From d020dbbf1b35ad5e6d1afa3a270a7abddb0626c1 Mon Sep 17 00:00:00 2001 From: Sam Andrello Date: Wed, 24 Jul 2024 12:30:24 -0400 Subject: [PATCH 1/9] added AUTHORS.rst --- AUTHORS.rst | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 AUTHORS.rst diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 00000000..c7329e2f --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,68 @@ +Authors +======= + +Billinge Group and community contibutors. + +---- + +This code was derived from the first PDFFIT program by Thomas Proffen. +The sources were converted to C++ by Jacques Bloch and then extensively hacked, +extended and purged from most glaring bugs by Chris Farrow and Pavol Juhas. +This code is currently maintained as part of the DiffPy project to create +python modules for structure investigations from diffraction data. + +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. + + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.pdffit2/graphs/contributors \ No newline at end of file From 806a9b263c025d9294cc219ed8c84fdb884aec4c Mon Sep 17 00:00:00 2001 From: Sam Andrello Date: Wed, 24 Jul 2024 12:31:17 -0400 Subject: [PATCH 2/9] Added CHANGELOG.rst --- CHANGELOG.rst | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 CHANGELOG.rst diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 00000000..843c40a4 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,26 @@ +============= +Release Notes +============= + +No notable functional changes from 1.4.1 + +-------------------------- +Version 1.4.2 – 2023-12-09 +-------------------------- + +Added +===== + +- Support for Python 3.11, 3.12 + +Changed +======= + +Deprecated +========== + +Removed +======= + +Fixed +===== \ No newline at end of file From eb866303629376fde3e13168e32005fff63928b0 Mon Sep 17 00:00:00 2001 From: Sam Andrello Date: Wed, 24 Jul 2024 12:31:38 -0400 Subject: [PATCH 3/9] Added code of conduct --- CODE_OF_CONDUCT.rst | 133 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 CODE_OF_CONDUCT.rst 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 `_ From 04c9200447bba7ed273d99c3180c280ede555a21 Mon Sep 17 00:00:00 2001 From: Sam Andrello Date: Wed, 24 Jul 2024 12:36:13 -0400 Subject: [PATCH 4/9] Added LICENSE.rst --- LICENSE.rst | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 LICENSE.rst diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 00000000..3949fdf0 --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,50 @@ +This program is part of the DiffPy and DANSE open-source projects +and is available subject to the conditions and terms laid out below. + +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) + +Copyright 2006-2007, Board of Trustees of Michigan State University, +Copyright 2008-2019, Board of Trustees of Columbia University in the +city of New York. (Copyright holder indicated in each source file). + +For more information please visit the project web-page: + http://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 880acae5ceaa98db118c2b9d2a438979db1847d9 Mon Sep 17 00:00:00 2001 From: Sam Andrello Date: Wed, 24 Jul 2024 12:37:05 -0400 Subject: [PATCH 5/9] Added isort config --- .isort.cfg | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .isort.cfg 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 From a09972c36b33e7c7f88f664d11bb25db15f4142a Mon Sep 17 00:00:00 2001 From: Sam Andrello Date: Wed, 24 Jul 2024 12:41:46 -0400 Subject: [PATCH 6/9] Added news directory w/ template --- news/TEMPLATE.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/TEMPLATE.rst diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst new file mode 100644 index 00000000..790d30b1 --- /dev/null +++ b/news/TEMPLATE.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From ee4dbba608bd6a8a1581a3f5857756987052a121 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 24 Jul 2024 16:56:44 +0000 Subject: [PATCH 7/9] [pre-commit.ci] auto fixes from pre-commit hooks --- AUTHORS.rst | 2 +- CHANGELOG.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index c7329e2f..8cae8521 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -65,4 +65,4 @@ Contributors ------------ For a list of contributors, visit -https://github.com/diffpy/diffpy.pdffit2/graphs/contributors \ No newline at end of file +https://github.com/diffpy/diffpy.pdffit2/graphs/contributors diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 843c40a4..55012a9d 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -23,4 +23,4 @@ Removed ======= Fixed -===== \ No newline at end of file +===== From 13c21502b41ead898a5b44bd13b2c042744ea2a6 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Thu, 25 Jul 2024 01:22:48 -0400 Subject: [PATCH 8/9] Update AUTHORS.rst --- AUTHORS.rst | 19 ++++--------------- 1 file changed, 4 insertions(+), 15 deletions(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index 8cae8521..d6679278 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -13,23 +13,12 @@ python modules for structure investigations from diffraction data. 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 +Previous significant contributors to this code were - Simon Billinge + Pavol Juhas, Chris Farrow, Jacques Bloch, Wenduo Zhou - 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 +Please see the github contributions and 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! From b52e7b442a512e90309783ec9a85b2d308d4864a Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Thu, 25 Jul 2024 01:24:11 -0400 Subject: [PATCH 9/9] columbia copyright updated to 2024 --- LICENSE.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE.rst b/LICENSE.rst index 3949fdf0..9618d51a 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -11,7 +11,7 @@ the following paper in your publication: crystals, J. Phys.: Condens. Matter 19, 335219 (2007) Copyright 2006-2007, Board of Trustees of Michigan State University, -Copyright 2008-2019, Board of Trustees of Columbia University in the +Copyright 2008-2024, Board of Trustees of Columbia University in the city of New York. (Copyright holder indicated in each source file). For more information please visit the project web-page: