diff --git a/Makefile b/Makefile
index 22f58715..0e1ef966 100644
--- a/Makefile
+++ b/Makefile
@@ -7,6 +7,9 @@ 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/)
@@ -166,7 +169,46 @@ changes:
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/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."
diff --git a/README.md b/README.md
index f4bd14f2..a20810ef 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,160 @@
diffpy.github.io
================
-Sphinx sources for the diffpy.org web page. This repository contains 3 branches:
+Sphinx sources for the [diffpy.org][site] web page.
-1. `source` sphinx sources for the web page
-2. `master` sources compiled to HTML format that are published via GitHub pages
-3. `archive` converted subversion repository for the old diffpy.org sources
+### 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)
+- [Publishing New Version of Existing Project](#new-version)
+- [Publishing New Project](#publishing-new-project)
+- [Publishing Changes](#publishing-changes)
+ - [Testing Changes](#testing-changes)
+ - [Contributors (Submitting Changes)](#submitting-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
Please, see the [Wiki](https://github.com/diffpy/diffpy.github.io/wiki) for more
information and tips about this project.
+
+
+# Where to Make Changes
+
+## Adding Citations
+
+
+### 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 Version of Existing Project
+
+For releasing an updated version of a project, first follow the release procedure outlined in the [group wiki](https://gitlab.thebillingegroup.com/resources/group-wiki/-/wikis/Finalizing-a-Project's-(Re)-Release) for packaging and deploying your project.
+
+In what follows, [pdfgetx v2.1.1](https://github.com/diffpy/diffpy.pdfgetx/releases/tag/v2.1.1) was chosen to show example commands for the steps outlined.
+
+After following the steps necessary for releasing your project, grab the set of documentation that will be provided with the deliverable upon user's request (typically, this would be something like the files hosted by GitHub on the GitHub releases page). Create a new directory for the updated version's documentation to live in
+```
+$ mkdir diffpy.github.io/doc/pdfgetx/2.1.1
+```
+Copy the updated documentation to this directory
+```
+$ tar --directory=static_root/doc/pdfgetx/2.1.1/ \
+ --strip-components=4 \
+ -vxzf ~/Downloads/diffpy.pdfgetx-2.1.1.tar.gz \
+ diffpy.pdfgetx-2.1.1/doc/manual/_build/PDFgetXNS3_manual.pdf
+
+$ tar --directory=static_root/doc/pdfgetx/2.1.1/ \
+ --strip-components=5 \
+ --exclude=objects.inv \
+ --exclude=.buildinfo \
+ -vxzf ~/Downloads/diffpy.pdfgetx-2.1.1.tar.gz \
+ diffpy.pdfgetx-2.1.1/doc/manual/_build/html/
+
+$ cp ~/Downloads/pdfgetxn3-examples.zip static_root/doc/pdfgetx/2.1.1/
+```
+Make sure to include all relevant files (e.g., `PDFgetXNS3_manual.pdf` and `pdfgetxn3-examples.zip`), exclude any files we don't want to provide to the user (e.g., `objects.inv` and `.buildinfo` from `diffpy.pdfgetx-2.1.1.tar.gz`)
+
+Finally, edit the [landing page of your project](https://github.com/diffpy/diffpy.github.io/blob/source/products/pdfgetx.rst) (in the [`source` branch][source]) to properly 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.
+
+
+# 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 reference.
+
+In what follows in this section, you will be working within the [`source`][source] branch, unless otherwise specified.
+
+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 (or make sure you have the necessary packages installed at a system level). If unsure how to achieve this, see the [Install Sphinx](https://gitlab.thebillingegroup.com/resources/group-wiki/-/wikis/Finalizing-a-Project's-(Re)-Release#install-sphinx) section of the projecct release wiki.
+
+## Testing Changes
+
+Make sure you have an active installation of Sphinx as per [Publishing Changes](#publishing-changes), 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:
+```
+$ make Makefile 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.
+
+Additionally, one can visually/user-experience validate that the changes are what is expected by running:
+```
+$ make Makefile html
+```
+Then opening `/_build/html/index.html` which will open a local instance of the website with the proposed changes in place.
+
+
+## Contributors (Submitting Changes)
+
+In order to update the contents of [diffpy.org][site], create a new branch off of [`source`][source] in your local fork of this repo and make whatever changes you need to. Once the desired edits are complete, follow the steps outlined in [Testing Changes](#testing-changes) to verify the site won't break as a result of these changes. Finally, after verifying that the changes won't break things, push your changes to your fork and open a pull-request to submit the changes back into this repo.
+
+
+## Maintainers (Publishing Changes)
+
+First, follow the steps outlines in [Testing Changes](#testing-changes) to verify that the changes won't mess things up (too bad). 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:
+```
+$ make Makefile html
+```
+
+Prepare the changes to be published:
+```
+$ make Makefile publish-prepare
+```
+
+Finally, publish the changes:
+```
+$ make Makefile publish-push
+```
+
+
+
+[site]: "diffpy.org"
+[source]: "source"
+[master]: "master"
+[archive]: "archive"
diff --git a/abbreviations.txt b/abbreviations.txt
index 5bb38611..13453731 100644
--- a/abbreviations.txt
+++ b/abbreviations.txt
@@ -293,3 +293,15 @@
.. |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/products/pdfgetx.rst b/products/pdfgetx.rst
index bab93999..430eb54e 100644
--- a/products/pdfgetx.rst
+++ b/products/pdfgetx.rst
@@ -67,7 +67,17 @@ Sorry for the complicated process. We hope you enjoy the software!
Documentation
=============
-Version 2.1.0 - latest
+Version 2.1.1 - latest
+----------------------
+
+* `installation instructions <../doc/pdfgetx/2.1.1/install.html>`__
+* `user manual <../doc/pdfgetx/2.1.1/index.html>`__,
+ `printable manual <../doc/pdfgetx/2.1.1/PDFgetXNS3_manual.pdf>`__
+* `tutorial files <../doc/pdfgetx/2.1.1/pdfgetxn3-examples.zip>`__
+* `release notes <../doc/pdfgetx/2.1.1/release.html>`__
+
+
+Version 2.1.0
----------------------
* `installation instructions <../doc/pdfgetx/2.1.0/install.html>`__
@@ -76,6 +86,7 @@ Version 2.1.0 - latest
* `tutorial files <../doc/pdfgetx/2.1.0/pdfgetxn3-examples.zip>`__
* `release notes <../doc/pdfgetx/2.1.0/release.html>`__
+
Version 2.0.0
-------------
diff --git a/publications.rst b/publications.rst
index e2f663e4..08042c92 100644
--- a/publications.rst
+++ b/publications.rst
@@ -6,8 +6,12 @@ References
The following papers in the literature describe the DiffPy products.
Please cite us if our software has been used in your research.
+* |citeLiuJac20|
+
* |citeJuhasJac18|
+* |citeShiJac18|
+
* |citeJuhasAca15|
* |citeGranlundAca15|
diff --git a/static_root/doc/pdfgetx/2.1.1/PDFgetXNS3_manual.pdf b/static_root/doc/pdfgetx/2.1.1/PDFgetXNS3_manual.pdf
new file mode 100644
index 00000000..0055447b
Binary files /dev/null and b/static_root/doc/pdfgetx/2.1.1/PDFgetXNS3_manual.pdf differ
diff --git a/static_root/doc/pdfgetx/2.1.1/_images/nickelfqgr.png b/static_root/doc/pdfgetx/2.1.1/_images/nickelfqgr.png
new file mode 100644
index 00000000..3fbc12de
Binary files /dev/null and b/static_root/doc/pdfgetx/2.1.1/_images/nickelfqgr.png differ
diff --git a/static_root/doc/pdfgetx/2.1.1/_images/nickelfqgrnoisy.png b/static_root/doc/pdfgetx/2.1.1/_images/nickelfqgrnoisy.png
new file mode 100644
index 00000000..caab8cf3
Binary files /dev/null and b/static_root/doc/pdfgetx/2.1.1/_images/nickelfqgrnoisy.png differ
diff --git a/static_root/doc/pdfgetx/2.1.1/_images/tunenickelfqgr.png b/static_root/doc/pdfgetx/2.1.1/_images/tunenickelfqgr.png
new file mode 100644
index 00000000..14accde4
Binary files /dev/null and b/static_root/doc/pdfgetx/2.1.1/_images/tunenickelfqgr.png differ
diff --git a/static_root/doc/pdfgetx/2.1.1/_images/tunenickelt4gr.png b/static_root/doc/pdfgetx/2.1.1/_images/tunenickelt4gr.png
new file mode 100644
index 00000000..c95278cd
Binary files /dev/null and b/static_root/doc/pdfgetx/2.1.1/_images/tunenickelt4gr.png differ
diff --git a/static_root/doc/pdfgetx/2.1.1/_images/twothetazerofit.svgz b/static_root/doc/pdfgetx/2.1.1/_images/twothetazerofit.svgz
new file mode 100644
index 00000000..80e48d71
Binary files /dev/null and b/static_root/doc/pdfgetx/2.1.1/_images/twothetazerofit.svgz differ
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/files.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/files.rst.txt
new file mode 100644
index 00000000..edc63d96
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/files.rst.txt
@@ -0,0 +1,102 @@
+Files used in PDF extraction
+========================================================================
+
+.. include:: abbreviations.txt
+.. _my-configfile:
+.. program:: pdfgetx3
+
+Configuration file
+------------------------------------------------------------------------
+
+Configuration files may define the PDF processing parameters.
+By default, the :program:`pdfgetx3` program attempts to read
+:file:`.pdfgetx3.cfg` file from the user HOME directory,
+then :file:`.pdfgetx3.cfg` and :file:`pdfgetx3.cfg` files
+from the current working directory.
+If configuration file has a different name, it needs to be specified
+with the :option:`-c, --config <-c>` option.
+The :program:`pdfgetn3` program works in the same way,
+except it checks for configuration files
+:file:`~/.pdfgetn3.cfg`, :file:`.pdfgetn3.cfg` and :file:`pdfgetn3.cfg`.
+
+The easiest way of creating a configuration file is to generate
+a template content using the :option:`--createconfig` option as ::
+
+ pdfgetx3 --createconfig=test.cfg
+
+and then change the generated test.cfg file in your favorite text
+editor. The configuration file follows a simple "varname=value" syntax,
+any lines starting with "#" are ignored as comments.
+
+The configuration file has several sections marked as ``[SECTIONNAME]``.
+The ``[DEFAULT]`` section is mandatory and it contains the default
+global settings. Any other sections are optional and they are applied
+only when selected with the :option:`-s, --section <-s>` option on the
+command line. Thus ::
+
+ pdfgetx3 --config=test.cfg --section=nacl
+
+would read the parameters from the ``[nacl]`` section after reading the
+defaults. Having several sections in the configuration
+file is useful when there are multiple measurements that share most of
+the parameters, but differ in a few of them, for example in chemical
+composition. The configuration file can then contain sections per each
+sample that define only the composition, while all other parameters are
+specified just once in the global DEFAULT section.
+
+
+Input files
+------------------------------------------------------------------------
+
+PDFgetX3 and PDFgetN3 accept input powder diffraction data
+in the form of two-column text file,
+where the first column x is either the scattering angle
+|twotheta| in degrees, momentum transfer *Q* in inverse nanometers or *Q*
+in inverse ångströms. The second column y contains the corresponding
+scattered intensities normalized per unit solid angle. The actual type
+of the x-values is identified by the :confval:`dataformat` parameter.
+The input files may contain header with comments or metadata, and the
+actual data are read from the first long section of numerical values.
+
+The input files are usually passed as command-line arguments to
+:program:`pdfgetx3` or :program:`pdfgetn3` programs and must be paths
+accessible from the current working directory.
+
+Input files can be also defined by setting the :confval:`inputfile`
+value in the configuration file. The :option:`-d, --datapath <-d>`
+option can be then used to provide additional data directories to
+search for these inputs and for the :confval:`backgroundfile`.
+This is to support configuration files located in a different
+directory than the data.
+
+When the :option:`--find <-f>` option is active, the pdfgetx3 arguments
+are understood as filename patterns and the input files are found
+in the current or specified directory.
+
+
+Output files
+------------------------------------------------------------------------
+
+PDFgetX3 and PDFgetN3 can produce up to four different output data files:
+
+* .iq -- |IQ|, the background-corrected
+ intensities sampled on a regular *Q*-space grid in inverse ångströms,
+
+* .sq -- |SQ|, the total scattering structure function,
+ with intensities normalized by average scattering factors and
+ corrected by a polynomial fit,
+
+* .fq -- |FQ|, the reduced structure function equal to *Q*\ (|SQ| - 1),
+
+* .gr -- |Gr|, the resultant PDF, where the first column is the
+ separation *r* in ångströms and the second is the function *G* in
+ Å\ :sup:`-2`.
+
+You can specify what output files should be produced by setting the
+:confval:`outputtypes` parameter in the configuration file or by
+passing the :option:`-t, --outputtypes <-t>` on the command line.
+
+The header of all output files contains the parameter values that were
+used in the calculation and thus it is by itself a valid configuration
+file. When passed as an argument to the :option:`--config <-c>` option,
+the PDFgetX3 will reproduce the previous calculation.
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/index.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/index.rst.txt
new file mode 100644
index 00000000..c7bf373e
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/index.rst.txt
@@ -0,0 +1,38 @@
+.. PDFgetX3 documentation master file, created by
+ sphinx-quickstart on Tue Sep 21 18:35:11 2010.
+ You can adapt this file completely to your liking,
+ but it should at least contain the root `toctree` directive.
