diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 534d55e3..00000000
--- a/.gitignore
+++ /dev/null
@@ -1,11 +0,0 @@
-_build
-*.bak
-*~
-
-#eclipse
-.project
-.pydevproject
-.settings
-
-# Include zip files present in static_root
-!/static_root/**/*.zip
diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 00000000..de749f99
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,50 @@
+This program is part of the DiffPy and DANSE open-source projects
+and is available subject to the conditions and terms laid out below.
+
+If you use this program to do productive scientific research that leads
+to publication, we ask that you acknowledge use of the program by citing
+the following paper in your publication:
+
+ C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin,
+ 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)
+
+Copyright 2006-2007, Board of Trustees of Michigan State University,
+Copyright 2008-2009, Board of Trustees of Columbia University in the
+city of New York. (Copyright holder indicated in each source file).
+
+For more information please visit the project web-page:
+ http://www.diffpy.org/
+or email Prof. Simon Billinge at sb2896@columbia.edu
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * 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.
+
+ * 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 COPYRIGHT HOLDER "AS IS". COPYRIGHT HOLDER
+EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER
+EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY
+FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM
+INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE
+SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY. IN NO EVENT SHALL
+COPYRIGHT HOLDER BE LIABLE TO ANY PARTY 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 OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 0e1ef966..00000000
--- a/Makefile
+++ /dev/null
@@ -1,267 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = _build
-
-CURRENT_DOC_DIR = ./static_root/doc
-TEMP_TEST_DOC_DIR = ./doc
-
-# 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) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.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 ' where 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) $(BUILDDIR)/html
- @echo
- @echo "Create hard-linked copy of 'static_root':"
- @echo
- rsync -aO -F --link-dest=$(CURDIR)/static_root/ \
- static_root/ $(BUILDDIR)/html/
- @echo
- @echo "Validate symbolic links:"
- @echo
- @find $(BUILDDIR)/html -type l \( -exec test -e {} \; -or -print \) | \
- sed 's/^/[broken] /' | ( ! grep . ) && echo "[OK]"
- @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/sphinxTestRun.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sphinxTestRun.qhc"
-
-devhelp:
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $$HOME/.local/share/devhelp/sphinxTestRun"
- @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/sphinxTestRun"
- @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:
- # For some reason, the doc directory for our sources is set to
- # ./static_root/doc but Sphinx expects it to be at ./doc and this has yet to
- # be addressed. The effect of this discontinuity is that when Sphinx is
- # running, it looks in the incorrect location with relative paths for static
- # files we are serving up. This ultimately is not an issue for the
- # functionality of the website as the links are indeed consistent in the
- # static files generated, but it causes tests such as `linkcheck` to fail.
- # For this reason, this make command has been modified to accoun for this
- # discontinuity to preserve the validity of the test, but this change may
- # have impact on future modifications to the website's internal structure
- # and/or a fix for this issue, hence the in-line documentation of the problem
- # (which gets printed to the console upon `linkcheck`'s failure).
- #
- # Here's what the make command was prior to this modification (and likely
- # should be converted back to after addressing the issue):
- #
- # $(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."
- #
- # Here's an overview of the logic for circumventing the issue:
- #
- # (1) Attempt to create the symlink to the actual doc directory in the
- # location that Sphinx expects it to be.
- # => Success
- # (a) Run linkcheck as we've properly configured our local structure
- # to be what Sphinx expects.
- # (b) Delete the symlink hack/patch, regardless of `linkcheck`'s
- # success as we know we create ./doc as a symlink in (1) (as
- # opposed to it being a directory containing its own data
- # possibly created at a later time without knowledge of this
- # fix).
- # => Failure
- # (a) Do no proceed and let this message be printed for future
- # debugging/maintainance effors.
- test -h $(TEMP_TEST_DOC_DIR) \
- || ln -sT $(CURRENT_DOC_DIR) $(TEMP_TEST_DOC_DIR) \
- && $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck \
- ; rm $(TEMP_TEST_DOC_DIR)
- @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."
-
-xml:
- $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
- @echo
- @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-pseudoxml:
- $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
- @echo
- @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
-
-# Publish to diffpy.github.io
-
-GITREPOPATH = $(CURDIR)/.git
-SOURCEBRANCH = $(shell git symbolic-ref --short HEAD)
-PUBLISHBRANCH = master
-PUBFIRSTREMOTE = $(shell git branch -r --list "*/$(PUBLISHBRANCH)" | head -1)
-GITREMOTE = $(shell git config --get branch.$(PUBLISHBRANCH).remote)
-GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url)
-GITLASTCOMMIT = $(shell git rev-parse --short HEAD)
-
-.create-publish-branch:
- @git rev-parse --verify --quiet $(PUBLISHBRANCH) >/dev/null || \
- echo $(PUBFIRSTREMOTE) | grep -q . || \
- ( echo "No remote found for branch $(PUBLISHBRANCH)" >&2; exit 1 )
- git rev-parse --verify --quiet $(PUBLISHBRANCH) >/dev/null || \
- git branch --track $(PUBLISHBRANCH) $(PUBFIRSTREMOTE)
-
-publish-prepare: .create-publish-branch
- @test -d $(BUILDDIR)/html || \
- ( echo >&2 "Run 'make html' first!"; false )
- test -d $(BUILDDIR)/webpage || \
- git clone -s -b $(PUBLISHBRANCH) $(GITREPOPATH) $(BUILDDIR)/webpage
- git -C $(BUILDDIR)/webpage fetch
- git -C $(BUILDDIR)/webpage checkout --force $(PUBLISHBRANCH)
- git -C $(BUILDDIR)/webpage pull $(GITREMOTEURL) $(PUBLISHBRANCH)
- rsync -aOcv --delete --exclude=.git --exclude=.rsync-exclude \
- --exclude-from=$(BUILDDIR)/webpage/.rsync-exclude \
- --link-dest=$(realpath $(BUILDDIR)/html) \
- $(BUILDDIR)/html/ $(BUILDDIR)/webpage/
- git -C $(BUILDDIR)/webpage add --force --all .
- git -C $(BUILDDIR)/webpage diff --cached --quiet || \
- git -C $(BUILDDIR)/webpage \
- commit -m "Sync with the source at $(GITLASTCOMMIT)"
- git -C $(BUILDDIR)/webpage push $(GITREPOPATH) $(PUBLISHBRANCH)
-
-publish-push:
- git push $(GITREMOTE) $(SOURCEBRANCH) $(PUBLISHBRANCH)
diff --git a/NSFnugget.rst b/NSFnugget.rst
deleted file mode 100644
index 9f72d93b..00000000
--- a/NSFnugget.rst
+++ /dev/null
@@ -1,41 +0,0 @@
-Enabling new science in nanoscale structure characterization of complex materials
-=================================================================================
-
-.. include:: abbreviations.txt
-
-*C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
-and S. J. L. Billinge (Michigan State University)*
-
-To understand and control the properties of materials it is necessary to have
-a detailed knowledge of their atomic structure. Increasingly, we are interested
-in exploiting materials with complex structures on the nanoscale, which presents
-special experimental challenges as crystallography, the standard approach to
-structure determination, loses its power on these length-scales. Alternative
-methods sensitive to nanoscale order are under development. The diffraction
-sub-group of the DANSE project recently released a new software tool that
-will have a large impact in nanostructure characterization using x-ray and
-neutron diffraction.
-
-
-
-.. figure:: images/PDFgui_screenshot_707.png
- :align: center
- :scale: 50 %
-
- Screen-shot of PDFgui during a refinement of multiple data-sets
-
-
-The diffraction data are Fourier transformed to obtain the atomic pair distribution
-function (PDF) and analyzed by quantitatively fitting nanostructure models to the
-data. PDFgui allows rapid setup of individual and multiple
-refinements. This program will be implemented at the
-POWGEN3 and NOMAD diffractometers at SNS with macros to allow real-time parametric
-refinements similar to those shown, allowing researchers to make scientific
-discoveries during data collection, at the beam-time, and not a-posteriori after
-the beamtime is over. PDFgui has numerous extensions
-that are described in more detail in [#]_. The beta version of PDFgui
-is now in public release, available for Windows, Linux and Mac OSX platforms,
-and in the first month has been downloaded 220 times. More information can be
-found at https://www.diffpy.org.
-
-.. [#] |citeFarrowJpcm07|
diff --git a/PublishedRevision b/PublishedRevision
new file mode 100644
index 00000000..ffea877c
--- /dev/null
+++ b/PublishedRevision
@@ -0,0 +1 @@
+HEAD
diff --git a/README.md b/README.md
deleted file mode 100644
index f15d06d4..00000000
--- a/README.md
+++ /dev/null
@@ -1,200 +0,0 @@
-diffpy.github.io
-================
-
-Sphinx sources for the [diffpy.org][site] web page.
