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Sep 4, 2024
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5684c18
Lint check & fix to python3 format (#18)
stevenhua0320 Jul 29, 2024
a4221ff
lint check & change to python3 & pre-commit check (#19)
stevenhua0320 Jul 29, 2024
866e714
lint check and fix print and exception python2 issue (#20)
stevenhua0320 Jul 29, 2024
c28b97b
lint check and fix python2 print and exception issues (#21)
stevenhua0320 Jul 29, 2024
ff0fc58
finish parenthesizing print statements (#24)
sbillinge Jul 29, 2024
7c77b11
fix too many leading #, import modules, and unused var (#29)
stevenhua0320 Jul 30, 2024
21d1a53
requirements (#30)
sbillinge Jul 30, 2024
181a54a
fix import module not used & string check (#25)
stevenhua0320 Jul 30, 2024
8772a95
fix too many leading "#" in string block (#26)
stevenhua0320 Jul 30, 2024
ffe5fc7
lint check, remove unused import modules & remove too many "#". (#27)
stevenhua0320 Jul 30, 2024
edaa35d
remove unused modules, ambiguous variable name (#28)
stevenhua0320 Jul 30, 2024
1f67292
cleaning (#31)
sbillinge Jul 30, 2024
30d0909
Copyright (#32)
sbillinge Jul 30, 2024
7dd69bc
lint check, fix break import modules, remove unused import modules, r…
stevenhua0320 Jul 30, 2024
81b261b
fix break import modules, remove unused import modules, fix docstring…
stevenhua0320 Jul 30, 2024
978dca1
fix formatting issue and typo in copyright (#35)
stevenhua0320 Jul 30, 2024
c0d43e6
clean out inits (#38)
sbillinge Jul 31, 2024
9a2d7cc
peakextraction.py and init (#40)
sbillinge Jul 31, 2024
d237df0
move untrack doc and requirement files (#41)
stevenhua0320 Jul 31, 2024
f3cdb58
add pyproject.toml (#42)
stevenhua0320 Jul 31, 2024
9ecf5e8
move diffpy files to src dir (#44)
stevenhua0320 Jul 31, 2024
e1a5e58
LICENSE (#45)
stevenhua0320 Jul 31, 2024
0b46507
add untrack files and add cookiecut.rst news (#46)
stevenhua0320 Jul 31, 2024
c1886a1
fix py2 -> py3, fix broken import, remove deprecation warning (#47)
stevenhua0320 Aug 2, 2024
f31d3d4
fix broken import, remove deprecated pkg_resource (#50)
stevenhua0320 Aug 2, 2024
ee8f1b2
change import path to make it work. (#48)
stevenhua0320 Aug 2, 2024
8f6c376
fix import modules, py2->py3 (#49)
stevenhua0320 Aug 2, 2024
9f81b5f
fix broken import in doc, change README to rst file. (#51)
stevenhua0320 Aug 6, 2024
8270200
fix p2 to p3 (#52)
stevenhua0320 Aug 6, 2024
89c8c0b
add test for dataclusters (#54)
stevenhua0320 Aug 10, 2024
5aad8bd
Eq tests (#59)
sbillinge Aug 10, 2024
5be09d5
add attributes in eq method (#60)
stevenhua0320 Aug 11, 2024
d1bf3d4
Add set data test cases (#61)
stevenhua0320 Aug 13, 2024
48c5d64
fix arbitrary.py to numpydoc format (#68)
stevenhua0320 Aug 14, 2024
20b4d01
print things correctly (#71)
stevenhua0320 Aug 14, 2024
6e62077
change createpeak to actualize function (#72)
stevenhua0320 Aug 15, 2024
578a972
fix import and counting to make it work (#74)
stevenhua0320 Aug 16, 2024
3773bcf
refactor makeclusters to make it work (#73)
stevenhua0320 Aug 16, 2024
abfdb5b
deprecation remove (#78)
stevenhua0320 Aug 16, 2024
e58e0c7
Revert "refactor makeclusters to make it work (#73)" (#79)
stevenhua0320 Aug 16, 2024
ee41be5
try out py2 before py3 refactor to make sure correct workflow (#75)
stevenhua0320 Aug 17, 2024
abe0c2a
fix false counting and numpy to int (#80)
stevenhua0320 Aug 19, 2024
8716a9d
numpydoc edition (#81)
stevenhua0320 Aug 19, 2024
e87962f
numpydoc build (#82)
stevenhua0320 Aug 19, 2024
6458a3e
numpydoc build on peakstability (#83)
stevenhua0320 Aug 19, 2024
35a2ef4
numpydoc build for ModelCluster (#85)
stevenhua0320 Aug 20, 2024
df43be6
numpydoc build for multimodelselection.py (#87)
stevenhua0320 Aug 20, 2024
4d3d8ff
numpydoc documentation build for ModelCluster class (#86)
stevenhua0320 Aug 20, 2024
def4a2d
numpydoc build for pdfdataset (#88)
stevenhua0320 Aug 21, 2024
4cb462e
numpydoc build for pdfpeakextraction.py (#89)
stevenhua0320 Aug 21, 2024
03b18c1
numpydoc build for gaussianoverr.py (#91)
stevenhua0320 Aug 22, 2024
d55b946
terminationripples.py numpydoc build (#92)
stevenhua0320 Aug 22, 2024
d722872
numpydoc build for gaussian.py (#90)
stevenhua0320 Aug 22, 2024
a66843b
numpydoc build for base.py (#95)
stevenhua0320 Aug 23, 2024
e7e53cb
numpydoc build for polynomial.py (#97)
stevenhua0320 Aug 23, 2024
608a1c1
numpydoc build for fromsequence.py (#99)
stevenhua0320 Aug 23, 2024
bb71671
numpydoc build for nanospherical.py (#98)
stevenhua0320 Aug 23, 2024
f7cc015
numpydoc build for base.py in Baseline class (#96)
stevenhua0320 Aug 23, 2024
2b8c446
numpydoc build for aic.py (#93)
stevenhua0320 Aug 23, 2024
caab0af
numpydoc build for aicc.py (#94)
stevenhua0320 Aug 23, 2024
16039d6
numpydoc build for ModelCovariance (#84)
stevenhua0320 Aug 23, 2024
38ab653
numpydoc build for modelparts.py (#100)
stevenhua0320 Aug 24, 2024
e47955f
numpydoc build for basefunction.py (#101)
stevenhua0320 Aug 24, 2024
356129a
api workflow build for diffpy.srmise (#102)
stevenhua0320 Aug 26, 2024
30f856e
add changed news (#103)
stevenhua0320 Sep 4, 2024
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1 change: 1 addition & 0 deletions .gitattributes
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diffpy.srmise/_version.py export-subst
11 changes: 11 additions & 0 deletions AUTHORS.rst
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Authors
=======