+
+########################################################################
+diffpy.pdfgetx
+########################################################################
+
+User manual for PDFgetX3, PDFgetN3, PDFgetS3 and Python package diffpy.pdfgetx.
+
+| Release |release|
+| |today|
+
+========================================================================
+Table of contents
+========================================================================
+
+
+.. toctree::
+ :maxdepth: 2
+
+ intro
+ install
+ quick-start
+ tutorial
+ files
+ interact
+ options
+ plotdata
+ release
+
+========================================================================
+Indices
+========================================================================
+
+* :ref:`genindex`
+* :ref:`search`
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/install.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/install.rst.txt
new file mode 100644
index 00000000..df692603
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/install.rst.txt
@@ -0,0 +1,146 @@
+Installation
+========================================================================
+
+.. include:: abbreviations.txt
+
+Software requirements
+------------------------------------------------------------------------
+
+This software is written in Python programming language, therefore
+you must have Python 3.8, 3.7, 3.6, 3.5 or 2.7 installed. In addition,
+the following third-party Python libraries are also required:
+
+* pip - Python package installer
+* setuptools - tools for installing Python packages
+* six - Python 2 and 3 compatibility library
+* NumPy - library for scientific computing with Python
+* matplotlib - Python plotting library
+* IPython - enhanced interactive Python shell
+
+Standard Python releases can be obtained from
+https://www.python.org/downloads.
+The third-party libraries can be found at the
+`Python Package Index `__
+or using any Internet search engine.
+
+Another more convenient option is to obtain one of the science-oriented
+Python distributions such as
+`Anaconda Python`_,
+`Enthought Canopy `_ or
+`PythonXY `_,
+These distributions already include all the necessary libraries, so the
+required Python software can be all installed in one step.
+
+On Linux operating systems the third-party libraries are usually
+included in a system software repository. For example on an
+Ubuntu Linux computer the software dependencies can be all installed
+with a single shell command ::
+
+ sudo apt-get install \
+ python3-pip python3-setuptools python3-six \
+ python3-numpy python3-matplotlib ipython3
+
+This may be, of course, as well accomplished using the GUI
+driven Synaptic package manager. Other Linux
+distributions may use different software management tools,
+but the names of the necessary packages should be very similar
+to those above.
+
+On Windows operating system, it may be necessary to add the
+``C:\Python37`` directory and the scripts directory
+``C:\Python37\Scripts`` to the system :envvar:`!PATH`. Some Python
+distributions already do so as a part of their installation process. The
+easiest way to check is to start the :program:`Command Prompt`, type
+there ``python`` and see if this starts the Python interpreter.
+
+Alternately, if you want to run the diffpy.pdfgetx software with a specific version of Python,
+we recommend using a virtual environment, such as ``conda``. For example, if you have Anaconda Python installed,
+you can create a conda virtual environment to install the software as follow ::
+
+ conda create --name pdfgetx_env numpy matplotlib ipython --python=3.8
+
+You can choose the name of the environment and python version as you desire. You can choose any of the
+supported Python versions. Then, activate this environment and follow the instructions in the
+next section to install the software ::
+
+ conda activate pdfgetx_env
+
+Installation
+------------------------------------------------------------------------
+
+The diffpy.pdfgetx software is distributed as a Python wheel file,
+which can be obtained from the
+`Columbia Technology Ventures
+`__.
+Once all the required software is in
+place, start the command prompt on Windows or a Unix terminal on Linux
+or Mac, navigate to the directory that contains the wheel file and
+execute the following command::
+
+ pip install ./diffpy.pdfgetx-VERSION.whl
+
+Here VERSION needs to be replaced to match the actual filename. It is
+critical that pip installer is from a supported Python version otherwise
+the program would not work. On Linux and Mac operating systems the installation may need to run with root user privileges, for example, by prepending ``sudo`` to the command line above. If root access is not available, use the ``pip install`` options :option:`!--user` or :option:`!--prefix` to install the software to a user-writable directory.
+
+The package provides three programs for PDF conversion, :program:`pdfgetx3`, :program:`pdfgetn3` and :program:`pdfgets3`. To check if they are correctly installed run ::
+
+ pdfgetx3 --version
+ pdfgetn3 --version
+ pdfgets3 --version
+
+This should display the software version, which should agree
+with the VERSION string in the wheel package name.
+The installation also includes a :program:`plotdata`
+command for an easy plotting of text data files. To verify
+if plotdata works, run the ``plotdata --version`` command.
+Finally, a comprehensive test of the installed software can
+be executed using ::
+
+ python -m diffpy.pdfgetx.tests.run
+
+.. note::
+
+ Older versions of diffpy.pdfgetx use Python egg format
+ instead of Python wheel.
+ To install these use the easy_install command as follows::
+
+ python -m easy_install ./diffpy.pdfgetx-VERSION.egg
+
+.. index:: %pdfgetx3 IPython magic
+.. index:: %pdfgetn3 IPython magic
+.. index:: %pdfgets3 IPython magic
+
+IPython magic command
+------------------------------------------------------------------------
+
+These instructions are intended for `IPython`_ users who would like to
+integrate PDFgetX3, PDFgetN3 and PDFgetS3 into their IPython environment. If
+you don't plan to customize IPython in such way you can safely skip
+this paragraph.
+
+When pdfgetx3 or pdfgetn3 or pdfgets3 is run in interactive mode, it start
+IPython interactive shell and define an extra ``%pdfgetx3``, ``%pdfgetn3`` and ``%pdfgets3`` magic commands within the IPython session. The IPython
+magic commands are not valid Python code, but work in a similar
+fashion as standard shell commands. The ``%pdfgetx3``, ``%pdfgetn3`` and ``%pdfgets3`` magics can be thus used with the same options and arguments as if run from the shell. This is useful for processing more files, while
+preserving all plots or variables that were already created
+in an IPython session.
+
+The ``%pdfgetx3``, ``%pdfgetn3`` and ``%pdfgets3`` magic commands can be defined
+permanently so they are available in all IPython sessions. To set
+this up
+
+#. find the ``profile_default/ipython_config.py`` file and open it
+ in a text editor. If that file does not exists,
+ create it first by executing ::
+
+ ipython profile create
+
+#. navigate to the paragraph that contains the
+ :py:data:`!c.InteractiveShellApp.extensions` and add there
+ the following line ::
+
+ c.InteractiveShellApp.extensions = ['diffpy.pdfgetx.ipy_magics']
+
+ There must be no leading indent, i.e., the text must start at the
+ very first column.
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/interact.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/interact.rst.txt
new file mode 100644
index 00000000..0d4fb746
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/interact.rst.txt
@@ -0,0 +1,154 @@
+Interactive mode
+========================================================================
+
+.. include:: abbreviations.txt
+.. program:: pdfgetx3
+.. py:currentmodule:: _interactive_
+
+The interactive mode is activated by using either the
+:option:`-i, --interact <-i>` option or a non-empty
+:option:`--plot <-p>` option. In the interactive mode
+the program starts an `IPython`_ interactive shell and pre-loads several
+functions and variables related to the PDF calculation. It also defines
+IPython commands ``%pdfgetx3`` and ``%pdfgetn3``, which can be used with
+the same syntax as the :program:`pdfgetx3` and :program:`pdfgetn3` in
+system shell.
+The interactive session is also initialized with all functions from the
+:py:mod:`matplotlib.pyplot` module for convenient plotting.
+The functions and variables related to PDF processing are:
+
+.. py:function:: pdfgetter(x=None, y=None, filename='', **kwargs)
+
+ Instance of the :py:class:`!PDFGetter` class which serves as a
+ low-level function that calculates the PDF. This is a callable
+ object, which takes as an argument a pair of input arrays for
+ (*Q*, intensity) or (|twotheta|, intensity) depending on
+ :confval:`dataformat`. It can be also called with a keyword
+ argument ``filename=FILE``, which would read the input arrays
+ from the specified file. When called with no arguments,
+ it calculates PDF from the last input data.
+
+ :parameters:
+ * **x** (*numpy.ndarray, optional*) --
+ The *Q* or |twotheta| values in powder diffraction pattern.
+
+ * **y** (*numpy.ndarray, optional*) --
+ The scattered intensities in powder diffraction pattern
+
+ * **filename** (*str, optional*) --
+ The text data file for loading the `x`, `y` values when
+ they are not specified.
+
+ * **kwargs** (*misc, optional*) --
+ Extra keyword arguments that are applied to
+ the :data:`!config` object, for example ``qmax=20``.
+
+ :return:
+ A pair of output arrays *(r, G)*.
+
+.. interactvar:: config
+
+ Instance of the :py:class:`!PDFConfig` class that stores the
+ :ref:`parameters and input files ` for the program.
+ Use ``print(config)`` to display the current configuration values.
+ This is the same object as :data:`!pdfgetter.config`. Configuration
+ may be changed by setting a respective attribute of the
+ :interactvar:`!config` object, for example::
+
+ In [1]: config.qmax = 21
+
+ The :py:data:`!config` values may be also changed by calling the
+ :py:func:`pdfgetter` or :py:func:`processfiles` function with a
+ corresponding keyword argument, for example
+ ``processfiles(qmax=20, force="once")``.
+
+.. interactvar:: iraw
+ iq
+ sq
+ fq
+ gr
+
+ These variables are assigned the input raw intensities and the
+ intermediate results, stored as matrix rows. The matrix rows
+ correspond to twotheta1, intensity1, twotheta2, intensity2, etc.
+ Because matrices are iterated row first, the raw intensities
+ from all input files can be plotted with the matplotlib plot
+ function as ``plot(*iraw)``.
+
+ These variables should be considered read-only and are reset
+ with subsequent PDF calculations.
+
+.. py:function:: tuneconfig(plotids=None, pdfgetter=None, axeslist=None)
+
+ Show a GUI dialog for interactive tuning of configuration variables.
+
+ :arg plotids:
+ The string or iterable that specify what interactive plots should be
+ tuned. By default the same as ``config.plot``. It can be also an
+ integer index or name of a transformation in :py:func:`pdfgetter` or
+ a reference to a :py:class:`!Transformation` object.
+
+ :arg pdfgetter:
+ The optional :py:class:`!PDFGetter` object to be tuned.
+ This is by default the interactive :py:func:`!pdfgetter` object.
+
+ :arg axeslist:
+ An optional list of matplotlib Axes for showing interactive plots.
+ When None, use ``subplot(N, 1, i)`` to create any necessary axes.
+
+ .. note::
+
+ Changes from :py:func:`!tuneconfig` apply only to the configuration
+ and results in memory. Use the :py:func:`processfiles` function
+ to save them to disk.
+
+ .. seealso:: :ref:`my-tuneconfig` tutorial
+
+.. py:function:: processfiles(filename=None, **kwargs)
+
+ Process all input files again with the current configuration values.
+ This is a higher-level function than :py:func:`pdfgetter`, as
+ it also saves output files and produces plots as specified by the
+ :interactvar:`config` object.
+
+ :arg filename:
+ One or more input files to be converted to PDFs and saved or
+ plotted according to the :py:data:`!config` settings. Use the
+ previous list of input files when not specified.
+
+ :arg kwargs:
+ An optional keyword arguments to set for the :py:data:`!config`
+ object, for example ``(force="once", qmax=18)``.
+
+ This function updates the :interactvar:`config.inputfiles `
+ list and the :interactvar:`iraw`, :interactvar:`iq`,
+ :interactvar:`sq`, :interactvar:`fq` and :interactvar:`gr`
+ interactive variables.
+
+.. py:function:: clearsession()
+
+ Clear all elements from the :interactvar:`config.inputfiles `
+ and also the
+ :interactvar:`iraw`, :interactvar:`iq`, :interactvar:`sq`,
+ :interactvar:`fq` and :interactvar:`gr` variables.
+
+ :return:
+ No return value.
+
+.. py:currentmodule:: diffpy.pdfgetx
+.. autofunction:: loaddata
+
+ This function can be imported from the
+ :py:mod:`!diffpy.pdfgetx` module.
+
+.. py:currentmodule:: diffpy.pdfgetx.plotdata
+.. autofunction:: plotdata
+
+ This function can be imported from the
+ :py:mod:`!diffpy.pdfgetx.plotdata` module.
+
+.. py:currentmodule:: diffpy.pdfgetx
+.. autofunction:: findfiles
+
+ This function can be imported from the
+ :py:mod:`!diffpy.pdfgetx` module.
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/intro.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/intro.rst.txt
new file mode 100644
index 00000000..a112ee9a
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/intro.rst.txt
@@ -0,0 +1,70 @@
+Introduction
+========================================================================
+
+diffpy.pdfgetx is a simple yet powerful software for converting X-ray or
+neutron powder diffraction data to atomic Pair Distribution Functions
+(PDFs). In addition, it also allows the extraction of PDFs from small-angle
+scattering (SAS) data. The software includes three command line programs
+PDFgetX3, PDFgetN3 and PDFgetS3 for processing X-ray,
+constant-wavelength neutron and small-angle diffraction data
+respectively. PDFgetX3, PDFgetN3 and PDFgetS3 can be used in a batch
+mode to convert a series of data files without user intervention. The
+programs can be also run in an interactive mode that allows to control
+process parameters and plot the PDFs and any intermediate results. Users
+can interactively tune the PDF processing parameters, visualize their effect on the results and adjust them to their optimum values. The programs are bundled with Python library diffpy.pdfgetx for PDF processing functions, which can be used in custom Python scripts.