-
-### Quick Jump:
-
-- [GitHub Structure](#github-structure)
-- [Where to Make Changes](#where-to-make-changes)
- - [Adding Citations](#adding-citations)
- - [Adding Publications that Describe a DiffPy Project (the "Reference" Section)](#reference-section-1)
- - [Adding Other Publications (the "Publication Using diffpy.cmi" Section)](#reference-section-2)
-- [New Version of Existing Project](#new-version)
-- [New Project](#publishing-new-project)
-- [Publishing Changes](#publishing-changes)
- - [Testing Changes](#testing-changes)
- - [Maintainers (Publishing Changes)](#publishing-changes)
-
-
-# GitHub Structure
-
-This repository contains 3 branches:
-
-1. [`source`][source] sphinx sources for the web page
-2. [`master`][master] sources compiled to HTML format that are published via GitHub pages
-3. [`archive`][archive] converted subversion repository for the old diffpy.org sources
-
-The basic logic is we edit on the source branch and follow instructions below to build the
-sources. The built sources, in the form of html files, are then copied to the master branch
-which is what GitHub pages is configured to render.
-
-
-# Publishing New Version of an Existing Project
-
-For releasing an updated version of a project, first generate the release for the project and
-make sure it is successfully deployed at Pypi and conda-forge.
-
-If you would like to see Connor's commented out comments about how to link pdf versions of
-documentation manuals please see the raw source code of this readme. However, we are moving
-away from having separately built manuals.
-
-
-With the [`source` branch][source] checed out, edit the landing page of your project] (e.g.,
-`products/pdfgetx.rst` for PDFgetx3) to document and provide the updated version of your project.
-
-Once the preceding steps are complete, see
-the instructions of the [Publishing Changes](#submitting-changes) section for publishing these changes.
-
-# Where to Make Changes
-
-Here is a brief map of where in the sources to make updates when different things happen
-
-## A new paper has appeared describing a diffpy product
-
-
-### Adding Publications that Describe a DiffPy Project (the "Reference" Section)
-
-When adding a new publication to the list of [references used within the website](https://www.diffpy.org/publications.html), add the
-citation text of the publication to the documentation *only once* as a named snippet in
-[abbreviations.txt](https://github.com/diffpy/diffpy.github.io/blob/source/abbreviations.txt#L286). For example:
-```
-.. |citeJuhasJac18| replace::
- P. Juhás, J. N. Louwen, L. van Eijck, E. T. C. Vogt, S. J. L. Billinge,
- `PDFgetN3: atomic pair distribution functions from
- neutron powder diffraction data using ad hoc corrections
- `__,
- *J. Appl. Crystallogr.*, **51**, 1492--1497 (2018)
- |downloadJuhasJac18|
-```
-Here, `|citeJuhasJac18|` is the name that can be used elsewhere in the documentation and
-the Sphinx documentation generator will replace all instances of this tag with the indented
-text following the `replace::` directive.
-
-**Important:** After defining the publication's tag as described above, make sure to add the
-publication to the list of publications maintained in [publications.rst](https://github.com/diffpy/diffpy.github.io/blob/source/publications.rst). Make sure that
-you add the reference to the proper section and do so in descending reverse chronological order
-(i.e., the newest citations should appear at the top of their respective sections).
-
-*Note:* In this example, the citation is for a publication
-which describes a product of the diffpy.cmi project (namely, PDFgetN3). For publications which
-describe a component of diffpy.cmi, we provide a link to download the publication directly from
-the [diffpy.org][site] website. Here, the link is provided via the `|downloadJuhasJac18|` tag
-which is the identifier for another snippet within [abbreviations.txt](https://github.com/diffpy/diffpy.github.io/blob/source/abbreviations.txt#L294) following the definition
-of `|citeJuhasJac18|`, seen here as:
-```
-.. |downloadJuhasJac18| image:: /images/pdficon_small.png
- :target: /doc/pdfgetx/Juhas-jac-2018.pdf
-```
-Furthermore, note that since the initial use of `|downloadJuhasJac18|` occurs within the indented text
-of the definition of `|citeJuhasJac18|`, the link to `|downloadJuhasJac18|` will appear
-everywhere `|citeJuhasJac18|` does.
