and choose
-            "Insert Data Set" in the pop-up menu.
-        (b) Load the "Ni-xray.gr" file.
-
-        Again, the right panel shows 3 tabs for properties of this dataset.
-
-    5.  Define what is refined:
-        (a) Click on the "Ni-xray.gr" data and select the "Constraints" tab.
-        (b) Type "@1" into "Scale Factor" edit box.
-        (c) Select the "Ni.stru" phase and its "Constraints" tab.
-        (d) Fill "a", "b", "c" boxes with "@5".
-
-        A refined variable can be expressed as math expression
-        f(@n1, @n2, @n3, ...) where
-            @n1  stands for fitted parameter and
-            n1, n2, ...   are arbitrary positive integers
-        This allows simple linking of related variables - for example, since
-        cell lengths a, b, c are all expressed as "@5", the refined structure
-        will remain cubic.
-
-    6.  Start the refinement:
-        (a) Select "Fit 1" in the left panel.  The parameters panel shows list
-            of used parameters and their initial values.
-        (b) Click the "gear" icon on the toolbar and watch the fit progress
-            in the terminal window.
-
-    7.  Plot the results:
-        (a) Select "PLOTTING" in the left-most vertical tab.
-        (b) Select the "Ni-xray.gr" dataset
-        (c) Select "r" as the X plotting variable.
-        (d) Hold down shift and select "Gcalc" and "Gtrunc" as the Y plotting
-            variables.
-        (d) Click "Plot" button.
-
-        A new window pops up with plots.  You can try out the buttons in
-        the toolbar below.
-
-    8.  Save your project for later use.
-
-------------------------------------------------------------------------------
-
-Lesson 2:  Build structure model using crystal symmetry
-
-  In the previous example the initial structure was defined by an existing
-  file.  However, PDFgui makes it very easy to build structure model from
-  scratch and constrain it with arbitrary crystal symmetry.
-
-    1.  Create blank structure:
-        (a) Click the FITTING tab
-        (b) Repeat steps 1-3a from Lesson 1, but choose the "New" button.
-            Rename "New Phase" to "Ni fcc".
-
-    2.  Define asymmetric unit:
-	(a) Right click the header of the empty atoms grid in the
-	    "Configure" page.
-        (b) Insert 1 atom using the popup menu.
-        (c) Change the elem cell to "Ni".
-        (d) Select the u11-u33 cells and type "0.004" and press Enter.
-
-    3.  Expand to all equivalent positions:
-        (a) Right click the first Ni atom and select "Expand space group". A
-            "Space Group Expansion" dialog should open.
-        (b) In the dialog, select Fm-3m or just type 225 in the "Space Group"
-            box and hit "OK".
-
-	You should now have four atoms in the atoms grid.
-
-    4.  Generate symmetry constraints:
-        (a) Select the "Constraints" tab.
-        (b) Select all atoms. This can be done by dragging the mouse over the
-            atom names or by clicking on the "elem" header.
-        (c) Right click in a selected cell and select "Symmetry constraints."
-	    A "Space Group Constraints" dialog should open.
-        (d) "Fm-3m" should already appear in the "Space Group" box. If it does
-            not, select it as you did in step 3 and hit "OK".
-
-	The u11-u33 cells should all read the same value.  The "x", "y" and
-	"z" cells should be all empty, because Ni atoms are at special
-	positions in Fm-3m.  You may try to select lower-symmetry space and
-	check what happens with the constraints.  The space group constraints
-	may be mixed by selecting different groups of atoms, for example when
-	only certain species show lowered symmetry.
-
-    5. Continue the fit as in Lesson 1.
-
-------------------------------------------------------------------------------
-
-Lesson 3:  Multi-stage fitting
-
-  Learn how to string together fits.
-
-    1.  Create a fit as in Lesson 1.
-
-    2.  Copy the fit.
-        (a) Right click on the fit name "Fit 1" in the right panel (the fit
-            tree).
-        (b) Select "Copy" from the pop-up menu.
-
-    3.  Paste the fit.
