From 6421b8158f71a0f8147fa752ab0432c218f8d2ec Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 1 Aug 2024 12:04:13 -0400 Subject: [PATCH 01/10] untracked files --- .isort.cfg | 4 + AUTHORS.rst | 10 +++ CODE_OF_CONDUCT.rst | 133 ++++++++++++++++++++++++++++ LICENSE.rst | 30 +++++++ requirements/README.txt | 11 +++ requirements/build.txt | 2 + requirements/docs.txt | 4 + requirements/pip.txt | 0 requirements/run.txt | 5 -- requirements/test.txt | 5 +- src/diffpy/pdfgui/tests/conftest.py | 19 ++++ 11 files changed, 216 insertions(+), 7 deletions(-) create mode 100644 .isort.cfg create mode 100644 AUTHORS.rst create mode 100644 CODE_OF_CONDUCT.rst create mode 100644 LICENSE.rst create mode 100644 requirements/README.txt create mode 100644 requirements/build.txt create mode 100644 requirements/docs.txt create mode 100644 requirements/pip.txt create mode 100644 src/diffpy/pdfgui/tests/conftest.py diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 00000000..e0926f42 --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,4 @@ +[settings] +line_length = 115 +multi_line_output = 3 +include_trailing_comma = True diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 00000000..c817445c --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,10 @@ +Authors +======= + +Billinge Group and community contibutors. + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.pdfgui/graphs/contributors diff --git a/CODE_OF_CONDUCT.rst b/CODE_OF_CONDUCT.rst new file mode 100644 index 00000000..ff9c3561 --- /dev/null +++ b/CODE_OF_CONDUCT.rst @@ -0,0 +1,133 @@ +===================================== + Contributor Covenant Code of Conduct +===================================== + +Our Pledge +---------- + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +Our Standards +------------- + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +Enforcement Responsibilities +---------------------------- + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +Scope +----- + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +Enforcement +----------- + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +Enforcement Guidelines +---------------------- + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +1. Correction +**************** + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +2. Warning +************* + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +3. Temporary Ban +****************** + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +4. Permanent Ban +****************** + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +Attribution +----------- + +This Code of Conduct is adapted from the `Contributor Covenant `_. + +Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder `_. + +For answers to common questions about this code of conduct, see the `FAQ `_. `Translations are available `_ diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 00000000..95a04ac9 --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,30 @@ +BSD 3-Clause License + +Copyright (c) 2024, The Trustees of Columbia University +in the City of New York. +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/requirements/README.txt b/requirements/README.txt new file mode 100644 index 00000000..dc34909d --- /dev/null +++ b/requirements/README.txt @@ -0,0 +1,11 @@ +# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! +# +# This directory is where you should place your project dependencies. +# "pip.txt" should contain all required packages not available on conda. +# All other files should contain only packages available to download from conda. +# build.txt should contain all packages required to build (not run) the project. +# run.txt should contain all packages (including optional packages) required for a user to run the program. +# test.txt should contain all packages required for the testing suite and to ensure all tests pass. +# docs.txt should contain all packages required for building the package documentation page. +# +# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! diff --git a/requirements/build.txt b/requirements/build.txt new file mode 100644 index 00000000..f72d870d --- /dev/null +++ b/requirements/build.txt @@ -0,0 +1,2 @@ +python +setuptools diff --git a/requirements/docs.txt b/requirements/docs.txt new file mode 100644 index 00000000..ab17b1c8 --- /dev/null +++ b/requirements/docs.txt @@ -0,0 +1,4 @@ +sphinx +sphinx_rtd_theme +doctr +m2r diff --git a/requirements/pip.txt b/requirements/pip.txt new file mode 100644 index 00000000..e69de29b diff --git a/requirements/run.txt b/requirements/run.txt index 40bce3f0..e69de29b 100644 --- a/requirements/run.txt +++ b/requirements/run.txt @@ -1,5 +0,0 @@ -numpy==1.26 -wxpython -diffpy.pdffit2 -diffpy.utils -matplotlib-base diff --git a/requirements/test.txt b/requirements/test.txt index 628a048a..6f9ccf84 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -1,4 +1,5 @@ +flake8 pytest -freezegun -coverage codecov +coverage +pytest-env diff --git a/src/diffpy/pdfgui/tests/conftest.py