Luke Granlund
Billinge Group and community contibutors.

Contributors
------------

For a list of contributors, visit
https://github.com/diffpy/diffpy.srmise/graphs/contributors
3 changes: 0 additions & 3 deletions AUTHORS.txt

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5 changes: 5 additions & 0 deletions CHANGELOG.rst
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=============
Release Notes
=============

.. current developments
133 changes: 133 additions & 0 deletions CODE_OF_CONDUCT.rst
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=====================================
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
[email protected]. 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 <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.

Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.

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>`_
44 changes: 44 additions & 0 deletions LICENSE.rst
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BSD 3-Clause License

Copyright 2014-2015, Board of Trustees of Michigan State University
2016-2024, The Trustees of Columbia University in the City of New York.
All rights reserved.

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:

L. Granlund, S.J.L. Billinge, P.M. Duxbury, Algorithm for
systematic peak extraction from atomic pair distribution
functions, Acta Crystallographica A 71(4), 392-409 (2015).
doi:10.1107/S2053273315005276

For more information please visit the diffpy web-page at
http://www.diffpy.org
or email Luke Granlund at [email protected], or Prof. Simon
Billinge at [email protected].

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.
46 changes: 0 additions & 46 deletions LICENSE.txt

This file was deleted.

51 changes: 51 additions & 0 deletions LICENSE_PDFgui.rst
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BSD 3-Clause License

Copyright 2006-2007, Board of Trustees of Michigan State University
2008-2024, The Trustees of Columbia University in the City of New York.
All rights reserved.

SrMise incorporates source code from diffpy.pdfgui in the file
pdfdataset.py. The PDFgui license is reproduced in full below.

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)

For more information please visit the diffpy web-page at
http://www.diffpy.org
or email Luke Granlund at [email protected], or Prof. Simon
Billinge at [email protected].

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.
56 changes: 0 additions & 56 deletions LICENSE_PDFgui.txt

This file was deleted.

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