-        (a) Right click in the empty space between the first fit in the fit
-            tree.
-        (b) Select "Paste Fit." This will create "Fit 1_copy", a copy of
-	    "Fit 1" in the fit tree.
-
-    4. Link the fits.
-        (a) Click on "Fit 1_copy" in the fit tree.
-        (b) In the "Parameters" panel, select the entire "Initial" column.
-        (c) Type "=Fit 1" and then press Enter. The "Initial" values of the
-            parameters should now read "=Fit1:n", where "n" is the index of the
-            parameter.
-
-            This is the linking syntax: "=name:index".
-            "name" is the name of another fit.
-            "index" is the index of a parameter in that fit.
-            If you omit "index", it will default to the index of the parameter
-            you are linking from.  A linked parameter uses the refined value
-	    of the link as its initial value. This is useful when you are
-	    running several related fits.
-
-    5.  Add more fit parameters.
-        (a) Select the "Constraints" tab of the  "Ni.stru" phase below
-            "Fit 1_copy".
-        (b) Write "@9" in the "delta2" box.
-
-    6. Run the fit and plot the results.
-        (a) Run the fit as in Lesson 1.
-        (b) Plot the fit as in Lesson 1, but this time hold down Control and
-            select the data sets from "Fit 1" and "Fit 1_copy". You can change
-            the "offset" in the plotting window to 0 to place the plots on top
-            of each other.
-
-------------------------------------------------------------------------------
-
-References:
-
-1. Proffen-jac-1999.pdf
-   Th. Proffen and S. J. L. Billinge, PDFFIT a program for full profile
-   structural refinement of the atomic pair distribution function,
-   J. Appl. Crystallogr. 32, 572-575 (1999)
-
-2. Farrow-jpcm-2007.pdf
-   C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, J. Bloch, Th. Proffen
-   and S. J. L. Billinge, PDFfit2 and PDFgui: Computer programs for studying
-   nanostructure in crystals, J. Phys.: Condens. Matter 19, 335219 (2007)
diff --git a/src/diffpy/pdfgui/doc/manual/Makefile b/src/diffpy/pdfgui/doc/manual/Makefile
deleted file mode 100644
index c1ee4b0e..00000000
--- a/src/diffpy/pdfgui/doc/manual/Makefile
+++ /dev/null
@@ -1,49 +0,0 @@
-# Makefile for compiling and publishing pdfgui manual
-# Available targets:
-#
-#   all      -- (default) build pdfgui manual in HTML and PDF formats
-#   clean    -- remove intermediate texinfo files
-#   cleanALL -- delete all generated files
-#   publish  -- copy the compiled manual files to WEBDIR directory
-#
-# Variables:
-#
-#   EQBUILD  -- extract PNG equations for HTML manual
-#   WEBDIR   -- the rsync target directory.  Required by "publish" target.
-
-
-all: pdfgui.pdf pdfgui.html
-
-
-pdfgui.html: pdfgui.texinfo
-	$(MAKE) -C images
-	texi2html $<
-ifdef EQBUILD
-	python extractEquations.py $<
-endif
-	python fixHTMLCode.py $@
-
-
-pdfgui.pdf: pdfgui.texinfo
-	$(MAKE) -C images
-	texi2pdf $<
-
-
-clean:
-	/bin/rm -f -- \
-	    pdfgui.vr pdfgui.tp pdfgui.pg pdfgui.ky pdfgui.fn \
-	    pdfgui.cps pdfgui.cp pdfgui.toc pdfgui.aux pdfgui.log \
-	    pdfgui.vrs
-
-
-cleanALL: clean
-	/bin/rm -f pdfgui.html pdfgui.pdf
-	$(MAKE) -C images clean
-
-
-publish: all
-ifndef WEBDIR
-	$(error Set WEBDIR to define rsync target directory.)
-endif
-	rsync -pRt --chmod=a+rwx,go-w,Fa-x \
-	    pdfgui.html pdfgui.pdf images/*.png $(WEBDIR)