-
-Lastly, make sure that the linked publication has been included within this project's files, placed in
-an appropriate directory (typically, the parent directory of the project that the paper relates to). In
-the above example, the publication covers the PDFgetN3 feature of the `pdfgetx` package, thus it is
-placed within `pdfgetx`'s documentation directory and referenced accordingly with the line
-```
- :target: /doc/pdfgetx/Juhas-jac-2018.pdf
-```
-
-
-
-### Adding Other Publications (the "Publication Using diffpy.cmi" Section)
-
-Adding references to publications that do not describe the release/use of a product within the diffpy.cmi
-project (e.g., papers which use some component of diffpy.cmi), we simply provide the usual citation text (with
-appropriate DOI link). To add a citation of this type, refer to the information in [Reference Section](#reference-section-1), but
-disregard everything starting at, and following, the [Note](#reference-section-note).
-
-
-# Publishing New Project
-
-For adding a new project to the website, see one of the existing projects (e.g., [pdfgetx](https://www.diffpy.org/products/pdfgetx.html)) as a reference.
-
-You will need to create a directory for the project to live in within (e.g., [/static_root/doc/pdfgetx](https://github.com/diffpy/diffpy.github.io/tree/source/static_root/doc/pdfgetx)), then
-write a landing page for the project (e.g., [/products/pdfgetx.rst](https://github.com/diffpy/diffpy.github.io/blob/source/products/pdfgetx.rst)) which will provide any necessary information
-or files needed for a user to use the project. Once this is complete, see
-[Publishing New Version of Existing Project](#new-version) for steps on publishing the project.
-
-
-# Publishing Changes
-
-In order to test and/or publish changes, activate a conda environment that has a working installation of Sphinx
-
-## Testing Changes
-
-With your sphinx containing env activated, run the set of Sphinx validation command(s) to check that the static
-files that Sphinx will create to be served on the website are written properly:
-```
-diffpy.github.io (source)$ make linkcheck SPHINXOPTS="-W"
-```
-*NOTE:* the `"-W"` flag forces warnings to be treated as errors. If you believe there is a falsely reported
-warning that should be ignored that is preventing the test from passing, rerun the above command with the
-`SPHINXOPTS="-W"` portion omitted. Note that on Windows this seemed to generate a number of warnings
-not seen on linux and which didn't indicate anything broken.
-
-Additionally, one can visually/user-experience validate that the changes are what is expected by running:
-```
-diffpy.github.io (source)$ make html
-```
-Then opening `/_build/html/index.html` which will open a local instance of the website with the proposed changes
-in place.
-
-
-## Maintainers (Publishing Changes)
-
-First, follow the steps outlines in [Testing Changes](#testing-changes). Note that these tests, as they currently exist, are
-not extensive and it's quite possible that something indeed may appear incorrectly on the website (hence the manual
-review portion). After reviewing the changes, have Sphinx generate the static files to be hosted on the website:
-```
-diffpy.github.io (source)$ make html
-```
-
-Note: this could not be run by successfully by simon on Git Bash. It can presumably be run from WSL?
-Prepare the changes to be published:
-```
-diffpy.github.io (source)$ make publish-prepare
-```
-
-Finally, publish the changes:
-```
-diffpy.github.io (source)$ make publish-push
-```
-
-
-
-[site]: "diffpy.org"
-[source]: "source"
-[master]: "master"
-[archive]: "archive"
diff --git a/_includes/substitutions.rst b/_includes/substitutions.rst
deleted file mode 100644
index 96287220..00000000
--- a/_includes/substitutions.rst
+++ /dev/null
@@ -1,2 +0,0 @@
-.. define global names and alias here
-.. |diffpycmi| replace:: diffpy.cmi
diff --git a/_static/.empty b/_static/.empty
deleted file mode 100644
index e69de29b..00000000
diff --git a/_static/diffpy-styles.css b/_static/diffpy-styles.css
deleted file mode 100644
index a13987f0..00000000
--- a/_static/diffpy-styles.css
+++ /dev/null
@@ -1 +0,0 @@
-/* Add CSS style overrides here */
diff --git a/_templates/layout.html b/_templates/layout.html
deleted file mode 100644
