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* Lint check & fix to python3 format (#18) * lint check and change files from python2 to python3 * pre-commit check for these files * lint check & change to python3 & pre-commit check (#19) * lint check & change to python3 & pre-commit check * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * lint check and fix print and exception python2 issue (#20) * lint check and fix python2 print and exception issues (#21) * lint check and fix python2 print and exception issues * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * finish parenthesizing print statements (#24) * finish parenthesizing print statements * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix too many leading #, import modules, and unused var (#29) * requirements (#30) * fix import module not used & string check (#25) * fix too many leading "#" in string block (#26) * lint check, remove unused import modules & remove too many "#". (#27) * remove unused modules, ambiguous variable name (#28) * cleaning (#31) * requirements * clean out __init__ * replace ### * ins not none in modelevaluators base * Copyright (#32) * requirements * basefunction * all the copyright statements * lint check, fix break import modules, remove unused import modules, remove some # (#33) * fix break import modules, remove unused import modules, fix docstring length (#34) * fix formatting issue and typo in copyright (#35) * clean out inits (#38) * clean out inits * [pre-commit.ci] auto fixes from pre-commit hooks * dataclusters.py, modelevaluators/aicc and modelparts.py --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * peakextraction.py and init (#40) * move untrack doc and requirement files (#41) * move untrack doc and requirement files * add requirement in run.txt * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * add pyproject.toml (#42) * add pyproject.toml * [pre-commit.ci] auto fixes from pre-commit hooks * update classifiers pyproject.toml * Delete setup.py --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * move diffpy files to src dir (#44) * move diffpy files to src dir * [pre-commit.ci] auto fixes from pre-commit hooks * add Luke to authors --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * LICENSE (#45) * add two LICENSE.rst files into cookiecutter * fix LICENSE.rst and LICENSE_PDFgui.rst with correct references and year * resolve pdfdataset.py conflict --------- Co-authored-by: Simon Billinge <[email protected]> * add untrack files and add cookiecut.rst news (#46) * add untrack files and add cookiecut.rst news * delete README.txt * fix py2 -> py3, fix broken import, remove deprecation warning (#47) * fix py2 -> py3, move deprecation warning * fix search & split in binary files * fix broken import, remove deprecated pkg_resource (#50) * change import path to make it work. (#48) * fix import modules, py2->py3 (#49) * fix broken import in doc, change README to rst file. (#51) * fix broken import in doc, change README to rst file. * fix os getcwd method * fix p2 to p3 (#52) * add test for dataclusters (#54) * add test for dataclusters * define eq method in dataclusters.py * change parametrization form * add one more case and change reference name to actual * delete comment * add two more tests for DataClusters class function. * change in docstring for clearer explanation for clear method, remove duplicated case for testing behavior, remove other tests. * change clear method docstring into numpydoc format. Delete dtype for numpy array. * remove block * Make edition to condition on res, refactor for setdata to make behavior of the test passed. * change condition on res * add condition on x and res are incompatible, update test. * revert change in setdata method. * Eq tests (#59) * remove diffpy/srmise tree * test for eq * add attributes in eq method (#60) * Add set data test cases (#61) * add test cases to test files and make edition to make sure the behavior of the test pass. * [pre-commit.ci] auto fixes from pre-commit hooks * change case in test__eq__ to be compatible with the behavior of setdata * delete text and redundant tests * tweaking error message in DataClusters * [pre-commit.ci] auto fixes from pre-commit hooks * update test for checking implicit attributes for setdata function * [pre-commit.ci] auto fixes from pre-commit hooks * update test for setdata function * update setdata test to right format. * update to constructor test & make setdata clear function private * final tweaks to tests by Simon * fix actual_attribute typo * final refactor of actual_attr --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Simon Billinge <[email protected]> * fix arbitrary.py to numpydoc format (#68) * fix arbitrary.py to numpydoc format * pre-commit fix * change start sentence to 'The' * print things correctly (#71) * print things correctly * change to f string * reduce print to one line * change createpeak to actualize function (#72) * fix import and counting to make it work (#74) * refactor makeclusters to make it work (#73) * deprecation remove (#78) * deprecation remove * fix to right behavior * Revert "refactor makeclusters to make it work (#73)" (#79) This reverts commit 3773bcf. * try out py2 before py3 refactor to make sure correct workflow (#75) * fix false counting and numpy to int (#80) * fix false counting and numpy to int * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * numpydoc edition (#81) * change peakextraction function to numpydoc * pre-commit run * remove unused import * numpydoc build (#82) * numpydoc build on peakstability (#83) * numpydoc build for ModelCluster (#85) * numpydoc build for multimodelselection.py (#87) * numpydoc documentation build for ModelCluster class (#86) * numpydoc build for pdfdataset (#88) * numpydoc build for pdfpeakextraction.py (#89) * numpydoc build for gaussianoverr.py (#91) * numpydoc build for gaussianoverr.py * [pre-commit.ci] auto fixes from pre-commit hooks * fix pre-commit --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * terminationripples.py numpydoc build (#92) * numpydoc build for gaussian.py (#90) * numpydoc build for gaussian.py * [pre-commit.ci] auto fixes from pre-commit hooks * pre-commit fix * update for FWHM and maxwidth * update for starting sentence --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * numpydoc build for base.py (#95) * numpydoc build for polynomial.py (#97) * numpydoc build for fromsequence.py (#99) * numpydoc build for nanospherical.py (#98) * numpydoc build for base.py in Baseline class (#96) * numpydoc build for base.py * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * numpydoc build for aic.py (#93) * numpydoc build for aicc.py (#94) * numpydoc build for ModelCovariance (#84) * numpydoc build for ModelCovariance * update format type and fix indentation issue * numpydoc build for modelparts.py (#100) * numpydoc build for modelparts.py * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * numpydoc build for basefunction.py (#101) * api workflow build for diffpy.srmise (#102) * api workflow build for diffpy.srmise * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * add changed news (#103) --------- Co-authored-by: Rundong Hua <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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diffpy.srmise/_version.py export-subst

