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Populate API
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Diff for: ‎doc/source/api/diffpy.pdfmorph.example_package.rst

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Diff for: ‎doc/source/api/diffpy.pdfmorph.morph_helpers.rst

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:tocdepth: -1
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diffpy.pdfmorph.morph_helpers package
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=====================================
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.. automodule:: diffpy.pdfmorph.morph_helpers
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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diffpy.pdfmorph.morph_helpers.transformpdftordf module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morph_helpers.transformpdftordf
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morph_helpers.transformrdftopdf module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morph_helpers.transformrdftopdf
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:members:
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:undoc-members:
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:show-inheritance:

Diff for: ‎doc/source/api/diffpy.pdfmorph.morphs.rst

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:tocdepth: -1
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diffpy.pdfmorph.morphs package
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==============================
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.. automodule:: diffpy.pdfmorph.morphs
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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diffpy.pdfmorph.morphs.morphishape module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphishape
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphchain module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphchain
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphresolution module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphresolution
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphshape module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphshape
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphshift module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphshift
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morph module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morph
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphrgrid module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphrgrid
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphsmear module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphsmear
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphstretch module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphstretch
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.morphs.morphscale module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.morphs.morphscale
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:members:
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:undoc-members:
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:show-inheritance:

Diff for: ‎doc/source/api/diffpy.pdfmorph.rst

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:tocdepth: -1
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diffpy.pdfmorph package
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=======================================
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=======================
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.. automodule:: diffpy.pdfmorph
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:members:
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-----------
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.. toctree::
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diffpy.pdfmorph.example_package
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:titlesonly:
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diffpy.pdfmorph.morphs
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diffpy.pdfmorph.morph_helpers
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Submodules
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----------
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diffpy.pdfmorph.example_submodule module
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------------------------------------------------------------
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diffpy.pdfmorph.pdfplot module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.pdfplot
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.pdfmorph_api module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.pdfmorph_api
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.refine module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.refine
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.tools module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.tools
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.pdfmorph_io module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.pdfmorph_io
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.log module
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.log
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.pdfmorph.pdfmorphapp module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.pdfmorph.example_submodule
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.. automodule:: diffpy.pdfmorph.pdfmorphapp
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:members:
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:undoc-members:
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:show-inheritance:

Diff for: ‎doc/source/conf.py

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# All configuration values have a default; values that are commented out
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# serve to show the default.
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import os
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import sys
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import time
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from importlib.metadata import version
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from pathlib import Path
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autodoc_mock_imports = [
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"diffpy.utils",
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]
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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# sys.path.insert(0, os.path.abspath('.'))
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sys.path.insert(0, os.path.abspath("../.."))
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sys.path.insert(0, os.path.abspath("../../src"))
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# abbreviations
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# documentation root, use Path().resolve() to make it absolute, like shown here.
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# sys.path.insert(0, str(Path(".").resolve()))
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sys.path.insert(0, str(Path("../..").resolve()))
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sys.path.insert(0, str(Path("../../src").resolve())) # abbreviations
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ab_authors = "Billinge Group members and community contributors"
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# -- General configuration ------------------------------------------------
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# ones.
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.intersphinx",
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"sphinx.ext.napoleon",
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"sphinx.ext.todo",
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"sphinx.ext.viewcode",
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"sphinx.ext.intersphinx",
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"sphinx_rtd_theme",
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"m2r",
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]
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Diff for: ‎doc/source/index.rst

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| Software version |release|.
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| Last updated |today|.
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Introduction
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++++++++++++
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``PDFmorph`` is a Python package that increases the insight
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researchers can obtain from measured atomic pair distribution functions
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(PDFs) in a model-independent way. It was designed to help a
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researcher answer the question: "Has my material undergone a phase
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transition between these two measurements?"
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One approach is to compare the two PDFs in a plot and view the
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difference curve underneath. However, significant signal can be seen in
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the difference curve from benign effects such as thermal expansion (peak
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shifts) and increased thermal motion (peak broadening) or a change in
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scale due to differences in incident flux, for example. ``PDFmorph`` will
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do its best to correct for these benign effects before computing and
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plotting the difference curve. One measured PDF (typically that
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collected under higher temperature) is identified as the target PDF and
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the second PDF is then morphed by "stretching" (changing the r-axis to
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simulate a uniform lattice expansion), "smearing" (broadening peaks
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through a uniform convolution to simulate increased thermal motion), and
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"scaling" (self-explanatory). PDFmorph will vary the amplitude of the
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morphing transformations to obtain the best fit between the morphed and
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the target PDFs, then plot them on top of each other with the difference
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plotted below.
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There are also a few other morphing transformations in the program.
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If no morphing transformation is specified, ``PDFmorph`` will return just
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the plotted PDFs.
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Finally, we note that though ``PDFmorph`` should work on other spectra
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that are not PDFs, it has not been extensively tested beyond the PDF.
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To get started, please download our :download:`user manual <../manual/pdfmorph.pdf>`
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or visit the :ref:`quick_start`.
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=======
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Authors
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=======
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diffpy.pdfmorph is developed by Billinge Group
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and its community contributors.
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``PDFmorph`` is developed by members of the Billinge Group at
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Columbia University and Brookhaven National Laboratory including
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Christopher L. Farrow, Christopher J. Wright, Pavol Juhás, Chia-Hao
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(Timothy) Liu, S. Matthew Román, and Simon J. L. Billinge.
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For a detailed list of contributors see
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https://github.com/diffpy/diffpy.pdfmorph/graphs/contributors.
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.. toctree::
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:titlesonly:
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quickstart
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license
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release
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Package API <api/diffpy.pdfmorph>

Diff for: ‎doc/source/quickstart.rst

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Welcome! This will be a quick tutorial to accquaint users with PDFmorph
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and some of what it can do. For a more detailed tutorial, check out
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our :download:`user manual <../pdfmorph.pdf>`.
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our :download:`user manual <../manual/pdfmorph.pdf>`.
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As we described in the README and installation instructions, please make
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sure that you are familiar with working with your command line terminal
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3. Using the ``mkdir`` command, create a directory where you'll
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:download:`here <../../../tutorial/tutorialData.zip>`.
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:download:`here <../../tutorial/tutorialData.zip>`.
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Then, ``cd`` into the ``tutorialData`` directory.
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* The files in this dataset were collected by Soham Banerjee
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.. Additional PDFmorph Functionality/Exploration
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.. ---------------------------------------------
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.. TODO include undoped PDF example
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Extra Tutorials
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===============
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PDFmorph has some more functionalities not showcased in the basic workflow above
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(see `pdfmorph --help` for an overview of these functionalities).
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Tutorials for these additional functionalities are included below. Additional
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files for these tutorials can be downloaded
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:download:`here <../../../tutorial/additionalData.zip>`.
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:download:`here <../../tutorial/additionalData.zip>`.
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Performing Multiple Morphs
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--------------------------

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