index 87639d83..00000000
--- a/_templates/layout.html
+++ /dev/null
@@ -1,5 +0,0 @@
-{# Import the theme's layout. #}
-{% extends "!layout.html" %}
-
-{# Custom CSS overrides #}
-{# placeholder, see git log this-file #}
diff --git a/_templates/menu01.html b/_templates/menu01.html
deleted file mode 100644
index 1a235d9b..00000000
--- a/_templates/menu01.html
+++ /dev/null
@@ -1,19 +0,0 @@
-
diff --git a/_templates/navbar.html b/_templates/navbar.html
deleted file mode 100644
index 3c98d0ea..00000000
--- a/_templates/navbar.html
+++ /dev/null
@@ -1,10 +0,0 @@
-{% extends "!navbar.html" %}
-
-{# disable the toc block #}
-{% block navbartoc %}
-{% endblock %}
-
-{# add menu to the extra block #}
-{% block navbarextra %}
- {% include "menu01.html" %}
-{% endblock %}
diff --git a/abbreviations.txt b/abbreviations.txt
deleted file mode 100644
index 0cab1d73..00000000
--- a/abbreviations.txt
+++ /dev/null
@@ -1,307 +0,0 @@
-.. vim: set ft=rst:
-
-.. Named web links -----------------------------------------------------
-
-.. |anaconda-download| replace:: https://www.anaconda.com/distribution
-.. _anaconda-download: https://www.anaconda.com/distribution
-.. _diffpy-users: https://groups.google.com/d/forum/diffpy-users
-.. _ctv-xpdfsuite: https://columbia.resoluteinnovation.com/technologies/M11-120
-
-.. GitHub repositories -------------------------------------------------
-
-.. _diffpy.mpdf: https://github.com/benfrandsen/diffpy.magpdf
-.. _diffpy.srfit: https://github.com/diffpy/diffpy.srfit
-.. _diffpy.srreal: https://github.com/diffpy/diffpy.srreal
-.. _diffpy.structure: https://github.com/diffpy/diffpy.structure
-.. _diffpy.utils: https://github.com/diffpy/diffpy.utils
-.. _libdiffpy: https://github.com/diffpy/libdiffpy
-.. _libobjcryst: https://github.com/diffpy/libobjcryst
-.. _pyobjcryst: https://github.com/diffpy/pyobjcryst
-.. _srfit-sasview: https://github.com/diffpy/srfit-sasview
-
-.. External online documentation ---------------------------------------
-
-.. _doc-diffpy.srfit: https://diffpy.github.io/diffpy.srfit
-.. _doc-diffpy.srreal: https://diffpy.github.io/diffpy.srreal
-.. _doc-diffpy.structure: https://diffpystructure.readthedocs.io
-.. _doc-diffpy.utils: https://diffpy.github.io/diffpy.utils
-.. _doc-libdiffpy: https://diffpy.github.io/libdiffpy
-.. _doc-pyobjcryst: https://diffpy.github.io/pyobjcryst
-
-.. Citations -----------------------------------------------------------
-
-.. |citeJuhasJac13| replace::
- P. Juhás and T. Davis, C. L. Farrow, S. J. L. Billinge, `PDFgetX3:
- A rapid and highly automatable program for processing powder
- diffraction data into total scattering pair distribution functions
- `__,
- *J. Appl. Crystallogr.* **46**, 560-566 (2013)
- |downloadJuhasJac13|
-
-.. |downloadJuhasJac13| image:: /images/pdficon_small.png
- :target: /doc/pdfgetx/Juhas-jac-2013.pdf
-
-
-.. |citeFarrowJpcm07| replace::
- C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
- Th. Proffen and S. J. L. Billinge, `PDFfit2 and PDFgui: computer
- programs for studying nanostructure in crystals
- `__,
- *J. Phys.: Condens. Mat.* **19**, 335219 (2007)
- |downloadFarrowJpcm07|
-
-.. |downloadFarrowJpcm07| image:: /images/pdficon_small.png
- :target: /doc/pdfgui/Farrow-jpcm-2007.pdf
-
-
-.. |citeProffenJac99| replace::
- 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 (1999)
- |downloadProffenJac99|
-
-.. |downloadProffenJac99| image:: /images/pdficon_small.png
- :target: /doc/pdffit/Proffen-jac-1999.pdf
-
-
-.. |DiffPyCMI| replace::
- :doc:`diffpy.cmi `
-
-.. |citeShiPRL14| replace:: Chenyang Shi, Majid Beidaghi, Michael
- Naguib, Olha Mashtalir, Yury Gogotsi, and Simon J. L. Billinge,
- |ShiPRL14title|_,
- *Phys. Rev. Lett.* **112**, 125501 (2014).
-
-.. |ShiPRL14title| replace::
- Structure of nanocrystalline Ti\ :sub:`3`\ C\ :sub:`2` MXene using
- atomic pair distribution function
-.. _ShiPRL14title: http://link.aps.org/doi/10.1103/PhysRevLett.112.125501
-
-.. |citeFarrowJac14| replace::
- Christopher L. Farrow, Chenyang Shi, Pavol Juhás, Xiaogang Peng, and
- Simon J. L. Billinge, `Robust structure and morphology parameters for
- CdS nanoparticles by combining small angle X-ray scattering and atomic
- pair distribution function data in a complex modeling framework
- `__,
- *J. Appl. Crystallogr.* **47**, 561-565 (2014).
