Untrack files and pyproject.toml edit

diffpy.srmise/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

diffpy.srmise/CHANGELOG.rst

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+=============
+Release Notes
+=============
+
+.. current developments

diffpy.srmise/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
+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 <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>`_

diffpy.srmise/LICENSE.rst

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+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.
+
+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 luke.r.granlund@gmail.com, or Prof. Simon
+Billinge at sb2896@columbia.edu.
+
+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.

diffpy.srmise/doc/source/license.rst

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+:tocdepth: -1
+
+.. index:: license
+
+License
+#######
+
+OPEN SOURCE LICENSE AGREEMENT
+=============================
+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.

diffpy.srmise/pyproject.toml

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+[build-system]
+requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "diffpy.srmise"
+dynamic=['version']
+authors = [
+  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+]
+maintainers = [
+  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+]
+description = "Peak extraction/fitting tool for pair distribution functions"
+keywords = ['peak extraction fitting PDF AIC multimodeling']
+readme = "README.rst"
+requires-python = ">=3.10"
+classifiers = [
+        # List of possible values at
+        # http://pypi.python.org/pypi?:action=list_classifiers
+        'Development Status :: 3 - Alpha',
+        'Environment :: Console',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Education',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: POSIX',
+        'Operating System :: Unix',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Chemistry',
+        'Topic :: Software Development :: Libraries',
+]
+
+[project.urls]
+Homepage = "https://github.com/diffpy/diffpy.srmise/"
+Issues = "https://github.com/diffpy/diffpy.srmise/issues/"
+
+[tool.setuptools-git-versioning]
+enabled = true
+template = "{tag}"
+dev_template = "{tag}"
+dirty_template = "{tag}"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["*"]  # package names should match these glob patterns (["*"] by default)
+exclude = ["diffpy.srmise.tests*"]  # exclude packages matching these glob patterns (empty by default)
+namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
+
+[tool.black]
+line-length = 115
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | \.rst
+  | \.txt
+  | _build
+  | buck-out
+  | build
+  | dist
+
+  # The following are specific to Black, you probably don't want those.
+  | blib2to3
+  | tests/data
+)/
+'''