+
+
+.. index:: license
+
+License notice
+------------------------------------------------------------------------
+
+.. include:: ../../LICENSENOTICE.txt
+
+
+.. index:: authors
+
+Authors
+------------------------------------------------------------------------
+
+This code was written by members of the Billinge Group at
+Columbia University and Brookhaven National Laboratory including
+Pavol Juhás,
+Timur Davis,
+Chia-Hao (Timothy) Liu,
+Christopher Wright,
+Christopher Farrow,
+Hung Vuong,
+Songsheng Tao,
+Simon Billinge.
+
+
+.. index:: citations, references
+
+References
+------------------------------------------------------------------------
+
+If you use this program for a scientific research that leads
+to publication, we ask that you acknowledge use of the program
+by citing the following paper in your publication:
+
+ 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)
+
+For research publications that use this software to process neutron
+diffraction data we ask you to also cite:
+
+ 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** (2018)
+
+For research publications utilising the sasPDF utility, PDFGetS3, we ask you to acknowledge the use of the program by citing following paper in your publication:
+
+ 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 `__.
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/options.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/options.rst.txt
new file mode 100644
index 00000000..c02220f2
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/options.rst.txt
@@ -0,0 +1,370 @@
+Options and parameters
+========================================================================
+
+.. include:: abbreviations.txt
+.. program:: pdfgetx3
+
+PDFgetX3, PDFgetN3 and PDFgetS3 are very flexible in allowing users to customize
+the actions of the program. They have a number of parameters that can
+be specified either in configuration file or as command line options.
+Here is a complete description of the parameters and options used by
+either program.
+
+
+.. Note ::
+
+ The command line options start with a leading "-" and can
+ be only used as command line arguments when starting the
+ :program:`pdfgetx3` program. Within configuration file the parameter
+ names are plain words without any leading dashes. Finally,
+ parameters can be also set in the interactive mode as attributes of
+ the :interactvar:`config` object, but the assignments must be valid
+ Python statements. Here are examples of setting composition of
+ a processed specimen using each of these forms:
+
+ #. assigned in configuration file::
+
+ ...
+ composition = CaTiO3
+ ...
+
+ #. set as a command-line option when starting :program:`pdfgetx3` or
+ :program:`pdfgetn3`::
+
+ pdfgetx3 --composition=CaTiO3
+
+ #. set in the IPython interactive mode::
+
+ pdfgetx3 -i
+ ...
+ In [1]: config.composition = "CaTiO3"
+
+
+Program operation
+------------------------------------------------------------------------
+
+.. option:: -h, --help
+
+ Display a brief usage information with a list of command line options
+ and exit.
+
+.. option:: -V, --version
+
+ Display the program version and exit.
+
+.. option:: --manual
+
+ Open this manual in a Web browser and exit.
+
+.. option:: -f, --find
+.. _my-findpatterns:
+
+ Select input files that match all patterns. The command
+ line arguments are by default taken as input files. However,
+ with the :option:`!--find` option they are processed as
+ file patterns and the matching files are then used as inputs.
+ The input files are by default searched in the current directory
+ unless there is a path entry (e.g., :file:`data/`) that
+ selects a different search path. The search patterns are
+ interpreted as fixed strings, all of which must be present
+ in the file name. A single argument ``+`` starts
+ a new group of patterns to match more files that are not
+ covered by one set of patterns. Additional pattern
+ groups reuse the current search path unless they provide
+ their own path value. Pattern groups containing only
+ a path entry reuse file patterns from the last group.
+ When pattern groups overlap the repeated matches are ignored
+ to make the resulting list of files unique. Files starting
+ with ``.`` are ignored unless there is ``^.`` pattern
+ that explicitly matches them. The search
+ syntax provides the following special patterns:
+
+ .. tabularcolumns:: |l|p{0.75\textwidth}|
+
+ +---------+------------------------------------------------------------+
+ | ^ | match at the beginning of the string, i.e., ``^start`` |
+ | | matches only filenames that start with "start". |
+ +---------+------------------------------------------------------------+
+ | $ | match at the end of string, for example, ``.chi$`` selects |
+ | | file names ending with ".chi". A ``$`` on its own |
+ | | matches every string and can be used to select all files. |
+ +---------+------------------------------------------------------------+
+ | | match number *N* preceded by any number of leading zeros, |
+ | | e.g., ``<7>`` would match in "f7.chi", "f007.chi", but not |
+ | | in "f77.chi". |
+ +---------+------------------------------------------------------------+
+ | | match an integer range from *N* to *M* inclusive. |
+ | | The matched number may have one or more leading zeros. |
+ +---------+------------------------------------------------------------+
+ | <7-> | match number 7 or larger. |
+ +---------+------------------------------------------------------------+
+ | <-7> | match number 7 or smaller. |
+ +---------+------------------------------------------------------------+
+ | <-> | match any integer number. |
+ +---------+------------------------------------------------------------+
+ | \+ | start a new pattern group, for example, ``.chi$ + .dat$`` |
+ +---------+------------------------------------------------------------+
+ | / | set search path. An argument containing the ``/`` symbol |
+ | | is taken as the search path, for example, ``data/`` or |
+ | | ``./``. Each pattern group may provide its own search |
+ | | path effective for that and any subsequent pattern group. |
+ +---------+------------------------------------------------------------+
+
+ The ``^$<>`` characters are often special to Unix or Windows
+ command shells, therefore they need to be enclosed in double
+ quotes (\\") when used on command line.
+
+ .. seealso:: tutorial on :ref:`my-findexamples`
+
+.. option:: -l, --list
+
+ List all input files and exit. This is useful with the
+ :option:`!--find` option to verify if input files
+ are matched as intended.
+
+
+Configuration file options
+------------------------------------------------------------------------
+
+.. option:: -c CONFIG, --config=CONFIG
+
+ Read custom configuration file after loading the default ones.
+ Do not load any configuration file when "NONE".
+
+.. option:: -s NAME, --section=NAME
+
+ Load the custom configuration file section ``[SectionName]`` after
+ loading the ``[DEFAULT]`` section. This is useful for creating
+ several configuration variants in a single configuration file.
+
+.. option:: --createconfig=FILE
+
+ Write template configuration to a new FILE and exit. Write
+ to the standard output when FILE is "-".
+
+See also the :ref:`configuration file ` section
+for further details.
+
+.. _my-ioparameters:
+
+Input and output options
+------------------------------------------------------------------------
+
+.. confval:: inputfile
+
+ This parameter allows to specify one or more input files in the
+ configuration file, one file per line. The :confval:`!inputfile`
+ is only used if no input files were provided on the
+ :program:`pdfgetx3` or :program:`pdfgetn3` command line.
+
+.. confval:: dataformat
+.. option:: --format=FORMAT
+
+ Format of input files. Available formats are: ``twotheta``, ``QA``,
+ ``Qnm`` corresponding to a two-column text data where the first
+ column is either the scattering angle |twotheta| in degrees, *Q* in
+ inverse ångströms or *Q* in inverse nanometers.
+
+.. confval:: backgroundfile
+.. option:: -b FILE, --background=FILE
+
+ Optional datafile with background intensities from an empty sample
+ holder. It must be in the same dataformat as other input files.
+
+.. Note ::
+
+ The following input is only used in ``sas`` mode.
+
+.. confval:: formfactorfile
+.. option:: -ff FILE, --formfactorfile=FILE
+
+ Form factor intensities of the scatterers. This is required for ``sas`` mode. The form factor file is expected to be in two-column format with (Q, f2avg) data or three-column format with (Q, f2avg, favg2) data. The unit of Q is required to be A^-1.
+
+.. _my-datapath:
+.. confval:: datapath
+.. option:: -d DATAPATH, --datapath=DATAPATH
+
+ One or more extra directories to be searched for input or
+ background data files. The :option:`!-d` option can be specified
+ several times to add more directories, these are prepended in front
+ of any default value. Within configuration file the datapath
+ directories have to be listed each on a separate line.
+
+ A special value "NONE" (or "none") clears any previously defined
+ paths and only the further paths, if any, would be searched for
+ inputs.
+
+.. confval:: output
+.. option:: -o OUTPUT, --output=OUTPUT
+
+ Output file name, write to the standard output when "-". The
+ :option:`-t, --outputtypes <-t>` option controls what results are
+ being saved. Normally the OUTPUT is used as a custom basename for
+ the output files. The OUTPUT may contain @f, @h, @r, @e, @t, @b, @o
+ tokens, which are expanded as follows:
+
+ ===== ================== =======================================
+ token example definition
+ ===== ================== =======================================
+ @h dir1/dir2 the input file directory or "."
+ @r dir1/dir2/filename the input path with extension removed
+ @e dat the input file extension without "."
+ @t filename.dat the tail component of the input file
+ @b filename the tail component with extension removed
+ @o gr the output extension iq, sq, fq or gr
+ ===== ================== =======================================
+
+ An empty value works the same as "@b.@o" and saves the data
+ in the current directory with a proper extension for the
+ saved results. When "@o" is not present in the OUTPUT, it is
+ appended as a default filename extension.
+
+.. confval:: outputtypes
+.. option:: -t TYPES, --outputtypes=TYPES
+
+ Result types to be saved, one or more comma separated values.
+ Supported values are "iq", "sq", "fq", "gr", corresponding to the
+ |IQ|, |SQ|, |FQ| and |Gr| curves; these are also used as output
+ file extensions.
+
+ Result files are not written when empty, "none" or "NONE".
+
+.. confval:: force
+.. option:: --force=FORCE
+
+ Overwrite existing output files. By default the output
+ files are not written if they already exist. Possible values
+ in a configuration file are "true", "yes", "on", "1" or
+ "false", "no", "off", "0" or "once". The special value "once"
+ permits one overwrite and then resets ``config.force`` to
+ ``False``. Note that in interactive mode the values assigned
+ to ``config.force`` are converted to Python :py:class:`bool`
+ unless equal to "once".
+
+
+.. _my-pdfparameters:
+
+PDF parameters
+------------------------------------------------------------------------
+
+
+.. confval:: mode
+.. option:: --mode=STRING
+
+ The PDF conversion mode, i.e., the name of the
+ :py:func:`.pdfgetter` setup. The available modes correspond
+ to the radiation type used in powder diffraction experiment and can
+ be "xray" or "neutron".
+
+.. confval:: wavelength
+.. option:: -w FLOAT, --wavelength=FLOAT
+
+ X-ray wavelength in ångströms. This value is required
+ for the "twotheta" dataformat in order to convert the scattering
+ angles |twotheta| to a momentum transfer *Q*. For other data formats
+ the wavelength is not necessary and may be left undefined.
+
+.. confval:: twothetazero
+.. option:: --twothetazero=FLOAT
+
+ Position of the zero scattering angle in diffractometer degrees.
+ This parameter corrects for a constant offset in the
+ measured |twotheta| values. When loading configuration file
+ it is assumed 0 unless specified otherwise. This parameter
+ is only effective for the "twotheta" dataformat.
+
+.. confval:: composition
+.. option:: --composition=STRING
+
+ Chemical composition of the sample. Supported formats are
+ "PbTi0.5Zr0.5O3", "Pb 1 Ti 1/2 Zr 1/2 O 3" or "CH3 (CH2)3 OH".
+ Space characters are ignored, unit counts can be omitted, but it is
+ important to use a proper upper and lower case in atom symbols.
+ Elements can appear several times in the formula, e.g., "CH3 CH3",
+ and the formula may contain parentheses or fractional
+ stoichiometries.
+
+.. confval:: bgscale
+.. option:: --bgscale=FLOAT
+
+ Scaling of the background intensities loaded from the
+ :confval:`backgroundfile`, by default 1.
+
+.. confval:: rpoly
+.. option:: --rpoly=FLOAT
+
+ *r*-limit for the maximum frequency in the |FQ| correction polynomial.
+ The PDF is unreliable at shorter *r*, however a
+ very small :confval:`!rpoly` would disable polynomial correction and
+ give noisy PDF.
+ Larger values produce closer fits with a higher degree polynomial,
+ but when too large, they might smooth-out a useful signal in the
+ data. The default is 0.9.
+
+.. confval:: qmaxinst
+.. option:: --qmaxinst
+
+ The *Q* cutoff for the meaningful input intensities in inverse
+ ångströms. Some data files may contain trailing zeros
+ or unreliable intensities at the upper bound of the detector range.
+ The :confval:`!qmaxinst` defines a threshold for unreliable data.
+ The parameter is also used as an upper boundary for the polynomial
+ fit correction of the |SQ| data.
+
+.. confval:: qmin
+.. option:: --qmin
+
+ The lower *Q*-limit for the Fourier transformation of the |FQ| curve
+ in inverse ångströms.
+
+.. confval:: qmax
+.. option:: --qmax
+
+ The upper *Q*-limit for the Fourier transformation of the |FQ| curve
+ in inverse ångströms. This is essentially a limit, where sample
+ signal decays to the level of data noise.
+
+.. confval:: rmin
+.. option:: --rmin=FLOAT
+
+ Lower bound of the *r*-grid for the calculated PDF in ångströms.
+
+.. confval:: rmax
+.. option:: --rmax=FLOAT
+
+ Upper bound of the *r*-grid for the calculated PDF in ångströms.
+
+.. confval:: rstep
+.. option:: --rstep=FLOAT
+
+ Spacing of the *r*-grid for the calculated PDF in ångströms.
+
+
+Other parameters
+------------------------------------------------------------------------
+
+.. confval:: plot
+.. option:: -p TYPES, --plot=TYPES
+
+ Plot the specified results. A comma separated list with one or
+ more items from "iq", "sq", "fq", "gr". No plot is produced when
+ empty, "none" or "NONE". Setting this option turns on the
+ interactive mode.
+
+.. confval:: interact
+.. option:: -i, --interact
+
+ Start an IPython interactive session after processing all files.