-
-.. |citeAbeykoonArxiv14| replace::
- Milinda Abeykoon, Hefei Hu, Lijun Wu, Yimei Zhu, and Simon J. L.
- Billinge, `Calibration and data collection protocols for reliable
- lattice parameter values in electron pair distribution function (ePDF)
- studies `__, *arXiv*, 1401.1850 (2014).
-
-.. |citeChoiNanol14| replace::
- Joshua J. Choi, Xiaohao Yang, Zachariah M. Norman, Simon J. L.
- Billinge, and Jonathan S. Owen, `Structure of methylammonium lead
- iodide on mesoporous titanium dioxide: active material in high
- performance metal-organic solar cells
- `__, *Nano Lett.*
- **14**, 127 (2014).
-
-
-.. |citeJacquesNc13| replace::
- Simon D. M. Jacques, Marco Di Michiel, Simon A. J. Kimber, Xiaohao
- Yang, Robert J. Cernik, Andrew M. Beale, and Simon J. L. Billinge,
- `Pair distribution function computed tomography
- `__,
- *Nat. Commun.* **4**, 2536 (2013).
-
-
-.. |citeDavisCgd13| replace::
- Timur Davis, Matthew Johnson, and Simon J. L. Billinge, `Towards
- phase quantification at the nanoscale using the total scattering pair
- distribution function (TSPDF) method: recrystallization of cryomilled
- sulfamerazine `__,
- *Cryst. Growth Des.* **13**, 4239–4244 (2013).
-
-.. |citeYangPccp13| replace::
- Xiaohao Yang, Ahmad S. Masadeh, James R. McBride, Emil S. Bozin,
- Sandra J. Rosenthal, and Simon J. L. Billinge, `Confirmation of
- disordered structure of ultrasmall CdSe nanoparticles from X-ray
- atomic pair distribution function analysis
- `__,
- *Phys. Chem. Chem. Phys.* **15**, 8480 (2013).
-
-.. |citeFarrowJacs13| replace::
- Christopher L. Farrow, D. Kwabena Bediako, Yogesh Surendranath,
- Daniel G. Nocera, and Simon J. L. Billinge, `Intermediate-range
- structure of self-assembled cobalt-based oxygen evolving catalysts
- `__,
- *J. Am. Chem. Soc.* **135**, 6403-6406 (2013).
-
-.. |citeTyrstedAcie12| replace::
- Christoffer Tyrsted, Kirsten M. Ø. Jensen, Espen D. Bøjesen,
- Nina Lock, Mogens Christensen, Simon J. L. Billinge and Bo
- B. Iversen, `Understanding the formation and evolution of ceria
- nanoparticles under hydrothermal conditions
- `__,
- *Angew. Chem. Int. Edit.* **51**, 9030-9033 (2012).
-
-.. |citeJensenJacs12| replace::
- Kirsten M. Ø. Jensen, Mogens Christensen, Pavol Juhás, Christoffer
- Tyrsted, Espen D. Bøjesen, Nina Lock, Simon J. L. Billinge, and Bo B.
- Iversen, `Revealing the mechanisms behind SnO2 nanoparticle formation
- and growth during hydrothermal synthesis: an in situ total scattering
- study `__,
- *J. Am. Chem. Soc.* **134**, 6785 (2012).
-
-.. |citeMengqiangZhuGca12| replace::
- Mengqiang Zhu, Christopher L. Farrow, Jeffrey E. Post, Kenneth J. T.
- Livi, Simon J. L. Billinge, Matthew Ginder-Vogel and Donald L.
- Sparks, `Structural study of biotic and abiotic poorly-crystalline
- manganese oxides using atomic pair distribution function analysis
- `__,
- *Geochim. Cosmochim. Ac.* **81**, 39-55 (2012).
-
-.. |citeMengqiangZhuESTL14| replace::
- Mengqiang Zhu, Paul Northrup, Chenyang Shi, Simon J. L. Billinge,
- Donald L. Sparks and Glenn A. Waychunas,
- `The structure of sulfate adsorption complexes on ferrihydrite
- `__,
- *Environ. Sci. Technol. Lett.* **1**, 97-101 (2014).