b/src/diffpy/pdfgui/tests/conftest.py new file mode 100644 index 00000000..e3b63139 --- /dev/null +++ b/src/diffpy/pdfgui/tests/conftest.py @@ -0,0 +1,19 @@ +import json +from pathlib import Path + +import pytest + + +@pytest.fixture +def user_filesystem(tmp_path): + base_dir = Path(tmp_path) + home_dir = base_dir / "home_dir" + home_dir.mkdir(parents=True, exist_ok=True) + cwd_dir = base_dir / "cwd_dir" + cwd_dir.mkdir(parents=True, exist_ok=True) + + home_config_data = {"username": "home_username", "email": "home@email.com"} + with open(home_dir / "diffpyconfig.json", "w") as f: + json.dump(home_config_data, f) + + yield tmp_path From e8594a9426062019c0deb64d6948aedc2fb254b3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 1 Aug 2024 16:06:27 +0000 Subject: [PATCH 02/10] [pre-commit.ci] auto fixes from pre-commit hooks --- src/diffpy/pdfgui/control/calculation.py | 11 ++--------- src/diffpy/pdfgui/control/fitting.py | 6 +----- src/diffpy/pdfgui/control/pdfguicontrol.py | 6 +----- src/diffpy/pdfgui/tests/testphaseconfigurepanel.py | 8 +------- 4 files changed, 5 insertions(+), 26 deletions(-) diff --git a/src/diffpy/pdfgui/control/calculation.py b/src/diffpy/pdfgui/control/calculation.py index 2cab84a3..13819b81 100644 --- a/src/diffpy/pdfgui/control/calculation.py +++ b/src/diffpy/pdfgui/control/calculation.py @@ -19,11 +19,7 @@ import copy import math -from diffpy.pdfgui.control.controlerrors import ( - ControlConfigError, - ControlKeyError, - ControlValueError, -) +from diffpy.pdfgui.control.controlerrors import ControlConfigError, ControlKeyError, ControlValueError from diffpy.pdfgui.control.pdfcomponent import PDFComponent from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps @@ -124,10 +120,7 @@ def setRGrid(self, rmin=None, rstep=None, rmax=None): def start(self): """entry function for calculation""" - from diffpy.pdfgui.control.fitting import ( - getEngineExceptions, - handleEngineException, - ) + from diffpy.pdfgui.control.fitting import getEngineExceptions, handleEngineException try: self.calculate() diff --git a/src/diffpy/pdfgui/control/fitting.py b/src/diffpy/pdfgui/control/fitting.py index 8e24aed5..0d56df89 100644 --- a/src/diffpy/pdfgui/control/fitting.py +++ b/src/diffpy/pdfgui/control/fitting.py @@ -18,11 +18,7 @@ import threading import time -from diffpy.pdfgui.control.controlerrors import ( - ControlError, - ControlStatusError, - ControlValueError, -) +from diffpy.pdfgui.control.controlerrors import ControlError, ControlStatusError, ControlValueError from diffpy.pdfgui.control.organizer import Organizer from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps diff --git a/src/diffpy/pdfgui/control/pdfguicontrol.py b/src/diffpy/pdfgui/control/pdfguicontrol.py index 15632a0d..c6619417 100644 --- a/src/diffpy/pdfgui/control/pdfguicontrol.py +++ b/src/diffpy/pdfgui/control/pdfguicontrol.py @@ -24,11 +24,7 @@ import six.moves.cPickle as pickle from diffpy.pdfgui.control.calculation import Calculation -from diffpy.pdfgui.control.controlerrors import ( - ControlError, - ControlFileError, - ControlTypeError, -) +from diffpy.pdfgui.control.controlerrors import ControlError, ControlFileError, ControlTypeError from diffpy.pdfgui.control.fitdataset import FitDataSet from diffpy.pdfgui.control.fitstructure import FitStructure from diffpy.pdfgui.control.fitting import Fitting diff --git a/src/diffpy/pdfgui/tests/testphaseconfigurepanel.py b/src/diffpy/pdfgui/tests/testphaseconfigurepanel.py index 5f41f64e..acc01ec6 100644 --- a/src/diffpy/pdfgui/tests/testphaseconfigurepanel.py +++ b/src/diffpy/pdfgui/tests/testphaseconfigurepanel.py @@ -23,13 +23,7 @@ from diffpy.pdfgui.gui.mainframe import MainFrame from diffpy.pdfgui.gui.phaseconfigurepanel import PhaseConfigurePanel -from diffpy.pdfgui.tests.testutils import ( - GUITestCase, - clickcell, - datafile, - overrideclipboard, - tooltiptext, -) +from diffpy.pdfgui.tests.testutils import GUITestCase, clickcell, datafile, overrideclipboard, tooltiptext # ---------------------------------------------------------------------------- From c754e1b34503e47ff56d01930772739cd4003313 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 1 Aug 2024 13:34:04 -0400 Subject: [PATCH 03/10] update LICENSE.rst --- LICENSE.rst | 48 +++++++++++++++++++++++++++++++++ LICENSE.txt | 78 ----------------------------------------------------- 2 files changed, 48 insertions(+), 78 deletions(-) delete mode 100644 LICENSE.txt diff --git a/LICENSE.rst b/LICENSE.rst index 95a04ac9..61942254 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -4,6 +4,54 @@ Copyright (c) 2024, The Trustees of Columbia University in the City of New York. All rights reserved. +This software was originally developed by the Billinge group as part +of the Distributed Data Analysis of Neutron Scattering Experiments +(DANSE) project funded by the US National Science Foundation under +grant DMR-0520547. Developments of PDFfit2 were funded by NSF grant +DMR-0304391 in the Billinge group, and with support