+ Useful for tuning the configuration parameters or interactive
+ plotting. This is always on when plot option has been set.
+ See also :doc:`interact` for further details.
+
+.. confval:: verbose
+.. option:: --verbose=VALUE
+
+ Level of detail for the program to report about its actions.
+ Possible values are "error", "warning", "info", "debug", "all" or an
+ integer number from 0 to 5. Messages are completely suppressed when
+ 0, all messages are printed when verbose is 5 ("all") or higher.
+ This option is useful for diagnostics of any unexpected behavior
+ in the program.
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/plotdata.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/plotdata.rst.txt
new file mode 100644
index 00000000..d1c02156
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/plotdata.rst.txt
@@ -0,0 +1,161 @@
+.. index:: plotdata (program)
+.. _cmd-plotdata:
+
+The plotdata program
+========================================================================
+
+.. include:: abbreviations.txt
+.. program:: plotdata
+
+The PDFgetX3 software includes a simple stand-alone utility
+:program:`plotdata` for plotting text data files. In most cases
+this program can be invoked from a command-shell as ::
+
+ plotdata file1.dat file2.dat
+
+which plots the numerical data from the text files :file:`file1.dat`,
+:file:`file2.dat` together in a single graph. By default the first
+column is used as an *x* variable and the second column is used for the
+*y* values. After displaying the plot the program starts an `IPython`_
+interactive session allowing the user to modify or save plots. The
+IPython session is initialized with the :data:`!filenames` variable
+containing a list of plotted files. It also pre-loads the
+|plotdata| and |findfiles| functions just as in PDFgetX3
+interactive session. The :py:func:`!plotdata`
+function works in a similar way as the :program:`plotdata` program,
+just its arguments need to be passed as Python function arguments
+instead of command-line options. Thus an equivalent call of the
+:py:func:`!plotdata` function would be::
+
+ In [1]: plotdata(['file1.dat', 'file2.dat'])
+
+
+Selecting files
+------------------------------------------------------------------------
+
+The :program:`plotdata` program includes a file searching feature
+that is useful for selecting a set of files in large
+directories. It is also convenient for Windows operating systems,
+where the command prompt cannot do filename expansion for patterns
+such as ``*.dat``. The file search feature is controlled by the
+following options:
+
+.. option:: -f, --find
+
+ Use command line arguments as filename patterns and plot all matching
+ files. This option works in the same way as for
+ :program:`pdfgetx3`, for full details see the
+ :option:`pdfgetx3 --find ` documentation. Note that
+ within command line the special patterns ``^$<>`` need to be quoted
+ in double quotes (\\") so they are not processed by command shell.
+
+.. option:: -l, --list
+
+ List the input files and exit. This is useful in conjunction
+ with the :option:`!-f, --find` option to check if data files
+ are selected as intended.
+
+Assuming the current directory contains 20 files named
+:file:`file1.dat`, :file:`file2.dat`, ..., :file:`file20.dat`,
+the plotting of files 9 to 13 could be done (with a check listing)
+as follows ::
+
+ $ plotdata -fl "<9-13>.dat"
+ file9.dat
+ file10.dat
+ file11.dat
+ file12.dat
+ file13.dat
+ $ plotdata -f "<9-13>.dat"
+
+Within an interactive IPython session the equivalent plot could be
+produced by combining the |plotdata| and |findfiles| functions as ::
+
+ In [1]: plotdata(findfiles("<9-13>.dat"))
+
+
+Selecting x and y data
+------------------------------------------------------------------------
+
+The :program:`plotdata` program provides several ways of selecting
+columns for *x* or *y* data and for specifying plot markers or line
+formats. The columns can be specified using their integer index,
+but one needs to keep in mind the index of the first column is "0"
+as per Python indexing conventions. Here is a list of options
+supported by the plotdata program (and function):
+
+
+.. option:: -x X
+
+ index or name of the *x*-column to plot. See the :option:`-y` option
+ for the supported syntax, but note that ``X`` may select only one
+ column. When set to "." use the data-row index for *x*.
+
+.. option:: -y Y
+
+ index or name of the *y*-column or columns to plot. The ``Y`` column
+ specification can be a comma separated list of indices, column names
+ or Python-like ranges, for example "1,2", "G", "1:4" (START:STOP,
+ same as "1,2,3"), "1:4:2" (START:STOP:STEP, same as "1,3"), or
+ "-2:" (same as "-2,-1", i.e, the last 2 columns). Because column
+ indexing starts at "0" the second column must be specified as "1".
+
+ The column names work if the data section in the file is preceded by
+ a headline of unique column names, for example::
+
+ x square cube
+ 1 1 1
+ 2 4 8
+ 3 9 27
+ 4 16 64
+
+ For such data file the plotdata program will recognize column names
+ "x", "square" and "cube" and an implicit "." for row index.
+
+.. option:: -s STYLE, --style=STYLE
+
+ optional plot format specification. See the
+ :func:`matplotlib.pyplot.plot` function
+ for a list of available formats.
+
+.. option:: -L LOG, --log=LOG
+
+ axes to be plotted with logarithmic scaling, for example, "x", "y" or
+ "xy". Axes not listed in ``LOG`` will use linear scaling.
+
+.. option:: -h, --help
+
+ display a brief usage info and exit.
+
+.. option:: -V, --version
+
+ show program version and exit.
+
+.. option:: --manual
+
+ Open this manual page in a Web browser and exit.
+
+
+Examples
+------------------------------------------------------------------------
+
+The examples directory :file:`plotdata` contains a :file:`sincos.dat`
+file that has 3-columns of values labeled as "x", "sin" and "cos".
+Here are several examples of the :program:`plotdata` capabilities
+when used from command line - the user is encouraged to try them out::
+
+ plotdata sincos.dat
+ plotdata -y 1,2 sincos.dat
+ plotdata -x . -y 0:3 sincos.dat
+ plotdata -y cos sincos.dat
+ plotdata -x sin -y cos -sr-- sincos.dat
+
+An equivalent usage from a general IPython session would be::
+
+ ipython --matplotlib=auto
+ In [1]: from diffpy.pdfgetx.plotdata import plotdata
+ In [2]: plotdata('sincos.dat')
+ In [3]: plotdata('sincos.dat', y=[1,2])
+ In [4]: plotdata('sincos.dat', x='.', y=':3')
+ In [5]: plotdata('sincos.dat', y='cos')
+ In [6]: plotdata('sincos.dat', x='sin', y='cos', style='r--')
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/quick-start.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/quick-start.rst.txt
new file mode 100644
index 00000000..0b2fffd1
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/quick-start.rst.txt
@@ -0,0 +1,163 @@
+Quick-start guide
+========================================================================
+
+.. include:: abbreviations.txt
+.. program:: pdfgetx3
+
+This guide assumes that the software has been correctly installed and
+its command line programs PDFgetX3, PDFgetN3 and PDFgetS3 can be
+executed by typing :program:`pdfgetx3`, :program:`pdfgetn3`, or
+:program:`pdfgets3` in a shell window. Please, refer to the :doc:`installation ` section if this is not working yet.
+
+.. index:: pdfgetx3 (program)
+.. _cmd-pdfgetx3:
+
+pdfgetx3 command
+------------------------------------------------------------------------
+
+The pdfgetx3 program is a command-line application, therefore all
+the input files and run-parameters are supplied either as command-line
+arguments or through a configuration file. In general, the pdfgetx3 is
+executed from a command shell as ::
+
+ pdfgetx3 [options] input1 input2 ... inputN
+
+The :file:`inputN` stands for an input powder diffraction data. The
+:file:`inputN` file is a simple two-column text file, where the first
+column corresponds to either the |twotheta| diffraction angle, or a
+momentum transfer, *Q*, in inverse nanometer or inverse ångström units.
+The second column contains the corresponding X-ray intensities. The
+input file may start with a header containing comments or metadata
+related to the measurement. PDFgetX3 will ignore any text leading to a
+long two-column section. The example input files in this manual were
+created with the
+`FIT2D program `_ using
+its "chi" output format, thus we will also refer to them as "chi-files".
+A typical content of a "chi" file looks as folows:
+
+.. code-block:: none
+
+ Pt_bulk-00055.tif: 2-theta Scan
+ 2-Theta Angle (Degrees)
+
+ 1465
+ 2.0003892E-02 0.0000000E+00
+ 6.0011677E-02 0.0000000E+00
+ 1.0001946E-01 0.0000000E+00
+ 1.4002724E-01 0.0000000E+00
+ 1.8003502E-01 0.0000000E+00
+ ...
+
+The command-line options are arguments that start with a dash "-" and
+are used to specify run-parameters or modify the program behavior. The
+options can be specified in a short form that consists of a dash and
+a single character, or in a long, more descriptive format starting with
+a doubled dash ``--``. Options may require values. For short options,
+the value may be joined to the option string, for example
+:option:`!-w0.142774`, while for the long options it has to be separated
+with an equal sign, e.g., :option:`!--wavelength=0.142774`. Although
+all the PDF calculation parameters can be passed as command line
+options, it is often more convenient to set them in a configuration
+file. When run parameter is present both in a configuration file and
+as command-line option, the command-line value takes precedence. The
+command-line options are all described in the :doc:`options` section of
+this manual. A brief summary of options can be also displayed by
+executing ::
+
+ pdfgetx3 --help
+
+The best way of getting familiar with PDFgetX3 is to process
+the example diffraction data described in the :doc:`tutorial`.
+In general, the first step is to create a commented configuration file ``pdfgetx3.cfg`` using::
+
+ pdfgetx3 --createconfig=pdfgetx3.cfg
+
+The configuration file can have any name, but it is preferable
+to use either :file:`pdfgetx3.cfg` or :file:`.pdfgetx3.cfg`,
+for these files are automatically loaded by PDFgetX3. All
+other configuration files must be passed explicitly to the program
+using the :option:`-c, --config <-c>` option.
+
+Open the pdfgetx3.cfg file in a **text** editor. The lines that
+start with a hash mark ``#`` are comments and are not used. The lines
+starting with a right brace ``[`` denote sections in the configuration
+file. The active lines are all formatted as
+"NAME=VALUE". Although PDFgetX3 has many options, in general only a few
+of them are critical for the PDF calculation:
+
+* :confval:`dataformat` -- specifies the input data format
+
+* :confval:`wavelength` -- radiation wavelength in Å required for the
+ "twotheta" format.
+
+* :confval:`composition` -- chemical composition of the sample
+
+* :confval:`qmaxinst` -- upper *Q* boundary for a meaningful measurement
+ intensities.
+
+* :confval:`qmax` -- *Q*-cutoff for the Fourier transformation that
+ yields the PDF.
+
+Save the updated configuration file and run pdfgetx3 on the input data
+:file:`FILENAME.chi` as ::
+
+ pdfgetx3 --verbose=info -t gr FILENAME.chi
+
+Here the :option:`--verbose=info <--verbose>` option makes pdfgetx3
+print
+more information about its operation. This helps to verify
+if the configuration file is indeed loaded and if the parameter
+values are assigned as intended. The PDFgetX3 will not write
+any output files unless told so. The :option:`-t gr <-t>` option
+tells the program to save the final |Gr| curve as a
+:file:`FILENAME.gr` file in the working directory.
+
+The saved .gr file contains a header with all the calculation
+parameters and the input file name. The .gr file can be therefore
+also used as a configuration file in order to redo the same
+calculation ::
+
+ pdfgetx3 -c FILENAME.gr --plot=fq,gr
+
+Note this command does not include any .chi file and this will as
+a result process the previously used input :file:`FILENAME.chi`.
+The :option:`--plot=fq,gr <-p>` option tells PDFgetX3 to
+display 2 plots for the reduced structure function |FQ| and the
+final PDF |Gr|. The :option:`!--plot` option also implies an
+:doc:`interactive mode `
+therefore the program does not exit, but starts an
+interactive `IPython`_ session. To exit the interactive mode,
+type ``exit()`` and press Enter.
+
+.. index:: pdfgetn3 (program)
+.. _cmd-pdfgetn3:
+
+pdfgetn3 command
+------------------------------------------------------------------------
+
+The pdfgetx3 and pdfgetn3 programs operate in a very similar fashion
+apart from being set to assume X-ray and neutron data respectively.
+The type of the scattering data can be also specified using the
+:option:`--mode` option. Running ``pdfgetn3`` is nearly identical
+to executing ``pdfgetx3 --mode=neutron``. The only difference between
+these commands is that pdfgetx3 checks for configuration files
+:file:`pdfgetx3.cfg` and :file:`.pdfgetx3.cfg`, whereas
+pdfgetn3 looks for :file:`pdfgetn3.cfg` and :file:`.pdfgetn3.cfg`.
+
+.. index:: pdfgets3 (program)
+.. _cmd-pdfgets3:
+
+pdfgets3 command
+------------------------------------------------------------------------
+
+The pdfgets3 program is virtually the same as its counterparts for x-ray
+(pdfgetx3) and neutron (pdfgetn3) diffraction data. The only difference
+is that instead of referencing the well documented x-ray or neutron
+scattering form factor data, a user-defined form factor data is used
+for getting the PDF from a small-angle scattering (SAS) data. This
+behavior is enabled by specifying ``mode = sas`` in the configuration
+file or in the command line tool. The pdfgets3 program by default
+searches for a configuration named :file:`pdfgets3.cfg` and
+:file:`.pdfgets3.cfg` in order, when no configuration file is specified.
+
+Please refer to the :doc:`tutorial section ` for a step-by-step processing of the example data files and for demonstration of the capabilities in PDFgetX3, PDFgetN3 and PDFgetS3.