-
-.. |citeGhidiuCC14| replace::
- Michael Ghidiu, Michael Naguib, Chenyang Shi, Olha Mashtalir, Limei
- Pan, Bo Zhang, Jian Yang, Yury Gogotsi, Simon J. L. Billinge and
- Michel W. Barsoum,
- |GhidiuCC14title|_,
- *Chem. Commun.* **50**, 9517-9520 (2014).
-
-.. |GhidiuCC14title| replace::
- Synthesis and charaterization of two-dimensional
- Nb\ :sub:`4`\ C\ :sub:`3` (MXene)
-.. _GhidiuCC14title: http://dx.doi.org/10.1039/C4CC03366C
-
-.. |citeBeecherJacs14| replace::
- Alexander N. Beecher, Xiaohao Yang, Joshua H. Palmer, Alexandra L.
- LaGrassa, Pavol Juhás, Simon J. L. Billinge and Jonathan S. Owen,
- `Atomic structures and gram scale synthesis of three tetrahedral
- quantum dots
- `__,
- *J. Am. Chem. Soc.* **136**, 10645-10653 (2014).
-
-.. |citeDoanNguyenAcsn14| replace::
- Vicky V. T. Doan-Nguyen, Simon A. J. Kimber, Diego Pontoni, Danielle
- Reifsnyder Hickey, Benjamin T. Diroll, Xiaohao Yang, Marcel
- Miglierini, Christopher B. Murray and Simon J. L. Billinge,
- `Bulk metallic glass-like scattering signal in small metallic
- nanoparticles `__,
- *ACS Nano* **8**, 6163–6170 (2014).
-
-.. |citePrillJac15| replace::
- Dragica Prill, Pavol Juhás, Martin U. Schmidt and Simon J. L.
- Billinge, `Modeling pair distribution functions (PDF) of organic
- compounds: describing both intra- and intermolecular correlation
- functions in calculated PDFs
- `__,
- *J. Appl. Crystallogr.* **48**, 171-178 (2015).
-
-.. |citeTerbanNan15| replace::
- Maxwell W. Terban, Matthew Johnson, Marco Di Michiel and Simon J. L.
- Billinge, `Detection and characterization of nanoparticles in suspension at
- low concentrations using the X-ray total scattering pair distribution
- function technique
- `__,
- *Nanoscale* **7**, 5480 (2015).
-
-.. |citeGranlundAca15| replace::
- L. Granlund, S. J. L. Billinge and P. M. Duxbury,
- `Algorithm for systematic peak extraction from atomic pair distribution
- functions
- `__,
- *Acta Crystallogr. A* **71**, 392-409 (2015).
- |downloadGranlundAca15|
-
-.. |downloadGranlundAca15| image:: /images/pdficon_small.png
- :target: /doc/srmise/Granlund-aca-2015.pdf
-
-.. |citePrillAca16| replace::
- Dragica Prill, Pavol Juhás, Simon J. L. Billinge and Martin U. Schmidt,
- `Towards solution and refinement of organic crystal structures by
- fitting to the atomic pair distribution function
- `__,
- *Acta Crystallogr. A* **72**, 62-72 (2016).
-
-.. |citeJuhasAca15| replace::
- P. Juhás, C. L. Farrow, X. Yang, K. R. Knox and S. J. L. Billinge,
- `Complex modeling: a strategy and software program for combining
- multiple information sources to solve ill posed structure and
- nanostructure inverse problems
- `__,
- *Acta Crystallogr. A* **71**, 562-568 (2015).
- |downloadJuhasJac15|
-
-.. |downloadJuhasJac15| image:: /images/pdficon_small.png
- :target: /doc/diffpy-cmi/Juhas-aca-2015.pdf
-
-.. |citeTerbanCgd16| replace::
- Maxwell W. Terban, Eugene Y. Cheung, Paul Krolikowski,
- Simon J. L. Billinge,
- `Recrystallization, phase composition, and local structure of
- amorphous lactose from the total scattering pair distribution
- function
- `__,
- *Cryst. Growth Des.* **16**, 210-220 (2016).
-
-
-.. |citeFrandsenPrl16| replace::
- Benjamin A. Frandsen, Michela Brunelli, Katharine Page,
- Yasutomo J. Uemura, Julie B. Staunton, Simon J. L. Billinge,
- |FrandsenPrl16title|_,
- *Phys. Rev. Lett.* **116**, 197204 (2016).