from Michigan State +University and Columbia University. Any opinions, findings, and conclusions +or recommendations expressed in this material are those of the author(s) +and do not necessarily reflect the views of the respective funding bodies. +Subsequent development was done in the Billinge group at Columbia University +and then in collaboration between the Billinge group at Columbia and Pavol +Juhas at Brookhaven National Laboratory. Moving forward, PDFgui will be +maintained as a community project with contributions welcomed from many people. + +If you use this program to do productive scientific research that leads +to publication, we ask that you acknowledge use of the program by citing +the following paper in your publication: + + C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin, + J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and + PDFgui: computer programs for studying nanostructure in + crystals, J. Phys.: Condens. Matter 19, 335219 (2007) + +Up to the release 1.1.2 (February 2017) the copyright was held by +the institutions that hosted the work as follows: +Copyright 2006-2007, Board of Trustees of Michigan State University, +Copyright 2008-2012, Board of Trustees of Columbia University in the +city of New York. +Copyright 2013, Brookhaven National Laboratory (Copyright holder +indicated in each source file). + +As of February 2017, and the 1.1.2 release, PDFgui has moved to a shared copyright model. + +PDFgui uses a shared copyright model. Each contributor maintains copyright over their +contributions to PDFgui. But, it is important to note that these contributions are +typically only changes to the repositories. Thus, the PDFgui source code, in its entirety, +is not the copyright of any single person or institution. Instead, it is the collective +copyright of the entire PDFgui Development Team. If individual contributors want to +maintain a record of what changes/contributions they have specific copyright on, they +should indicate their copyright in the commit message of the change, when they commit +the change to one of the PDFgui repositories. + +The PDFgui Development Team is the set of all contributors to the PDFgui project. +A full list can be obtained from the git version control logs. + +For more information please visit the project web-page: + https://www.diffpy.org +or email Prof. Simon Billinge at sb2896@columbia.edu + Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/LICENSE.txt b/LICENSE.txt deleted file mode 100644 index f451dcb7..00000000 --- a/LICENSE.txt +++ /dev/null @@ -1,78 +0,0 @@ -This software was originally developed by the Billinge group as part -of the Distributed Data Analysis of Neutron Scattering Experiments -(DANSE) project funded by the US National Science Foundation under -grant DMR-0520547. Developments of PDFfit2 were funded by NSF grant -DMR-0304391 in the Billinge group, and with support from Michigan State -University and Columbia University. Any opinions, findings, and conclusions -or recommendations expressed in this material are those of the author(s) -and do not necessarily reflect the views of the respective funding bodies. -Subsequent development was done in the Billinge group at Columbia University -and then in collaboration between the Billinge group at Columbia and Pavol -Juhas at Brookhaven National Laboratory. Moving forward, PDFgui will be -maintained as a community project with contributions welcomed from many people. - -If you use this program to do productive scientific research that leads -to publication, we ask that you acknowledge use of the program by citing -the following paper in your publication: - - C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin, - J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and - PDFgui: computer programs for studying nanostructure in - crystals, J. Phys.: Condens. Matter 19, 335219 (2007) - -Up to the release 1.1.2 (February 2017) the copyright was held by -the institutions that hosted the work as follows: -Copyright 2006-2007, Board of Trustees of Michigan State University, -Copyright 2008-2012, Board of Trustees of Columbia University in the -city of New York. -Copyright 2013, Brookhaven National Laboratory (Copyright holder -indicated in each source file). - -As of February 2017, and the 1.1.2 release, PDFgui has moved to a shared copyright model. - -PDFgui uses a shared copyright model. Each contributor maintains copyright over their -contributions to PDFgui. But, it is important to note that these contributions are -typically only changes to the repositories. Thus, the PDFgui source code, in its entirety, -is not the copyright of any single person or institution. Instead, it is the collective -copyright of the entire PDFgui Development Team. If individual contributors want to -maintain a record of what changes/contributions they have specific copyright on, they -should indicate their copyright in the commit message of the change, when they commit -the change to one of the PDFgui