diffpy.srfit 3.1.0__py3-none-any.whl

diffpy/srfit/version.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2008-2025 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Christopher Farrow, Pavol Juhas, and members of the
+# Billinge Group.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srfit/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Definition of __version__."""
+
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
+
+# obtain version information
+from importlib.metadata import version
+
+__version__ = version("diffpy.srfit")
+
+# End of file

diffpy_srfit-3.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: diffpy.srfit
+Version: 3.1.0
+Summary: Configurable code for solving atomic structures.
+Author-email: Simon Billinge <sb2896@columbia.edu>
+Maintainer-email: Simon Billinge <sb2896@columbia.edu>
+Project-URL: Homepage, https://github.com/diffpy/diffpy.srfit/
+Project-URL: Issues, https://github.com/diffpy/diffpy.srfit/issues/
+Keywords: regression,modelling,fitting,diffraction,PDF
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+License-File: LICENSE_DANSE.rst
+License-File: AUTHORS.rst
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: scipy
+Dynamic: license-file
+
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.srfit
+.. _title: https://diffpy.github.io/diffpy.srfit
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.srfit
+        :height: 100px
+
+|PyPI| |Forge| |PythonVersion| |PR|
+
+|CI| |Codecov| |Black| |Tracking|
+
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
+
+.. |CI| image:: https://github.com/diffpy/diffpy.srfit/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.srfit/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.srfit/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.srfit
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.srfit
+        :target: https://anaconda.org/conda-forge/diffpy.srfit
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srfit
+        :target: https://pypi.org/project/diffpy.srfit/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.srfit
+        :target: https://pypi.org/project/diffpy.srfit/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.srfit/issues
+
+diffpy.srfit
+============
+
+Configurable code for solving atomic structures.
+
+The diffpy.srfit package provides the framework for building a global optimizer
+on the fly from components such as function calculators (that calculate
+different data spectra), regression algorithms and structure models.  The
+software is capable of co-refinement using multiple information sources or
+models. It provides a uniform interface for various regression algorithms. The
+target function being optimized can be specified by the user according to the
+data available.
+
+Within the diffpy.srfit framework, any parameter used in describing the
+structure of a material can be passed as a refinable variable to the global
+optimizer.  Once parameters are declared as variables they can easily be turned
+"on" or "off", i.e. fixed or allowed to vary. Additionally, variables may be
+constrained to obey mathematical relationships with other parameters or
+variables used in the structural model. Restraints can be applied to
+variables, which adds a penalty to the refinement process commensurate with the
+deviation from the known value or range. The cost function can also be
+customized by the user. If the refinement contains multiple models, each model
+can have its own cost function which will be properly weighted and combined to
+obtain the total cost function. Additionally, diffpy.srfit is designed to be
+extensible, allowing the user to integrate external calculators to perform
+co-refinements with other techniques.
+
+For more information about the diffpy.srfit library, please consult our `online documentation <https://diffpy.github.io/diffpy.srfit>`_.
+
+Citation
+--------
+
+If you use diffpy.srfit in a scientific publication, we would like you to cite this package as
+
+
+   P. Juhás, C. L. Farrow, X. Yang, K. R. Knox and S. J. L. Billinge,
+   `Complex modeling: a strategy and software program for combining
+   multiple information sources to solve ill posed structure and
+   nanostructure inverse problems
+   <http://dx.doi.org/10.1107/S2053273315014473>`__,
+   *Acta Crystallogr. A* **71**, 562-568 (2015).
+
+Installation
+------------
+
+The preferred method is to use `Miniconda Python
+<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
+and install from the "conda-forge" channel of Conda packages.
+
+To add "conda-forge" to the conda channels, run the following in a terminal. ::
+
+        conda config --add channels conda-forge
+
+We want to install our packages in a suitable conda environment.
+The following creates and activates a new environment named ``diffpy.srfit_env`` ::
+
+        conda create -n diffpy.srfit_env diffpy.srfit
+        conda activate diffpy.srfit_env
+
+To confirm that the installation was successful, type ::
+
+        python -c "import diffpy.srfit; print(diffpy.srfit.__version__)"
+
+The output should print the latest version displayed on the badges above.
+
+This will install the minimal `diffpy.srfit` installation.  It will often be used
+as along with other packages for manipulating and computing crystal structures
+and so on.  We also therefore recommend installing the following:
+
+* ``diffpy.structure`` - crystal structure container and parsers,
+  https://github.com/diffpy/diffpy.structure
+* ``pyobjcryst`` - Crystal and Molecule storage, rigid units, bond
+  length and bond angle restraints, https://github.com/diffpy/pyobjcryst
+
+Optimizations involving pair distribution functions PDF or bond valence
+sums require
+
+* ``diffpy.srreal`` - python library for PDF calculation,
+  https://github.com/diffpy/diffpy.srreal
+
+Optimizations involving small angle scattering or shape characteristic
+functions from the diffpy.srfit.sas module require
+
+* ``sas`` - module for calculation of P(R) in small-angle scattering
+  from the SasView project, http://www.sasview.org
+
+Fallback Installation
+---------------------
+
+If the above does not work, you can use ``pip`` to download and install the latest release from
+`Python Package Index <https://pypi.python.org>`_.
+To install using ``pip`` into your ``diffpy.srfit_env`` environment, type ::
+
+        pip install diffpy.srfit
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.srfit/>`_. Once installed, ``cd`` into your ``diffpy.srfit`` directory
+and run the following ::
+
+        pip install .
+
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.srfit>`_ for tutorials and API references.
+
+Support and Contribute
+----------------------
+
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srfit/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srfit/pulls>`_.
+
+Feel free to fork the project and contribute. To install diffpy.srfit
+in a development mode, with its sources being directly used by Python
+rather than copied to a package directory, use the following in the root
+directory ::
+
+        pip install -e .
+
+To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
+hooks.
+
+1. Install pre-commit in your working environment by running ``conda install pre-commit``.
+
+2. Initialize pre-commit (one time only) ``pre-commit install``.
+
+Thereafter your code will be linted by black and isort and checked against flake8 before you can commit.
+If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should
+pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before
+trying to commit again.
+
+Improvements and fixes are always appreciated.
+
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srfit/blob/main/CODE_OF_CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on diffpy.srfit please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+
+Acknowledgements
+----------------
+
+``diffpy.srfit`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
+The source code in *observable.py* was derived from the 1.0 version
+of the Caltech "Pyre" project.