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/release.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/release.rst.txt
new file mode 100644
index 00000000..7ede93fa
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/release.rst.txt
@@ -0,0 +1,3 @@
+.. index:: release notes
+
+.. mdinclude:: ../../CHANGELOG.md
diff --git a/static_root/doc/pdfgetx/2.1.1/_sources/tutorial.rst.txt b/static_root/doc/pdfgetx/2.1.1/_sources/tutorial.rst.txt
new file mode 100644
index 00000000..af6ef5db
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_sources/tutorial.rst.txt
@@ -0,0 +1,744 @@
+Tutorial
+========================================================================
+
+.. include:: abbreviations.txt
+.. program:: pdfgetx3
+.. index:: example files
+.. py:currentmodule:: diffpy.pdfgetx
+
+In this tutorial we will convert several X-ray powder diffraction
+patterns to corresponding PDFs. Open a terminal on a Unix-based system
+or a Command Prompt on Windows and navigate to the :file:`examples`
+folder included with the PDFgetX3 distribution. The :file:`examples`
+folder can be found in the parent "doc" directory relative to this
+document or another option is to just search your file system for
+one of the input files mentioned below.
+The example files are also available at
+|zipped-examples|.
+
+
+.. index:: examples
+
+Nickel X-ray PDF
+------------------------------------------------------------------------
+
+predefined configuration file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+Change to the :file:`Ni` directory. The file named
+:file:`ni300mesh_300k_nor_1-5.chi` contains powder X-ray data
+measured from nickel at the Advanced Photon Source beamline
+6ID-D. The file contains two columns for the |twotheta| scattering
+angles and X-ray intensities. The second file
+:file:`kapton_bgrd_300k_nor_2-3.chi` contains the background
+measurement, i.e., the intensities from an empty capillary.
+Finally, the :file:`pdfgetx3.cfg` contains a complete configuration
+parameters for converting the powder pattern to a PDF. Since all
+processing parameters are already defined in the configuration file,
+the first PDF calculation is very simple and involves running the
+:ref:`pdfgetx3 ` program
+with the powder data file as an argument::
+
+ $ pdfgetx3 ni300mesh_300k_nor_1-5.chi
+
+For the first run there should be no output on the screen,
+however a new file, :file:`ni300mesh_300k_nor_1-5.gr` should appear
+in the work directory.
+We can use the :ref:`plotdata ` program,
+included with this software, to plot the output data::
+
+ $ plotdata ni300mesh_300k_nor_1-5.gr
+
+This will open a graph window and start an `IPython`_ interactive session.
+To exit and close the figure, type ``exit()`` on the IPython prompt.
+Let's run the program again, but now with a
+:option:`--verbose=info <--verbose>`
+option, to show more details about the program actions. ::
+
+ $ pdfgetx3 --verbose=info ni300mesh_300k_nor_1-5.chi
+
+ INFO:applying pdfgetx3 defaults
+ INFO:set config.mode = xray
+ INFO:searching for default config file /home/user/.pdfgetx3.cfg
+ INFO:searching for default config file .pdfgetx3.cfg
+ INFO:searching for default config file pdfgetx3.cfg
+ INFO:loaded default config file pdfgetx3.cfg
+ INFO:reset config.twothetazero = 0.0
+ INFO:parsing config file section [DEFAULT]
+ INFO:set config.dataformat = twotheta
+ INFO:set config.backgroundfile = kapton_bgrd_300k_nor_2-3.chi
+ INFO:set config.outputtypes = gr
+ INFO:set config.wavelength = 0.142774
+ INFO:set config.composition = Ni
+ INFO:set config.qmaxinst = 26.5
+ INFO:set config.qmax = 26.0
+ INFO:set config.rmin = 0.0
+ INFO:set config.rmax = 30.0
+ INFO:set config.rstep = 0.01
+ INFO:finished parsing config file
+ INFO:processing command line options
+ INFO:set config.verbose = info
+ INFO:finished with command line options
+ INFO:using 1 input files from the command line.
+ INFO:configuring PDFGetter mode 'xray'
+ INFO:calling config_xray
+ INFO:started PDF processing.
+ INFO:processing 'ni300mesh_300k_nor_1-5.chi'
+ INFO:resolved output file '' as 'ni300mesh_300k_nor_1-5.gr'
+ WARNING:ni300mesh_300k_nor_1-5.gr already exists.
+ WARNING:Use "--force=yes" or "--force=once" to overwrite.
+ INFO:elapsed time: 0.095
+
+Here we can see what configuration files are searched, which of them
+get loaded and what are the effective values of the processing
+parameters. Unless the :option:`!--verbose` option is in effect, the
+program will show only messages that have either WARNING or ERROR
+importance. The warning line above indicates no output has been
+written, because that file already exists. This safety check can be
+overruled with the :option:`--force=yes <--force>` option, upon
+which pdfgetx3 would overwrite any existing files.
+
+PDFgetX3 output files start with a header that lists all the processing
+parameters and can be used as a valid configuration file with the
+:option:`-c` option. Another option, :option:`--plot=[iq,sq,fq,gr]
+<-p>` turns on plotting of the final PDF or of some other result. A
+side effect of the :option:`!--plot` option is that pdfgetx3 starts in
+an interactive mode, so the user can manipulate or save the plots. To
+put it all together, we are now going to redo the original PDF and plot
+its reduced total scattering function |FQ| and the PDF curve |Gr|. This
+time the chi file is not necessary, because the input file is already
+listed in the gr file that is now used as a custom configuration::
+
+ $ pdfgetx3 -c ni300mesh_300k_nor_1-5.gr --plot=fq,gr
+
+ WARNING:ni300mesh_300k_nor_1-5.gr already exists.
+ WARNING:Use "--force=yes" or "--force=once" to overwrite.
+
+ Variables related to PDF processing:
+
+ pdfgetter -- PDFGetter used for calculation.
+ config -- configuration data used by PDFGetter.
+ See config.inputfiles for a list of inputs.
+ iraw -- matrix of input raw intensities with 2 rows per file.
+ iq sq fq gr -- intermediate results per each input file stored
+ as matrix rows.
+
+ Functions:
+
+ tuneconfig -- dynamically tune configuration variables.
+ processfiles -- process specified data files.
+ clearsession -- clear all elements from the inputfiles, iraw,
+ iq, sq, fq and gr variables.
+ plotdata -- plot all or selected columns from a text data file.
+ loaddata -- load all or selected columns from a text data file.
+ findfiles -- search for files matching the specified patterns.
+
+ Use "%pdfgetx3" for a fresh run without exiting IPython.
+ In [1]:
+
+This will open a plot figure similar to
+
+.. image:: images/nickelfqgr.png
+
+Because of the :doc:`interactive mode ` implied by plotting,
+the program enters an IPython session.
+The IPython environment is preloaded with several extra functions
+and variables related to the PDF processing. For example, the
+:interactvar:`config` variable stores all the configuration parameters,
+and its content can be displayed with the :py:func:`print`
+function as ::
+
+ In [1]: print(config)
+
+ configfile = ni300mesh_300k_nor_1-5.gr
+ configsection = DEFAULT
+ dataformat = twotheta
+ ...
+ qmax = 26.0
+ ...
+
+The :py:func:`.processfiles` function allows to redo the
+whole calculation and plotting process for additional input files or
+for new parameter values. To plot the |FQ| and |Gr|
+curves calculated at |Qmax| = 22 |Ainv|, we can call
+:py:func:`!processfiles` and pass it a keyword argument for
+the new qmax as follows::
+
+ In [2]: processfiles(qmax=22)
+
+ # the qmax parameter was updated to a new value, thus
+ In [3]: config.qmax
+ Out[3]: 22
+
+There should be now two lines in each plot axis corresponding to
+the results at |Qmax| equal 26 and 22 |Ainv|. To exit the program,
+type ``exit()``.
+
+
+processing from scratch
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We have already encountered the command-line :option:`option -c <-c>`
+for specifying a custom configuration file. A special argument "NONE",
+will make pdfgetx3 ignore any configuration files and start up in a
+default state. We can use this feature to process the nickel PDF as if
+we did not have any configuration file::
+
+ $ pdfgetx3 -c NONE ni300mesh_300k_nor_1-5.chi
+
+ WARNING:Nothing to do, use "-t" or "--plot" options.
+ ERROR:Configuration error: wavelength not specified.
+ ERROR:See "--help" for more hints.
+
+There is an error, for the wavelength is necessary to convert
+the scattering angle |twotheta| to momentum transfer *Q*. The
+X-ray wavelength was 0.142774 Å, which can be passed with the
+:option:`-w, --wavelength <-w>` option::
+
+ $ pdfgetx3 -c NONE ni300mesh_300k_nor_1-5.chi -w 0.142774
+
+ ...
+ ERROR:Configuration error: Chemical composition not known.
+ ERROR:See "--help" for more hints.
+
+There is still an error. The PDF calculation needs an average
+X-ray scattering factor of the material, which is obtained from
+sample chemical composition. The composition can be specified
+with the :option:`--composition` option. The example
+below uses a "\\\\" character to indicate the command continues
+on the next line. Such syntax works in Unix terminals, but
+on Windows the command has to be typed all on a single line::
+
+ $ pdfgetx3 -c NONE ni300mesh_300k_nor_1-5.chi -w 0.142774 \
+ --composition=Ni
+
+ WARNING:Nothing to do, use "-t" or "--plot" options.
+ ...
+
+There was no error message this time, but the program complains
+about a lack of action. The pdfgetx3 program does not write any results
+unless instructed by the :option:`-t, --outputtypes <-t>` option.
+The outputtypes option recognizes the following result types:
+"iq", "sq", "fq", "gr". One or more of these type strings,
+separated by a comma, can be included with the
+:option:`!-t` option, which will produce the corresponding
+output files. An empty string, such as ``-t ""``, or ``-t NONE``
+may be used to clear any outputtypes defined in the configuration file,
+and avoid the unseemly file-exists warnings.
+
+At this point, we will not write any output files, but will use the
+:option:`--plot <-p>` option to display the calculated curves. The
+:option:`!--plot` accepts the same arguments as outputtypes, so to
+display the |FQ| and |Gr| curves we shall run ::
+
+ $ pdfgetx3 -c NONE ni300mesh_300k_nor_1-5.chi -w 0.142774 \
+ --composition=Ni --plot=fq,gr
+
+ WARNING:qmaxinst reset to last nonzero point qmaxinst=28.0865680161
+ WARNING:qmax reset to the data boundary qmaxinst=28.0865680161
+
+which should open the following plot window:
+
+.. image:: images/nickelfqgrnoisy.png
+
+The graphs look terrible. The PDF is very noisy and the |FQ| curve
+shows a sudden break at about 27 |Ainv|. What happened? The powder
+intensities are inaccurate at a very top of the detector angular range.
+The interactive session is setup with
+:interactvar:`iraw`, :interactvar:`iq`, :interactvar:`sq`,
+:interactvar:`fq`, :interactvar:`gr`
+variables for the original raw data and intermediate results. We
+are going to plot the "iq" variable that has the input intensities
+resampled on the *Q* grid. The matplotlib function
+:py:func:`~matplotlib.pyplot.clf` clears the figure,
+the iq variable is a two-row matrix with *Q* and *I* rows, and the
+:py:func:`~matplotlib.pyplot.axis`
+function lets us zoom to a given range::
+
+ In [1]: clf()
+ In [2]: plot(iq[0], iq[1])
+ Out[2]: []
+ In [3]: axis([20, 29, 0, 3000])
+ Out[3]: [20, 29, 0, 3000]
+
+The graph shows a sudden drop in the raw intensities at 27 |Ainv|.
+The :confval:`qmaxinst` variable defines a *Q* cutoff for a meaningful
+instrument intensities and, to be on a safe side, we are going to set
+it to 26.5 |Ainv| ::
+
+ In [4]: processfiles(qmaxinst=26.5)
+ WARNING:qmax reset to the data boundary qmaxinst=26.5
+
+The updated curves looks reasonable without any oscillations and
+breakpoints. The :py:func:`.tuneconfig` function provides a
+GUI-driven way for visualizing the processing parameters and their
+effect on the results. Type ``tuneconfig()`` to execute the function,
+which should open a new window with several sliders. Try to move
+different sliders and see how do the |FQ| and |Gr| curves change.
+The :confval:`rpoly` parameter controls the degree of data-correction
+polynomial and is an approximate low-*r* bound of reliable *G*
+values. Once the parameters are tuned, they may be set to
+exact values. We will also turn on the writing of the |Gr|
+curve and save it to an output file :file:`nicmd.gr`::
+
+ In [14]: config.qmax = 26
+ In [15]: config.outputtypes = 'gr'
+ In [16]: config.output = 'nicmd'
+ In [17]: processfiles()
+
+
+Platinum X-ray series
+------------------------------------------------------------------------
+
+PDFgetX3 has been designed to handle large series of data files.
+With the fast area-detectors it is easy to measure hundreds of X-ray
+patterns in a time or temperature series. Normally, these input
+files need to be entered as command line arguments to the pdfgetx3
+program. This is usually no problem with Unix-like shells, which
+expand filename patterns to a list of matching files.
+However, such file generation is in general not available on Windows.
+The input file names tend to include scan numbers which are useful
+for selecting desired data, yet even with Unix shells it is
+difficult to match a range of scan numbers
+(`z-shell `_ being a notable exception).
+
+.. _my-findexamples:
+
+matching input files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The :program:`pdfgetx3` program includes a built-in function for finding
+a set of input files. The command line arguments are normally taken as
+input file names. However, if the :option:`-f, --find <-f>` option is
+present, the arguments are understood as patterns and the program looks
+for files that match ALL of them. Another option
+:option:`-l, --list <-l>` makes pdfgetx3 print out the matching files
+without any other action, which can be used to verify if the patterns
+match intended files.
+
+We will try out this file search on platinum example files. Open a
+terminal and navigate to the :file:`Pt` directory. There should be a
+:file:`series` subdirectory with 6 chi files indexed from 903 to 908.
+At first, let's stay in the :file:`Pt` directory and run the following
+command ::
+
+ $ pdfgetx3 --list --find
+
+ Pt_bulk-00055-pdfgetx2.gr
+ Pt_bulk-00055-pdfgetx3.gr
+ Pt_bulk-00055.chi
+ empty_capillary-00032.chi
+ pdfgetx3.cfg
+ plotpdfcomparison.py
+
+Without any patterns the file search matches all files in the current
+directory. Now let's try to add name patterns. There are few special
+patterns, for example ``^`` matches at the beginning of the filename, ``$`` at the end and ```` matches a range of integer values from
+*N* to *M*. The patterns containing ``^$<>`` need to be quoted as
+these characters have special meaning in the shell. Here are some
+examples how it works.
+
+Filenames containing "y"::
+
+ $ pdfgetx3 --list --find y
+ empty_capillary-00032.chi
+ plotpdfcomparison.py
+
+Filenames that containing both "y" and "chi", here we use the
+options :option:`!--list` and :option:`!--find` in an abbreviated
+form :option:`!-l` and :option:`!-f`::
+
+ $ pdfgetx3 -lf y chi
+ empty_capillary-00032.chi
+
+Filenames that start with "e"::
+
+ $ pdfgetx3 --list --find "^e"
+ empty_capillary-00032.chi
+
+Filenames that contain *character* "2"::
+
+ $ pdfgetx3 --list --find 2
+ Pt_bulk-00055-pdfgetx2.gr
+ empty_capillary-00032.chi
+
+Filenames that contain *numeric value* "2"::
+
+ $ pdfgetx3 -lf "<2>"
+ Pt_bulk-00055-pdfgetx2.gr
+
+The special argument ``+`` starts a new group of patterns to
+generate extra files when they cannot be all covered by
+a single set of patterns. For example, to match files that
+contain contain both "bulk" and "chi" substrings and then
+also those that have "empty" and "chi" in their names, use::
+
+ $ pdfgetx3 -lf bulk chi + empty chi
+ Pt_bulk-00055.chi
+ empty_capillary-00032.chi
+
+When pattern groups overlap the resulting matches are
+made unique and each file is listed only once ::
+
+ $ pdfgetx3 -lf bulk chi + chi
+ Pt_bulk-00055.chi
+ empty_capillary-00032.chi
+
+
+data search path
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Each group of PDFgetX3 patterns can have one entry containing
+forward slash "/" to specify a non-current path that is searched
+for input files. The path specification affects the current and
+the following pattern groups unless they provide their own path.
+The chi files numbered "903" to "905" and "908" from the
+:file:`series` subdirectory can be therefore matched using ::
+
+ $ pdfgetx3 -lf series/ "<903-905>" + 908
+ series/Pt_bulk_ramp03-00903.chi
+ series/Pt_bulk_ramp03-00904.chi
+ series/Pt_bulk_ramp03-00905.chi
+ series/Pt_bulk_ramp03-00908.chi
+
+The current directory can be selected using `./` ::
+
+ $ pdfgetx3 -lf series/ 903 + ./ bulk chi
+ series/Pt_bulk_ramp03-00903.chi
+ Pt_bulk-00055.chi
+
+When additional pattern groups contain only the path
+argument, they reuse the existing set of patterns. The
+".chi"-ending files in the current and :file:`series`
+directories can be thus found using ::
+
+ $ pdfgetx3 -lf ".chi$" + series/
+ Pt_bulk-00055.chi
+ empty_capillary-00032.chi
+ series/Pt_bulk_ramp03-00903.chi
+ series/Pt_bulk_ramp03-00904.chi
+ series/Pt_bulk_ramp03-00905.chi
+ series/Pt_bulk_ramp03-00906.chi
+ series/Pt_bulk_ramp03-00907.chi
+ series/Pt_bulk_ramp03-00908.chi
+
+
+output file names
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+By default the output files are saved in the current directory. The
+output path, can be changed with the :option:`-o, --output <-o>` option.
+The :option:`!-o` recognizes several tokens that are replaced with
+parts of the input file name, for example, "@b" expands to an
+extension-stripped base name. In similar faction, "@o" is replaced
+with the output type extension. Thus to generate PDFs for all files
+in the :file:`series` directory and save them in the
+:file:`series-gr` subfolder do ::
+
+ $ pdfgetx3 --find series/ "<900-910>.chi" --output=series-gr/@b.@o
+
+The extension ".@o" is automatic when not included anywhere in the
+output file name. Thus to process the Pt series at |Qmax| = 18 |Ainv|
+while saving the results in the same folder, but with a "_qmax18" suffix
+in their filenames do ::
+
+ $ pdfgetx3 --find series/ "<900-910>.chi" --qmax=18 -o series-gr/@b_qmax18
+
+For input file :file:`Pt_bulk_ramp03-00903.chi` the :option:`!-o` option
+above expands to output path :file:`series-gr/Pt_bulk_ramp03-00903_qmax18.gr`.
+The :file:`series-gr` directory should now contain 12 "gr" files,
+6 of them processed at |Qmax| = 27 |Ainv| as given by configuration
+file and 6 others processed at |Qmax| = 18 |Ainv|.
+
+.. seealso:: :option:`-o, --output <-o>` for a list of output tokens
+
+.. index:: tuneconfig (example)
+.. _my-tuneconfig:
+
+Interactive tuning of parameters
+------------------------------------------------------------------------
+
+One of the most powerful features of PDFgetX3 is the ability to tune
+PDF processing parameters in an interactive mode and immediately
+visualize their effect on the results. To demonstrate this feature,
+navigate to the :file:`Ni` directory in the shell and process
+the nickel PDF while plotting the |FQ| and |Gr| curves.
+Because of plotting the program will open an interactive IPython
+session. The tuning mode can be then entered by calling the
+:py:func:`.tuneconfig`
+function from the IPython environment ::
+
+ $ pdfgetx3 --plot=fq,gr ni300mesh_300k_nor_1-5.chi
+ ...
+ In [1]: tuneconfig()
+
+The
+:py:func:`!tuneconfig`
+function will by default add a second set of live lines
+for the plotted curves and open a GUI dialog with sliders for the
+tunable process parameters. Changing any slider would immediately
+recalculate the PDF and update live lines in the plot.
+
+.. image:: images/tunenickelfqgr.png
+
+The *constant data scale* check-box rescales the result curves to a
+constant maximum value. This is useful for assessing if a parameter
+change produces different curve shape or if it just rescales the
+results. The tunable parameters are described in the
+:ref:`PDF parameters section `.
+Only the active parameters are displayed in the tuneconfig GUI,
+thus there would be no slider for the :confval:`bgscale` parameter
+if PDF has been processed without any background data.
+
+By default the
+:py:func:`!tuneconfig`
+function displays the same curves as
+specified by the :option:`--plot <-p>` option, however it can be
+configured to show arbitrary intermediate results or even visualize
+selected steps in the PDF processing. We shall demonstrate this by
+showing a live-plot of the polynomial correction together with the final
+PDF. At first, we shall use the :py:meth:`!describe` method of the
+:py:func:`.pdfgetter` object to print out the chain of
+transformations involved in the PDF processing and obtain a reference to
+the transformation object *t4* that applies the polynomial correction.
+The transformation object can be then included in a list of plot
+identifiers that are passed to the :py:func:`!tuneconfig` function ::
+
+ $ pdfgetx3 -i ni300mesh_300k_nor_1-5.chi
+ ...
+ Use "%pdfgetx3" for a fresh run without exiting IPython.
+
+ In [1]: fig, ax = subplots(2)
+ In [2]: pdfgetter.describe()
+ 0 TransformTwoThetaToQA
+ convert x data from twotheta to Q in 1/A
+ 1 TransformQGridRegular
+ Remove the data outside the (qmin, qmaxinst) range
+ 2 TransformBackground
+ subtract background intensity
+ 3 TransformXrayASFnormChris
+ scale and normalize intensities by x-ray scattering factors
+ 4 TransformSQnormRPoly
+ Normalize S(Q) by fitting a polynomial
+ 5 TransformSQToFQ
+ Convert S(Q) to F(Q).
+ 6 TransformFQgrid
+ Resample F(Q) to a regular grid suitable for FFT
+ 7 TransformFQToGr
+ Convert F(Q) to G(r).
+ In [3]: t4 = pdfgetter.getTransformation(4)
+ In [4]: tuneconfig([t4, 'gr'], axeslist=ax)
+ In [5]: ax[0].legend(loc=2)
+
+The :py:func:`~matplotlib.pyplot.subplots` function above
+is to create a new figure with 2 axes on top of each other.
+Overall, the code above should display the following plot
+and a GUI window:
+
+.. image:: images/tunenickelt4gr.png
+
+The tuning can be finished by clicking the ``Done`` button or closing the
+tuneconfig GUI window. The parameter values can be thereafter adjusted
+to a rounded values by setting an attribute of the :interactvar:`config`
+object, for example::
+
+ In [5]: config.bgscale = 1.5
+
+Finally, to save the new results, we shall first confirm
+:confval:`outputtypes` have been correctly set and then use the
+:py:func:`.processfiles` function to redo the calculations, plots and
+data output for the updated configuration. Note that the
+:py:func:`!processfiles` function accepts keyword arguments for
+configuration parameters. This is used at line ``In [8]`` to
+turn on the :confval:`force` flag and is in effect a shortcut
+for an extra ``config.force = True`` statement. ::
+
+ In [6]: config.outputtypes
+ Out[6]: ['gr']
+ In [7]: processfiles()
+ WARNING:ni300mesh_300k_nor_1-5.gr already exists.
+ WARNING:Use "--force=yes" or "--force=once" to overwrite.
+ In [8]: processfiles(force=True)
+
+:file:`ni300mesh_300k_nor_1-5.gr` was successfully saved at an
+updated configuration for there were no warnings after the last call.
+
+
+Neutron PDF
+------------------------------------------------------------------------
+
+This example illustrates PDF extraction from
+neutron powder data using :ref:`pdfgetn3 `.
+Navigate to the :file:`n-Sapphire` directory in the shell.
+The :file:`sapphire755.dat` file contains powder diffraction data from
+sapphire (α-Al\ :sub:`2`\ O\ :sub:`3`)
+measured at the constant-wavelength PEARL instrument
+at the Delft University of Technology.
+The :file:`pdfgetn3.cfg` configuration file specifies
+processing parameters such as :confval:`wavelength`,
+:confval:`twothetazero`, :confval:`composition`, and :confval:`mode`.
+
+To extract the sapphire neutron PDF run ::
+
+ $ pdfgetn3 --verbose=info sapphire755.dat
+
+ INFO:applying pdfgetn3 defaults
+ INFO:set config.mode = neutron
+ INFO:searching for default config file /home/user/.pdfgetn3.cfg
+ INFO:searching for default config file .pdfgetn3.cfg
+ INFO:searching for default config file pdfgetn3.cfg
+ INFO:loaded default config file pdfgetn3.cfg
+ INFO:reset config.twothetazero = 0.0
+ INFO:parsing config file section [DEFAULT]
+ INFO:set config.dataformat = twotheta
+ INFO:set config.backgroundfile =
+ INFO:set config.outputtypes = fq, gr
+ INFO:set config.mode = neutron
+ INFO:set config.wavelength = 1.0989
+ INFO:set config.twothetazero = -0.38
+ INFO:set config.composition = Al2O3
+ INFO:set config.qmaxinst = 11.2
+ INFO:set config.qmax = 11.2
+ INFO:set config.rmin = 0.0
+ INFO:set config.rmax = 20.0
+ INFO:set config.rstep = 0.01
+ INFO:finished parsing config file
+ INFO:processing command line options
+ INFO:set config.verbose = info
+ INFO:finished with command line options
+ INFO:using 1 input files from the command line.
+ INFO:configuring PDFGetter mode 'neutron'
+ INFO:calling config_neutron
+ INFO:started PDF processing.
+ INFO:processing 'sapphire755.dat'
+ INFO:resolved output file '' as 'sapphire755.fq'
+ INFO:written outpufile sapphire755.fq
+ INFO:resolved output file '' as 'sapphire755.gr'
+ INFO:written outpufile sapphire755.gr
+ INFO:elapsed time: 0.097
+
+This will produce two files :file:`sapphire755.fq`, :file:`sapphire755.gr`
+for the |FQ| and |Gr| functions.
+To compare them with expected results use ::
+
+ $ plotdata sapphire755-expected.fq sapphire755.fq
+ $ plotdata sapphire755-expected.gr sapphire755.gr
+
+
+Fit twothetazero
+------------------------------------------------------------------------
+
+For a good quality PDF it is essential to use powder patterns with
+accurate values of *Q*. Some instruments may produce spectra with
+a slightly offset scattering angle |twotheta| which
+causes inaccurate *Q* and a noticeably worse PDF.
+In this example we fit a constant-wavelength neutron PDF from nickel
+together with the :confval:`twothetazero` correction parameter for
+diffractometer offset.
+The procedure can be used to calibrate the zero correction from
+a standard sample and then use it for subsequent PDF extractions.
+The protocol can be also applied to fit zero correction in
+a full-fledged PDF refinement in case
+the zero offset may change for different samples.