repositories. - -The PDFgui Development Team is the set of all contributors to the PDFgui project. -A full list can be obtained from the git version control logs. - -For more information please visit the project web-page: - https://www.diffpy.org -or email Prof. Simon Billinge at sb2896@columbia.edu - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions -are met: - - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - - * Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - - * Neither the name of the copyright holder nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER "AS IS". COPYRIGHT HOLDER -EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER -EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY -FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM -INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE -SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY. IN NO EVENT SHALL -COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR ANY DIRECT, INDIRECT, -INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT -NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF -USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF -THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE -POSSIBILITY OF SUCH DAMAGE. From 5c2524ee3c3e86a1caf25d30641ce6a0f6cc361c Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 1 Aug 2024 13:42:40 -0400 Subject: [PATCH 04/10] update AUTHORS.rst and remove AUTHORS.txt --- AUTHORS.rst | 42 +++++++++++++++++++++++++++++++++++++++++- AUTHORS.txt | 50 -------------------------------------------------- 2 files changed, 41 insertions(+), 51 deletions(-) delete mode 100644 AUTHORS.txt diff --git a/AUTHORS.rst b/AUTHORS.rst index c817445c..0046b39c 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -1,10 +1,50 @@ Authors ======= -Billinge Group and community contibutors. +DiffPy was initiated as part of the Distributed Data Analysis of Neutron +Scattering Experiments (DANSE) project, funded by the National Science +Foundation under grant DMR-0520547. More information on DANSE can be +found at http://danse.us. Any opinions, findings, and conclusions or +recommendations expressed in this material are those of the author(s) +and do not necessarily reflect the views of the NSF. + +Main Contributors +----------------- + +This code was developed as part of the DiffPy project to create python +modules for structure investigations from diffraction data. The main +contributors to this package were + + Chris Farrow + Jiwu Liu + Pavol Juhas + Dmitriy Bryndin Contributors ------------ +Please see the header of each source file for a detailed list of +contributors. This is an open-source project and we hope and expect +that the list of contributors will expand with time. Many thanks to +all current and future contributors! + +For more information on the DiffPy project email sb2896@columbia.edu For a list of contributors, visit https://github.com/diffpy/diffpy.pdfgui/graphs/contributors + +Acknowledgments +--------------- + +We are truly grateful to all the people who have contributed, in all +different ways, to this project: Thomas Proffen, Xiangyun Qiu, Pete +Peterson and Jacques Bloch, previous Billinge-group members whose +contributions to the codes are living well beyond their affiliation with +the group; The hard working DANSE group at Caltech, University of +Maryland, Iowa State and University of Tennessee, especially Brent Fultz +for doggedly putting DANSE all together and Michael Aivazis, and the +indomitable Mike McKerns for their design input and MM's gargantuan +excel spreadsheets; The former members of the Billinge-group members, +especially HyunJeong Kim and Ahmad Masadeh for enthusiastic testing and +feature requests; Last but not least, our long suffering family members, +and the whole coffee and tea industries at large, without whom none of +this would have been possible. diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index a6b9bc57..00000000 --- a/AUTHORS.txt +++ /dev/null @@ -1,50 +0,0 @@ -This code was developed as part of the DiffPy project to create python -modules for structure investigations from diffraction data. The main -contributors to this package were - - Chris Farrow - Jiwu Liu - Pavol Juhas - Dmitriy Bryndin - -The DiffPy team is located in the Billinge-group at the Applied Physics -and Applied Mathematics Department of the Columbia University in New York. -Currently the team consists of - - Simon Billinge - Pavol Juhas - Chris Farrow - Emil Bozin - Wenduo Zhou - Peng Tian - Timur Dykhne - -Please see the header of each source file for a detailed list of -contributors. This is an open-source project and we hope and expect -that the list of contributors will expand with time. Many thanks to -all current and future contributors! - -For more information on the DiffPy project email sb2896@columbia.edu - -DiffPy was initiated as part of the Distributed Data Analysis of Neutron -Scattering Experiments (DANSE) project, funded by the National