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Authors
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=======
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Luke Granlund
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Billinge Group and community contibutors.
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Contributors
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------------
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For a list of contributors, visit
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https://github.com/diffpy/diffpy.srmise/graphs/contributors

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=============
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Release Notes
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=============
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.. current developments

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=====================================
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Contributor Covenant Code of Conduct
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=====================================
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Our Pledge
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----------
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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Our Standards
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-------------
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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Enforcement Responsibilities
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----------------------------
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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Scope
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-----
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official email address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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Enforcement
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-----------
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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[email protected]. All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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Enforcement Guidelines
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----------------------
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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1. Correction
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****************
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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2. Warning
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*************
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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3. Temporary Ban
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******************
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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4. Permanent Ban
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******************
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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Attribution
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-----------
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This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
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Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.
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For answers to common questions about this code of conduct, see the `FAQ <https://www.contributor-covenant.org/faq>`_. `Translations are available <https://www.contributor-covenant.org/translations>`_

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BSD 3-Clause License
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Copyright 2014-2015, Board of Trustees of Michigan State University
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2016-2024, The Trustees of Columbia University in the City of New York.
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All rights reserved.
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If you use this program to do productive scientific research that
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leads to publication, we ask that you acknowledge use of the
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program by citing the following paper in your publication:
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L. Granlund, S.J.L. Billinge, P.M. Duxbury, Algorithm for
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systematic peak extraction from atomic pair distribution
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functions, Acta Crystallographica A 71(4), 392-409 (2015).
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doi:10.1107/S2053273315005276
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For more information please visit the diffpy web-page at
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http://www.diffpy.org
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or email Luke Granlund at [email protected], or Prof. Simon
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Billinge at [email protected].
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its contributors
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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BSD 3-Clause License
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Copyright 2006-2007, Board of Trustees of Michigan State University
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2008-2024, The Trustees of Columbia University in the City of New York.
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All rights reserved.
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SrMise incorporates source code from diffpy.pdfgui in the file
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pdfdataset.py. The PDFgui license is reproduced in full below.
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This program is part of the DiffPy and DANSE open-source projects
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and is available subject to the conditions and terms laid out
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below.
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If you use this program to do productive scientific research that
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leads to publication, we ask that you acknowledge use of the
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program by citing the following paper in your publication:
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C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin,
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J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and
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PDFgui: computer programs for studying nanostructure in
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crystals, J. Phys.: Condens. Matter 19, 335219 (2007)
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For more information please visit the diffpy web-page at
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http://www.diffpy.org
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or email Luke Granlund at [email protected], or Prof. Simon
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Billinge at [email protected].
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its contributors
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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