+
+This tutorial requires either Linux or Mac OS X platforms,
+because the PDF fitting is conducted with
+`DiffPy-CMI `__,
+which is not yet available for Windows.
+If DiffPy-CMI is not yet installed,
+we recommend to use `Anaconda Python`_ and set up a dedicated
+Anaconda environment *nbcmi* for this tutorial.
+This can be accomplished using the following steps::
+
+ $ conda create -n nbcmi -c diffpy python=2 diffpy-cmi
+ $ conda activate nbcmi
+ $ pip install path/to/diffpy.pdfgetx-VERSION.whl
+
+When these prerequisites are in place,
+change to the :file:`n-twothetazero-fit` directory
+and open the self documented Jupyter notebook as follows ::
+
+ $ jupyter notebook fit-twothetazero.ipynb
+
+.. |tthzero| replace:: :confval:`!twothetazero`
+
+The notebook sets up and executes several PDF refinements and
+compares the results from fits on uncorrected data and with
+a fitted |tthzero|.
+After running all cells the notebook should produce similar graphs
+as in the figure below.
+
+.. figure:: images/twothetazerofit.*
+
+ Refinement of nickel neutron PDF for **(a)** uncorrected data
+ and **(b)** with a refined zero correction.
+ The extracted PDFs are plotted as blue circles,
+ simulated PDFs as red lines and
+ the difference is plotted offset in green below.
+
+The final refined zero offset in the notebook should be approximately -0.36°.
+The correction produces experimental PDF with a remarkably better fit
+residual R\ :sub:`w` which is lowered from (a) 0.18 to (b) 0.05.
+
+
+Small-angle-scattering PDF (sasPDF)
+------------------------------------------------------------------------
+
+Here we illustrate how to extract a PDF from small-angle-scattering (sas) data using :ref:`pdfgets3 `.
+To do this, navigate to the :file:`Au_DNA_NPA` directory in your terminal.
+In this folder, you will find :file:`Au_DNA_NPA.chi` and
+:file:`Au_DNA_FF.chi` files which correspond to diffraction data from
+DNA-capped Au nanoparticle assemblies and from a DNA-capped Au
+nanoparticle colloidal solution respectively. Those two files were
+measured at X21 beamline, NSLS and published in `D. Nykypanchuk, M. M.
+Maye, D. van der Lelie, and O. Gang, Nature 451, 549 (2008).
+`_. We thank Prof. Oleg Gang (Columbia University) for sharing this data. The :file:`pdfgets3.cfg`
+configuration file specifies processing parameters such as :confval:`formfactorfile` (required by ``sas`` mode), :confval:`qmin`, :confval:`qmax`, and :confval:`mode`.
+
+To extract the PDF of DNA-capped DNA nanoparticle assemblies ::
+
+ $ pdfgets3 --verbose=info Au_DNA_NPA.chi
+
+ INFO:applying pdfgets3 defaults
+ INFO:set config.mode = sas
+ INFO:searching for default config file /home/user/.pdfgets3.cfg
+ INFO:searching for default config file .pdfgets3.cfg
+ INFO:searching for default config file pdfgets3.cfg
+ INFO:loaded default config file pdfgets3.cfg
+ INFO:reset config.twothetazero = 0.0
+ INFO:parsing config file section [DEFAULT]
+ INFO:set config.dataformat = QA
+ INFO:set config.backgroundfile =
+ INFO:set config.datapath = []
+ INFO:set config.formfactorfile = Au_DNA_FF.chi
+ INFO:set config.output =
+ INFO:set config.outputtypes = fq, gr
+ INFO:set config.force = yes
+ INFO:set config.mode = sas
+ INFO:set config.rpoly = 240.605
+ INFO:set config.qmaxinst = 0.075
+ INFO:set config.qmin = 0.01
+ INFO:set config.qmax = 0.072
+ INFO:set config.rmin = 100.0
+ INFO:set config.rmax = 5000.0
+ INFO:set config.rstep = 1.0
+ INFO:set config.plot = iq, fq, gr
+ INFO:set config.verbose = info
+ INFO:finished parsing config file
+ INFO:processing command line options
+ INFO:set config.verbose = info
+ INFO:finished with command line options
+ INFO:using 1 input files from the command line.
+ INFO:configuring PDFGetter mode 'sas'
+ INFO:calling config_sas
+ INFO:started PDF processing.
+ INFO:processing 'Au_DNA_NPA.chi'
+ INFO:resolved output file '' as 'Au_DNA_NPA.fq'
+ INFO:written outpufile Au_DNA_NPA.fq
+ INFO:resolved output file '' as 'Au_DNA_NPA.gr'
+ INFO:written outpufile Au_DNA_NPA.gr
+ INFO:elapsed time: 0.947
+
+
+This will save two files :file:`Au_DNA_NPA.fq`, :file:`Au_DNA_NPA.gr` in the same directoy for the |FQ| and |Gr| functions. This also plots |FQ| and |Gr| functions in a pop-up window and the processing parameters such as :confval:`rpoly` or so may be tuned interactively by issuing command :py:func:`!tuneconfig` in the `IPython`_ session as discussed above.
diff --git a/static_root/doc/pdfgetx/2.1.1/_static/basic.css b/static_root/doc/pdfgetx/2.1.1/_static/basic.css
new file mode 100644
index 00000000..01192852
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_static/basic.css
@@ -0,0 +1,768 @@
+/*
+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+ clear: both;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+ width: 100%;
+ font-size: 90%;
+}
+
+div.related h3 {
+ display: none;
+}
+
+div.related ul {
+ margin: 0;
+ padding: 0 0 0 10px;
+ list-style: none;
+}
+
+div.related li {
+ display: inline;
+}
+
+div.related li.right {
+ float: right;
+ margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+ padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+ float: left;
+ width: 230px;
+ margin-left: -100%;
+ font-size: 90%;
+ word-wrap: break-word;
+ overflow-wrap : break-word;
+}
+
+div.sphinxsidebar ul {
+ list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+ margin-left: 20px;
+ list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+ margin-top: 10px;
+}
+
+div.sphinxsidebar input {
+ border: 1px solid #98dbcc;
+ font-family: sans-serif;
+ font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox form.search {
+ overflow: hidden;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+ float: left;
+ width: 80%;
+ padding: 0.25em;
+ box-sizing: border-box;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+ float: left;
+ width: 20%;
+ border-left: none;
+ padding: 0.25em;
+ box-sizing: border-box;
+}
+
+
+img {
+ border: 0;
+ max-width: 100%;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+ margin: 10px 0 0 20px;
+ padding: 0;
+}
+
+ul.search li {
+ padding: 5px 0 5px 20px;
+ background-image: url(file.png);
+ background-repeat: no-repeat;
+ background-position: 0 7px;
+}
+
+ul.search li a {
+ font-weight: bold;
+}
+
+ul.search li div.context {
+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+ width: 90%;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+table.contentstable p.biglink {
+ line-height: 150%;
+}
+
+a.biglink {
+ font-size: 1.3em;
+}
+
+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+ width: 100%;
+}
+
+table.indextable td {
+ text-align: left;
+ vertical-align: top;
+}
+
+table.indextable ul {
+ margin-top: 0;
+ margin-bottom: 0;
+ list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+ padding-left: 0em;
+}
+
+table.indextable tr.pcap {
+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+div.modindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+ padding: 2px;
+ border-collapse: collapse;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+div.body {
+ min-width: 450px;
+ max-width: 800px;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+ -moz-hyphens: auto;
+ -ms-hyphens: auto;
+ -webkit-hyphens: auto;
+ hyphens: auto;
+}
+
+a.headerlink {
+ visibility: hidden;
+}
+
+a.brackets:before,
+span.brackets > a:before{
+ content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+ content: "]";
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
+ visibility: visible;
+}
+
+div.body p.caption {
+ text-align: inherit;
+}
+
+div.body td {
+ text-align: left;
+}
+
+.first {
+ margin-top: 0 !important;
+}
+
+p.rubric {
+ margin-top: 30px;
+ font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+img.align-default, .figure.align-default {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+.align-left {
+ text-align: left;
+}
+
+.align-center {
+ text-align: center;
+}
+
+.align-default {
+ text-align: center;
+}
+
+.align-right {
+ text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+ margin: 0 0 0.5em 1em;
+ border: 1px solid #ddb;
+ padding: 7px 7px 0 7px;
+ background-color: #ffe;
+ width: 40%;
+ float: right;
+}
+
+p.sidebar-title {
+ font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+ border: 1px solid #ccc;
+ padding: 7px 7px 0 7px;
+ margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+ font-size: 1.1em;
+ font-weight: bold;
+ margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 7px;
+}
+
+div.admonition dt {
+ font-weight: bold;
+}
+
+div.admonition dl {
+ margin-bottom: 0;
+}
+
+p.admonition-title {
+ margin: 0px 10px 5px 0px;
+ font-weight: bold;
+}
+
+div.body p.centered {
+ text-align: center;
+ margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+ border: 0;
+ border-collapse: collapse;
+}
+
+table.align-center {
+ margin-left: auto;
+ margin-right: auto;
+}
+
+table.align-default {
+ margin-left: auto;
+ margin-right: auto;
+}
+
+table caption span.caption-number {
+ font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
+table.docutils td, table.docutils th {
+ padding: 1px 8px 1px 5px;
+ border-top: 0;
+ border-left: 0;
+ border-right: 0;
+ border-bottom: 1px solid #aaa;
+}
+
+table.footnote td, table.footnote th {
+ border: 0 !important;
+}
+
+th {
+ text-align: left;
+ padding-right: 5px;
+}
+
+table.citation {
+ border-left: solid 1px gray;
+ margin-left: 1px;
+}
+
+table.citation td {
+ border-bottom: none;
+}
+
+th > p:first-child,
+td > p:first-child {
+ margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+ margin-bottom: 0px;
+}
+
+/* -- figures --------------------------------------------------------------- */
+
+div.figure {
+ margin: 0.5em;
+ padding: 0.5em;
+}
+
+div.figure p.caption {
+ padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number {
+ font-style: italic;
+}
+
+div.figure p.caption span.caption-text {
+}
+
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+ border: 0 !important;
+}
+
+.field-list ul {
+ margin: 0;
+ padding-left: 1em;
+}
+
+.field-list p {
+ margin: 0;
+}
+
+.field-name {
+ -moz-hyphens: manual;
+ -ms-hyphens: manual;
+ -webkit-hyphens: manual;
+ hyphens: manual;
+}
+
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+ vertical-align: top;
+}
+
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+ list-style: decimal;
+}
+
+ol.loweralpha {
+ list-style: lower-alpha;
+}
+
+ol.upperalpha {
+ list-style: upper-alpha;
+}
+
+ol.lowerroman {
+ list-style: lower-roman;
+}
+
+ol.upperroman {
+ list-style: upper-roman;
+}
+
+li > p:first-child {
+ margin-top: 0px;
+}
+
+li > p:last-child {
+ margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+ float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+ margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+ content: "";
+ clear: both;
+}
+
+dl.field-list {
+ display: grid;
+ grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+ font-weight: bold;
+ word-break: break-word;
+ padding-left: 0.5em;
+ padding-right: 5px;
+}
+
+dl.field-list > dt:after {
+ content: ":";
+}
+
+dl.field-list > dd {
+ padding-left: 0.5em;
+ margin-top: 0em;
+ margin-left: 0em;
+ margin-bottom: 0em;
+}
+
+dl {
+ margin-bottom: 15px;
+}
+
+dd > p:first-child {
+ margin-top: 0px;
+}
+
+dd ul, dd table {
+ margin-bottom: 10px;
+}
+
+dd {
+ margin-top: 3px;
+ margin-bottom: 10px;
+ margin-left: 30px;
+}
+
+dt:target, span.highlighted {
+ background-color: #fbe54e;
+}
+
+rect.highlighted {
+ fill: #fbe54e;
+}
+
+dl.glossary dt {
+ font-weight: bold;
+ font-size: 1.1em;
+}
+
+.optional {
+ font-size: 1.3em;
+}
+
+.sig-paren {
+ font-size: larger;
+}
+
+.versionmodified {
+ font-style: italic;
+}
+
+.system-message {
+ background-color: #fda;
+ padding: 5px;
+ border: 3px solid red;
+}
+
+.footnote:target {
+ background-color: #ffa;
+}
+
+.line-block {
+ display: block;
+ margin-top: 1em;
+ margin-bottom: 1em;
+}
+
+.line-block .line-block {
+ margin-top: 0;
+ margin-bottom: 0;
+ margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+ font-family: sans-serif;
+}
+
+.accelerator {
+ text-decoration: underline;
+}
+
+.classifier {
+ font-style: oblique;
+}
+
+.classifier:before {
+ font-style: normal;
+ margin: 0.5em;
+ content: ":";
+}
+
+abbr, acronym {
+ border-bottom: dotted 1px;
+ cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+ overflow: auto;
+ overflow-y: hidden; /* fixes display issues on Chrome browsers */
+}
+
+span.pre {
+ -moz-hyphens: none;
+ -ms-hyphens: none;
+ -webkit-hyphens: none;
+ hyphens: none;
+}
+
+td.linenos pre {
+ padding: 5px 0px;
+ border: 0;
+ background-color: transparent;
+ color: #aaa;
+}
+
+table.highlighttable {
+ margin-left: 0.5em;
+}
+
+table.highlighttable td {
+ padding: 0 0.5em 0 0.5em;
+}
+
+div.code-block-caption {
+ padding: 2px 5px;
+ font-size: small;
+}
+
+div.code-block-caption code {
+ background-color: transparent;
+}
+
+div.code-block-caption + div > div.highlight > pre {
+ margin-top: 0;
+}
+
+div.doctest > div.highlight span.gp { /* gp: Generic.Prompt */
+ user-select: none;
+}
+
+div.code-block-caption span.caption-number {
+ padding: 0.1em 0.3em;
+ font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+ padding: 1em 1em 0;
+}
+
+div.literal-block-wrapper div.highlight {
+ margin: 0;
+}
+
+code.descname {
+ background-color: transparent;
+ font-weight: bold;
+ font-size: 1.2em;
+}
+
+code.descclassname {
+ background-color: transparent;
+}
+
+code.xref, a code {
+ background-color: transparent;
+ font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+ background-color: transparent;
+}
+
+.viewcode-link {
+ float: right;
+}
+
+.viewcode-back {
+ float: right;
+ font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+ margin: -1px -10px;
+ padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+ vertical-align: middle;
+}
+
+div.body div.math p {
+ text-align: center;
+}
+
+span.eqno {
+ float: right;
+}
+
+span.eqno a.headerlink {
+ position: relative;
+ left: 0px;
+ z-index: 1;
+}
+
+div.math:hover a.headerlink {
+ visibility: visible;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+ div.document,
+ div.documentwrapper,
+ div.bodywrapper {
+ margin: 0 !important;
+ width: 100%;
+ }
+
+ div.sphinxsidebar,
+ div.related,
+ div.footer,
+ #top-link {
+ display: none;
+ }
+}
\ No newline at end of file
diff --git a/static_root/doc/pdfgetx/2.1.1/_static/classic.css b/static_root/doc/pdfgetx/2.1.1/_static/classic.css
new file mode 100644
index 00000000..3496a7bb
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_static/classic.css
@@ -0,0 +1,271 @@
+/*
+ * classic.css_t
+ * ~~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- classic theme.