Science -Foundation under grant DMR-0520547. More information on DANSE can be -found at http://danse.us. Any opinions, findings, and conclusions or -recommendations expressed in this material are those of the author(s) -and do not necessarily reflect the views of the NSF. - -Acknowledgments: - -We are truly grateful to all the people who have contributed, in all -different ways, to this project: Thomas Proffen, Xiangyun Qiu, Pete -Peterson and Jacques Bloch, previous Billinge-group members whose -contributions to the codes are living well beyond their affiliation with -the group; The hard working DANSE group at Caltech, University of -Maryland, Iowa State and University of Tennessee, especially Brent Fultz -for doggedly putting DANSE all together and Michael Aivazis, and the -indomitable Mike McKerns for their design input and MM's gargantuan -excel spreadsheets; The former members of the Billinge-group members, -especially HyunJeong Kim and Ahmad Masadeh for enthusiastic testing and -feature requests; Last but not least, our long suffering family members, -and the whole coffee and tea industries at large, without whom none of -this would have been possible. From d1eb042db112e54dc60843a11deb35ea971bf2e2 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 1 Aug 2024 20:20:37 -0400 Subject: [PATCH 05/10] tipping our hat --- AUTHORS.rst | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/AUTHORS.rst b/AUTHORS.rst index 0046b39c..c942b8dd 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -20,6 +20,17 @@ contributors to this package were Pavol Juhas Dmitriy Bryndin +Other current and former contributors of the DiffPy project include + + Simon Billinge + Chris Farrow + Emil Bozin + Wenduo Zhou + Peng Tian + +The DiffPy team is part of the Billinge Group at Columbia University in New York, +within the Department of Applied Physics and Applied Mathematics. + Contributors ------------ Please see the header of each source file for a detailed list of From 4026cfa6e974db93c66b97e6bf2666517e582436 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 2 Aug 2024 10:35:39 -0400 Subject: [PATCH 06/10] Remove BSD 3-Clause, leaving Columbia copyright --- LICENSE.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/LICENSE.rst b/LICENSE.rst index 61942254..0cebd08f 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -1,5 +1,3 @@ -BSD 3-Clause License - Copyright (c) 2024, The Trustees of Columbia University in the City of New York. All rights reserved. From ec29956b5d3363e582ef7361bbac83e07df4b259 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 2 Aug 2024 10:38:15 -0400 Subject: [PATCH 07/10] remove README from requirements --- requirements/README.txt | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 requirements/README.txt diff --git a/requirements/README.txt b/requirements/README.txt deleted file mode 100644 index dc34909d..00000000 --- a/requirements/README.txt +++ /dev/null @@ -1,11 +0,0 @@ -# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! -# -# This directory is where you should place your project dependencies. -# "pip.txt" should contain all required packages not available on conda. -# All other files should contain only packages available to download from conda. -# build.txt should contain all packages required to build (not run) the project. -# run.txt should contain all packages (including optional packages) required for a user to run the program. -# test.txt should contain all packages required for the testing suite and to ensure all tests pass. -# docs.txt should contain all packages required for building the package documentation page. -# -# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! From ff7fb3db39e41b92329ecb5197e19c51ca270384 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Fri, 2 Aug 2024 15:55:35 -0400 Subject: [PATCH 08/10] replace requirements --- requirements/run.txt | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/requirements/run.txt b/requirements/run.txt index e69de29b..37edf04d 100644 --- a/requirements/run.txt +++ b/requirements/run.txt @@ -0,0 +1,4 @@ +numpy==1.26 +diffpy.pdffit2 +diffpy.utils +matplotlib-base From c0a61e553b9e63d1f1a8eafe649eed01dcf036d5 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Fri, 2 Aug 2024 15:58:26 -0400 Subject: [PATCH 09/10] adding wxpython back --- requirements/run.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/run.txt b/requirements/run.txt index 37edf04d..1bad6988 100644 --- a/requirements/run.txt +++ b/requirements/run.txt @@ -1,4 +1,5 @@ numpy==1.26 +wxpython diffpy.pdffit2 diffpy.utils matplotlib-base From 860a6b7040b2db65ce2b3dbfad02bb45076bd4af Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Fri, 2 Aug 2024 15:59:00 -0400 Subject: [PATCH 10/10] adding back freezegun --- requirements/test.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/test.txt b/requirements/test.txt index 6f9ccf84..977a5764 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -1,4 +1,5 @@ flake8 +freezegun pytest codecov coverage