-
-.. |FrandsenPrl16title| replace::
- Verification of Anderson Superexchange in MnO via magnetic pair
- distribution function analysis and *ab initio* theory
-.. _FrandsenPrl16title: http://link.aps.org/doi/10.1103/PhysRevLett.116.197204
-
-
-.. |citeJensenNc16| replace::
- Kirsten M. Ø. Jensen, Pavol Juhás, Marcus A. Tofanelli,
- Christine L. Heinecke, Gavin Vaughan, Christopher J. Ackerson,
- Simon J. L. Billinge,
- |JensenNc16title|_,
- *Nat. Commun.* **7**, 11859 (2016)
-
-.. |JensenNc16title| replace::
- Polymorphism in magic-sized Au\ :sub:`144`\ (SR)\ :sub:`60` clusters
-.. _JensenNc16title: http://dx.doi.org/10.1038/ncomms11859
-
-
-.. |citeShiJac18| replace::
- C. Shi,
- `xINTERPDF: a graphical user interface for analyzing
- intermolecular pair distribution functions of organic compounds
- from X-ray total scattering data
- `__,
- *J. Appl. Crystallogr.* **51**, 1498-1499 (2018)
- |downloadShiJac18|
-
-.. |downloadShiJac18| image:: /images/pdficon_small.png
- :target: /doc/xinterpdf/Shi-jac-2018.pdf
-
-
-.. |citeJuhasJac18| replace::
- P. Juhás, J. N. Louwen, L. van Eijck, E. T. C. Vogt, S. J. L. Billinge,
- `PDFgetN3: atomic pair distribution functions from
- neutron powder diffraction data using ad hoc corrections
- `__,
- *J. Appl. Crystallogr.*, **51**, 1492--1497 (2018)
- |downloadJuhasJac18|
-
-.. |downloadJuhasJac18| image:: /images/pdficon_small.png
- :target: /doc/pdfgetx/Juhas-jac-2018.pdf
-
-
-.. |citeLiuJac20| replace::
- CH Liu, E. Janke, R. Li, P. Juhás, O. Gang, D. V. Talapin,
- S. J. L. Billinge,
- `sasPDF: pair distribution function analysis of nanoparticle assemblies
- from small-angle-scattering data
- `__.
- |downloadLiuJac20|
-
-.. |downloadLiuJac20| image:: /images/pdficon_small.png
- :target: /doc/pdfgetx/Liu-jac-2020.pdf
diff --git a/acknowledgements.rst b/acknowledgements.rst
deleted file mode 100644
index eb0b3667..00000000
--- a/acknowledgements.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-Acknowledgements
-================
-
-
-Developers
-----------
-
-The active DiffPy development team is Pavol Juhas, Long Yang, Kevin Knox,
-Xiaohao Yang, Michael McKerns, Chris Farrow, and Simon J. L. Billinge.
-Former members of the project are Emil Bozin, Wenduo Zhou, Peng Tian,
-Timur Davis, Jiwu Liu, and Dmitriy Bryndin.
-
-
-Funding
--------
-
-The DiffPy project is currently supported by Laboratory Directed
-Research and Development (LDRD) Program 12-007 (Complex Modeling) at
-Brookhaven National Laboratory (BNL). BNL is funded by the US
-Department of Energy Office of Science, Office of Basic Energy Sciences
-under contract DE-AC02-98CH10886. Previous funding for DiffPy was
-provided by the Distributed Data Analysis of Neutron Scattering
-Experiments (DANSE) project funded by the US National Science Foundation
-under award DMR-0520547. More information on DANSE can be found
-at http://danse.us. The early developments of PDFfit2 were funded by
-NSF grant DMR-0304391 in the Billinge-group, and with support from
-Michigan State University. Any opinions, findings, and conclusions or
-recommendations expressed in this material are those of the author(s)
-and do not necessarily reflect the views of the respective funding
-bodies.
-
-Additional Contributions
-------------------------
-
-The DiffPy team would like to thank multiple users for their help and
-comments during the development of this release: Dragica Podgorski,
-Valentina Felsen, and Kirsten M. Ø. Jensen.
diff --git a/static_root/bugreport/pdfgui/index.html b/bugreport/pdfgui/index.shtml
similarity index 91%
rename from static_root/bugreport/pdfgui/index.html
rename to bugreport/pdfgui/index.shtml
index 0ab3b4d5..882fad66 100644
--- a/static_root/bugreport/pdfgui/index.html
+++ b/bugreport/pdfgui/index.shtml
@@ -16,7 +16,7 @@
-