+ *
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+html {
+ /* CSS hack for macOS's scrollbar (see #1125) */
+ background-color: #FFFFFF;
+}
+
+body {
+ font-family: 'Palatino', 'Palatino Linotype', 'URW Palladio L', 'Century Schoolbook L', 'Georgia', serif;
+ font-size: 100%;
+ background-color: white;
+ color: #000;
+ margin: 0;
+ padding: 0;
+}
+
+div.document {
+ background-color: white;
+}
+
+div.documentwrapper {
+ float: left;
+ width: 100%;
+}
+
+div.bodywrapper {
+ margin: 0 0 0 230px;
+}
+
+div.body {
+ background-color: white;
+ color: #222222;
+ padding: 0 20px 30px 20px;
+}
+
+div.footer {
+ color: #555555;
+ width: 100%;
+ padding: 9px 0 9px 0;
+ text-align: center;
+ font-size: 75%;
+}
+
+div.footer a {
+ color: #555555;
+ text-decoration: underline;
+}
+
+div.related {
+ background-color: white;
+ line-height: 30px;
+ color: #666666;
+}
+
+div.related a {
+ color: #444444;
+}
+
+div.sphinxsidebar {
+}
+
+div.sphinxsidebar h3 {
+ font-family: 'Myriad Pro', 'Trebuchet Ms', 'Segoe UI', sans-serif;
+ color: #444444;
+ font-size: 1.4em;
+ font-weight: normal;
+ margin: 0;
+ padding: 0;
+}
+
+div.sphinxsidebar h3 a {
+ color: #444444;
+}
+
+div.sphinxsidebar h4 {
+ font-family: 'Myriad Pro', 'Trebuchet Ms', 'Segoe UI', sans-serif;
+ color: #444444;
+ font-size: 1.3em;
+ font-weight: normal;
+ margin: 5px 0 0 0;
+ padding: 0;
+}
+
+div.sphinxsidebar p {
+ color: #444444;
+}
+
+div.sphinxsidebar p.topless {
+ margin: 5px 10px 10px 10px;
+}
+
+div.sphinxsidebar ul {
+ margin: 10px;
+ padding: 0;
+ color: #444444;
+}
+
+div.sphinxsidebar a {
+ color: #444444;
+}
+
+div.sphinxsidebar input {
+ border: 1px solid #444444;
+ font-family: sans-serif;
+ font-size: 1em;
+}
+
+
+/* for collapsible sidebar */
+div#sidebarbutton {
+ background-color: #3c6e83;
+}
+
+
+/* -- hyperlink styles ------------------------------------------------------ */
+
+a {
+ color: #00608f;
+ text-decoration: none;
+}
+
+a:visited {
+ color: #30306f;
+ text-decoration: none;
+}
+
+a:hover {
+ text-decoration: underline;
+}
+
+
+
+/* -- body styles ----------------------------------------------------------- */
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+ font-family: 'Myriad Pro', 'Trebuchet Ms', 'Segoe UI', sans-serif;
+ background-color: white;
+ font-weight: normal;
+ color: #1a1a1a;
+ border-bottom: 1px solid #ccc;
+ margin: 20px -20px 10px -20px;
+ padding: 3px 0 3px 10px;
+}
+
+div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h2 { font-size: 160%; }
+div.body h3 { font-size: 140%; }
+div.body h4 { font-size: 120%; }
+div.body h5 { font-size: 110%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+ color: #aaaaaa;
+ font-size: 0.8em;
+ padding: 0 4px 0 4px;
+ text-decoration: none;
+}
+
+a.headerlink:hover {
+ background-color: #aaaaaa;
+ color: white;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+ text-align: justify;
+ line-height: 130%;
+}
+
+div.admonition p.admonition-title + p {
+ display: inline;
+}
+
+div.admonition p {
+ margin-bottom: 5px;
+}
+
+div.admonition pre {
+ margin-bottom: 5px;
+}
+
+div.admonition ul, div.admonition ol {
+ margin-bottom: 5px;
+}
+
+div.note {
+ background-color: #eee;
+ border: 1px solid #ccc;
+}
+
+div.seealso {
+ background-color: #ffc;
+ border: 1px solid #ff6;
+}
+
+div.topic {
+ background-color: #eee;
+}
+
+div.warning {
+ background-color: #ffe4e4;
+ border: 1px solid #f66;
+}
+
+p.admonition-title {
+ display: inline;
+}
+
+p.admonition-title:after {
+ content: ":";
+}
+
+pre {
+ padding: 5px;
+ background-color: #eeffcc;
+ color: #333333;
+ line-height: 120%;
+ border: 1px solid #ac9;
+ border-left: none;
+ border-right: none;
+}
+
+code {
+ background-color: #ecf0f3;
+ padding: 0 1px 0 1px;
+ font-size: 0.95em;
+}
+
+th, dl.field-list > dt {
+ background-color: #ede;
+}
+
+.warning code {
+ background: #efc2c2;
+}
+
+.note code {
+ background: #d6d6d6;
+}
+
+.viewcode-back {
+ font-family: 'Palatino', 'Palatino Linotype', 'URW Palladio L', 'Century Schoolbook L', 'Georgia', serif;
+}
+
+div.viewcode-block:target {
+ background-color: #f4debf;
+ border-top: 1px solid #ac9;
+ border-bottom: 1px solid #ac9;
+}
+
+div.code-block-caption {
+ color: #efefef;
+ background-color: #1c4e63;
+}
\ No newline at end of file
diff --git a/static_root/doc/pdfgetx/2.1.1/_static/copybutton.js b/static_root/doc/pdfgetx/2.1.1/_static/copybutton.js
new file mode 100644
index 00000000..ca9f489f
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_static/copybutton.js
@@ -0,0 +1,57 @@
+$(document).ready(function() {
+ /* Add a [>>>] button on the top-right corner of code samples to hide
+ * the >>> and ... prompts and the output and thus make the code
+ * copyable. */
+ var div = $('.highlight-python .highlight,' +
+ '.highlight-pycon .highlight,' +
+ '.highlight-python3 .highlight')
+ var pre = div.find('pre');
+
+ // get the styles from the current theme
+ pre.parent().parent().css('position', 'relative');
+ var hide_text = 'Hide the prompts and output';
+ var show_text = 'Show the prompts and output';
+ var border_width = pre.css('border-top-width');
+ var border_style = pre.css('border-top-style');
+ var border_color = pre.css('border-top-color');
+ var button_styles = {
+ 'cursor':'pointer', 'position': 'absolute', 'top': '0', 'right': '0',
+ 'border-color': border_color, 'border-style': border_style,
+ 'border-width': border_width, 'color': border_color, 'text-size': '75%',
+ 'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em',
+ 'border-radius': '0 3px 0 0'
+ }
+
+ // create and add the button to all the code blocks that contain >>>
+ div.each(function(index) {
+ var jthis = $(this);
+ if (jthis.find('.gp').length > 0) {
+ var button = $('>>>');
+ button.css(button_styles)
+ button.attr('title', hide_text);
+ jthis.prepend(button);
+ }
+ // tracebacks (.gt) contain bare text elements that need to be
+ // wrapped in a span to work with .nextUntil() (see later)
+ jthis.find('pre:has(.gt)').contents().filter(function() {
+ return ((this.nodeType == 3) && (this.data.trim().length > 0));
+ }).wrap('');
+ });
+
+ // define the behavior of the button when it's clicked
+ $('.copybutton').toggle(
+ function() {
+ var button = $(this);
+ button.parent().find('.go, .gp, .gt').hide();
+ button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden');
+ button.css('text-decoration', 'line-through');
+ button.attr('title', show_text);
+ },
+ function() {
+ var button = $(this);
+ button.parent().find('.go, .gp, .gt').show();
+ button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible');
+ button.css('text-decoration', 'none');
+ button.attr('title', hide_text);
+ });
+});
diff --git a/static_root/doc/pdfgetx/2.1.1/_static/doctools.js b/static_root/doc/pdfgetx/2.1.1/_static/doctools.js
new file mode 100644
index 00000000..daccd209
--- /dev/null
+++ b/static_root/doc/pdfgetx/2.1.1/_static/doctools.js
@@ -0,0 +1,315 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+ "profile", "profileEnd"];
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+ return decodeURIComponent(x).replace(/\+/g, ' ');
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s === 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
+ }
+ return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node, addItems) {
+ if (node.nodeType === 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 &&
+ !jQuery(node.parentNode).hasClass(className) &&
+ !jQuery(node.parentNode).hasClass("nohighlight")) {
+ var span;
+ var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+ if (isInSVG) {
+ span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+ } else {
+ span = document.createElement("span");
+ span.className = className;
+ }
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ if (isInSVG) {
+ var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+ var bbox = node.parentElement.getBBox();
+ rect.x.baseVal.value = bbox.x;
+ rect.y.baseVal.value = bbox.y;
+ rect.width.baseVal.value = bbox.width;
+ rect.height.baseVal.value = bbox.height;
+ rect.setAttribute('class', className);
+ addItems.push({
+ "parent": node.parentNode,
+ "target": rect});
+ }
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this, addItems);
+ });
+ }
+ }
+ var addItems = [];
+ var result = this.each(function() {
+ highlight(this, addItems);
+ });
+ for (var i = 0; i < addItems.length; ++i) {
+ jQuery(addItems[i].parent).before(addItems[i].target);
+ }
+ return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+ jQuery.uaMatch = function(ua) {
+ ua = ua.toLowerCase();
+
+ var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+ /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+ /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+ /(msie) ([\w.]+)/.exec(ua) ||
+ ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+ [];
+
+ return {
+ browser: match[ 1 ] || "",
+ version: match[ 2 ] || "0"
+ };
+ };
+ jQuery.browser = {};
+ jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+ init : function() {
+ this.fixFirefoxAnchorBug();
+ this.highlightSearchWords();
+ this.initIndexTable();
+ if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+ this.initOnKeyListeners();
+ }
+ },
+
+ /**
+ * i18n support
+ */
+ TRANSLATIONS : {},
+ PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
+ LOCALE : 'unknown',
+
+ // gettext and ngettext don't access this so that the functions
+ // can safely bound to a different name (_ = Documentation.gettext)
+ gettext : function(string) {
+ var translated = Documentation.TRANSLATIONS[string];
+ if (typeof translated === 'undefined')
+ return string;
+ return (typeof translated === 'string') ? translated : translated[0];
+ },
+
+ ngettext : function(singular, plural, n) {
+ var translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated === 'undefined')
+ return (n == 1) ? singular : plural;
+ return translated[Documentation.PLURALEXPR(n)];
+ },
+
+ addTranslations : function(catalog) {
+ for (var key in catalog.messages)
+ this.TRANSLATIONS[key] = catalog.messages[key];
+ this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+ this.LOCALE = catalog.locale;
+ },
+
+ /**
+ * add context elements like header anchor links
+ */
+ addContextElements : function() {
+ $('div[id] > :header:first').each(function() {
+ $('\u00B6').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this headline')).
+ appendTo(this);
+ });
+ $('dt[id]').each(function() {
+ $('\u00B6').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this definition')).
+ appendTo(this);
+ });
+ },
+
+ /**
+ * workaround a firefox stupidity
+ * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
+ */
+ fixFirefoxAnchorBug : function() {
+ if (document.location.hash && $.browser.mozilla)
+ window.setTimeout(function() {
+ document.location.href += '';
+ }, 10);
+ },
+
+ /**
+ * highlight the search words provided in the url in the text
+ */
+ highlightSearchWords : function() {
+ var params = $.getQueryParameters();
+ var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+ if (terms.length) {
+ var body = $('div.body');
+ if (!body.length) {
+ body = $('body');
+ }
+ window.setTimeout(function() {
+ $.each(terms, function() {
+ body.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ }, 10);
+ $('