Cookie (#105)

* Lint check & fix to python3 format (#18)

* lint check and change files from python2 to python3

* pre-commit check for these files

* lint check & change to python3 & pre-commit check (#19)

* lint check & change to python3 & pre-commit check

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* lint check and fix print and exception python2 issue (#20)

* lint check and fix python2 print and exception issues (#21)

* lint check and fix python2 print and exception issues

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* finish parenthesizing print statements (#24)

* finish parenthesizing print statements

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* fix too many leading #, import modules, and unused var (#29)

* requirements (#30)

* fix import module not used & string check (#25)

* fix too many leading "#" in string block (#26)

* lint check, remove unused import modules & remove too many "#". (#27)

* remove unused modules, ambiguous variable name (#28)

* cleaning (#31)

* requirements

* clean out __init__

* replace ###

* ins not none in modelevaluators base

* Copyright (#32)

* requirements

* basefunction

* all the copyright statements

* lint check, fix break import modules, remove unused import modules, remove some # (#33)

* fix break import modules, remove unused import modules, fix docstring length (#34)

* fix formatting issue and typo in copyright (#35)

* clean out inits (#38)

* clean out inits

* [pre-commit.ci] auto fixes from pre-commit hooks

* dataclusters.py, modelevaluators/aicc and modelparts.py

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* peakextraction.py and init (#40)

* move untrack doc and requirement files (#41)

* move untrack doc and requirement files

* add requirement in run.txt

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* add pyproject.toml (#42)

* add pyproject.toml

* [pre-commit.ci] auto fixes from pre-commit hooks

* update classifiers pyproject.toml

* Delete setup.py

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* move diffpy files to src dir (#44)

* move diffpy files to src dir

* [pre-commit.ci] auto fixes from pre-commit hooks

* add Luke to authors

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* LICENSE (#45)

* add two LICENSE.rst files into cookiecutter

* fix LICENSE.rst and LICENSE_PDFgui.rst with correct references and year

* resolve pdfdataset.py conflict

---------

Co-authored-by: Simon Billinge <[email protected]>

* add untrack files and add cookiecut.rst news (#46)

* add untrack files and add cookiecut.rst news

* delete README.txt

* fix py2 -> py3, fix broken import, remove deprecation warning (#47)

* fix py2 -> py3, move deprecation warning

* fix search & split in binary files

* fix broken import, remove deprecated pkg_resource (#50)

* change import path to make it work. (#48)

* fix import modules, py2->py3 (#49)

* fix broken import in doc, change README to rst file. (#51)

* fix broken import in doc, change README to rst file.

* fix os getcwd method

* fix p2 to p3 (#52)

* add test for dataclusters (#54)

* add test for dataclusters

* define eq method in dataclusters.py

* change parametrization form

* add one more case and change reference name to actual

* delete comment

* add two more tests for DataClusters class function.

* change in docstring for clearer explanation for clear method, remove duplicated case for testing behavior, remove other tests.

* change clear method docstring into numpydoc format. Delete dtype for numpy array.

* remove block

* Make edition to condition on res, refactor for setdata to make behavior of the test passed.

* change condition on res

* add condition on x and res are incompatible, update test.

* revert change in setdata method.

* Eq tests (#59)

* remove diffpy/srmise tree

* test for eq

* add attributes in eq method (#60)

* Add set data test cases (#61)

* add test cases to test files and make edition to make sure the behavior of the test pass.

* [pre-commit.ci] auto fixes from pre-commit hooks

* change case in test__eq__ to be compatible with the behavior of setdata

* delete text and redundant tests

* tweaking error message in DataClusters

* [pre-commit.ci] auto fixes from pre-commit hooks

* update test for checking implicit attributes for setdata function

* [pre-commit.ci] auto fixes from pre-commit hooks

* update test for setdata function

* update setdata test to right format.

* update to constructor test & make setdata clear function private

* final tweaks to tests by Simon

* fix actual_attribute typo

* final refactor of actual_attr

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Simon Billinge <[email protected]>

* fix arbitrary.py to numpydoc format (#68)

* fix arbitrary.py to numpydoc format

* pre-commit fix

* change start sentence to 'The'

* print things correctly (#71)

* print things correctly

* change to f string

* reduce print to one line

* change createpeak to actualize function (#72)

* fix import and counting to make it work (#74)

* refactor makeclusters to make it work (#73)

* deprecation remove (#78)

* deprecation remove

* fix to right behavior

* Revert "refactor makeclusters to make it work (#73)" (#79)

This reverts commit 3773bcf.

* try out py2 before py3 refactor to make sure correct workflow (#75)

* fix false counting and numpy to int (#80)

* fix false counting and numpy to int

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* numpydoc edition (#81)

* change peakextraction function to numpydoc

* pre-commit run

* remove unused import

* numpydoc build (#82)

* numpydoc build on peakstability (#83)

* numpydoc build for ModelCluster (#85)

* numpydoc build for multimodelselection.py (#87)

* numpydoc documentation build for ModelCluster class (#86)

* numpydoc build for pdfdataset (#88)

* numpydoc build for pdfpeakextraction.py (#89)

* numpydoc build for gaussianoverr.py (#91)

* numpydoc build for gaussianoverr.py

* [pre-commit.ci] auto fixes from pre-commit hooks

* fix pre-commit

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* terminationripples.py numpydoc build (#92)

* numpydoc build for gaussian.py (#90)

* numpydoc build for gaussian.py

* [pre-commit.ci] auto fixes from pre-commit hooks

* pre-commit fix

* update for FWHM and maxwidth

* update for starting sentence

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* numpydoc build for base.py (#95)

* numpydoc build for polynomial.py (#97)

* numpydoc build for fromsequence.py (#99)

* numpydoc build for nanospherical.py (#98)

* numpydoc build for base.py in Baseline class (#96)

* numpydoc build for base.py

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* numpydoc build for aic.py (#93)

* numpydoc build for aicc.py (#94)

* numpydoc build for ModelCovariance (#84)

* numpydoc build for ModelCovariance

* update format type and fix indentation issue

* numpydoc build for modelparts.py (#100)

* numpydoc build for modelparts.py

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* numpydoc build for basefunction.py (#101)

* api workflow build for diffpy.srmise (#102)

* api workflow build for diffpy.srmise

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* add changed news (#103)

---------

Co-authored-by: Rundong Hua <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.gitattributes

@@ -0,0 +1 @@
+diffpy.srmise/_version.py export-subst

AUTHORS.rst

@@ -0,0 +1,11 @@
+Authors
+=======
+
+Luke Granlund
+Billinge Group and community contibutors.
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srmise/graphs/contributors

CHANGELOG.rst

@@ -0,0 +1,5 @@
+=============
+Release Notes
+=============
+
+.. current developments

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
+[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>`_

LICENSE.rst

@@ -0,0 +1,44 @@
+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.

LICENSE_PDFgui.rst

@@ -0,0 +1,51 @@
+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.