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* untracked files * [pre-commit.ci] auto fixes from pre-commit hooks * update LICENSE.rst * update AUTHORS.rst and remove AUTHORS.txt * tipping our hat * Remove BSD 3-Clause, leaving Columbia copyright * remove README from requirements * replace requirements * adding wxpython back * adding back freezegun --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Simon Billinge <[email protected]>
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‎.isort.cfg

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[settings]
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line_length = 115
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multi_line_output = 3
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include_trailing_comma = True

‎AUTHORS.txt ‎AUTHORS.rst

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Authors
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=======
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DiffPy was initiated as part of the Distributed Data Analysis of Neutron
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Scattering Experiments (DANSE) project, funded by the National Science
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Foundation under grant DMR-0520547. More information on DANSE can be
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found at http://danse.us. Any opinions, findings, and conclusions or
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recommendations expressed in this material are those of the author(s)
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and do not necessarily reflect the views of the NSF.
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Main Contributors
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-----------------
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This code was developed as part of the DiffPy project to create python
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modules for structure investigations from diffraction data. The main
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contributors to this package were
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Pavol Juhas
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Dmitriy Bryndin
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The DiffPy team is located in the Billinge-group at the Applied Physics
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and Applied Mathematics Department of the Columbia University in New York.
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Currently the team consists of
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Other current and former contributors of the DiffPy project include
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Simon Billinge
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Pavol Juhas
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Chris Farrow
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Emil Bozin
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Wenduo Zhou
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Peng Tian
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Timur Dykhne
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The DiffPy team is part of the Billinge Group at Columbia University in New York,
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within the Department of Applied Physics and Applied Mathematics.
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Contributors
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------------
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Please see the header of each source file for a detailed list of
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contributors. This is an open-source project and we hope and expect
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that the list of contributors will expand with time. Many thanks to
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all current and future contributors!
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For more information on the DiffPy project email [email protected]
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DiffPy was initiated as part of the Distributed Data Analysis of Neutron
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Scattering Experiments (DANSE) project, funded by the National Science
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Foundation under grant DMR-0520547. More information on DANSE can be
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found at http://danse.us. Any opinions, findings, and conclusions or
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recommendations expressed in this material are those of the author(s)
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and do not necessarily reflect the views of the NSF.
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For a list of contributors, visit
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https://github.com/diffpy/diffpy.pdfgui/graphs/contributors
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Acknowledgments:
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Acknowledgments
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---------------
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We are truly grateful to all the people who have contributed, in all
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different ways, to this project: Thomas Proffen, Xiangyun Qiu, Pete

‎CODE_OF_CONDUCT.rst

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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>`_

‎LICENSE.txt ‎LICENSE.rst

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Copyright (c) 2024, The Trustees of Columbia University
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in the City of New York.
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All rights reserved.
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This software was originally developed by the Billinge group as part
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of the Distributed Data Analysis of Neutron Scattering Experiments
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(DANSE) project funded by the US National Science Foundation under
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or email Prof. Simon 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
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are met:
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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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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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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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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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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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 COPYRIGHT HOLDER "AS IS". COPYRIGHT HOLDER
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EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER
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EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY
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FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM
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INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE
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SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY. IN NO EVENT SHALL
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COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR ANY DIRECT, INDIRECT,
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INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
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THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE
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POSSIBILITY OF SUCH DAMAGE.
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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.

‎requirements/build.txt

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python
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setuptools

‎requirements/docs.txt

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sphinx
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sphinx_rtd_theme
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doctr
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m2r

‎requirements/pip.txt

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‎requirements/run.txt

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numpy==1.26
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wxpython
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diffpy.pdffit2
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diffpy.utils
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matplotlib-base
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numpy==1.26
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wxpython
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diffpy.pdffit2
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diffpy.utils
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matplotlib-base

‎requirements/test.txt

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pytest
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flake8
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freezegun
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coverage
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pytest
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codecov
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coverage
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pytest-env

‎src/diffpy/pdfgui/control/calculation.py

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import copy
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import math
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from diffpy.pdfgui.control.controlerrors import (
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ControlConfigError,
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ControlKeyError,
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ControlValueError,
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)
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from diffpy.pdfgui.control.controlerrors import ControlConfigError, ControlKeyError, ControlValueError
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from diffpy.pdfgui.control.pdfcomponent import PDFComponent
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from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps
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def start(self):
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"""entry function for calculation"""
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from diffpy.pdfgui.control.fitting import (
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getEngineExceptions,
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handleEngineException,
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)
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from diffpy.pdfgui.control.fitting import getEngineExceptions, handleEngineException
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try:
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self.calculate()

‎src/diffpy/pdfgui/control/fitting.py

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import threading
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import time
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ControlError,
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ControlStatusError,
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ControlValueError,
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)
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from diffpy.pdfgui.control.controlerrors import ControlError, ControlStatusError, ControlValueError
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from diffpy.pdfgui.control.organizer import Organizer
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‎src/diffpy/pdfgui/control/pdfguicontrol.py

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import six.moves.cPickle as pickle
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from diffpy.pdfgui.control.controlerrors import (
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ControlError,
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ControlFileError,
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ControlTypeError,
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)
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from diffpy.pdfgui.control.controlerrors import ControlError, ControlFileError, ControlTypeError
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from diffpy.pdfgui.control.fitdataset import FitDataSet
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from diffpy.pdfgui.control.fitstructure import FitStructure
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from diffpy.pdfgui.control.fitting import Fitting

‎src/diffpy/pdfgui/tests/conftest.py

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import json
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from pathlib import Path
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import pytest
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@pytest.fixture
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def user_filesystem(tmp_path):
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base_dir = Path(tmp_path)
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home_dir = base_dir / "home_dir"
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home_dir.mkdir(parents=True, exist_ok=True)
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cwd_dir = base_dir / "cwd_dir"
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cwd_dir.mkdir(parents=True, exist_ok=True)
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home_config_data = {"username": "home_username", "email": "[email protected]"}
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with open(home_dir / "diffpyconfig.json", "w") as f:
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json.dump(home_config_data, f)
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yield tmp_path

‎src/diffpy/pdfgui/tests/testphaseconfigurepanel.py

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from diffpy.pdfgui.gui.mainframe import MainFrame
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from diffpy.pdfgui.gui.phaseconfigurepanel import PhaseConfigurePanel
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from diffpy.pdfgui.tests.testutils import (
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GUITestCase,
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clickcell,
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datafile,
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overrideclipboard,
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tooltiptext,
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)
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from diffpy.pdfgui.tests.testutils import GUITestCase, clickcell, datafile, overrideclipboard, tooltiptext
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# ----------------------------------------------------------------------------
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