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diffpy_srfit-3.1.0.dist-info/licenses/AUTHORS.rst

@@ -0,0 +1,10 @@
+Authors
+=======
+
+Christopher Farrow, Pavol Juhas, Simon J. L. Billinge, and members of the Billinge Group
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srfit/graphs/contributors

diffpy_srfit-3.1.0.dist-info/licenses/LICENSE.rst

@@ -0,0 +1,138 @@
+OPEN SOURCE LICENSE AGREEMENT
+=============================
+
+Copyright (c) 2009-2011, University of Tennessee
+Copyright (c) 1989, 1991 Free Software Foundation, Inc.
+Copyright (c) 2006, The Regents of the University of California through
+    Lawrence Berkeley National Laboratory
+Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
+Copyright (c) 2006-2007, Board of Trustees of Michigan State University
+Copyright (c) 2008-2012, The Trustees of Columbia University in the City
+    of New York
+Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National
+    Laboratory
+Copyright (c) 2020-2025, The Trustees of Columbia University in the City
+    of New York
+
+
+The "DiffPy-CMI" is distributed subject to the following license conditions:
+
+
+SOFTWARE LICENSE AGREEMENT
+
+    Software: DiffPy-CMI
+
+
+(1) The "Software", below, refers to the aforementioned DiffPy-CMI (in either
+source code, or binary form and accompanying documentation).
+
+Part of the software was derived from the DANSE, ObjCryst++ (with permission),
+PyCifRW, Python periodictable, CCTBX, and SasView open source projects, of
+which the original Copyrights are contained in each individual file.
+
+Each licensee is addressed as "you" or "Licensee."
+
+
+(2) The copyright holders shown above and their third-party Licensors hereby
+grant licensee a royalty-free nonexclusive license, subject to the limitations
+stated herein and U.S. Government license rights.
+
+
+(3) You may modify and make a copy or copies of the software for use within
+your organization, if you meet the following conditions:
+
+    (a) Copies in source code must include the copyright notice and this
+        software license agreement.
+
+    (b) Copies in binary form must include the copyright notice and this
+        Software License Agreement in the documentation and/or other materials
+        provided with the copy.
+
+
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+
+    (a) Copies in source code must include the copyright notice and this
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+
+    (d) Neither the name of Brookhaven Science Associates or Brookhaven
+        National Laboratory nor the names of its contributors may be used to
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+
+
+(5) Portions of the Software resulted from work developed under a U.S.
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+Brookhaven National Laboratory Notice
+=====================================
+
+Acknowledgment of sponsorship
+-----------------------------
+
+This software was produced by the Brookhaven National Laboratory, under
+Contract DE-AC02-98CH10886 with the Department of Energy.
+
+
+Government disclaimer of liability
+----------------------------------
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+
+
+END OF LICENSE

diffpy_srfit-3.1.0.dist-info/licenses/LICENSE_DANSE.rst

@@ -0,0 +1,34 @@
+This program is part of the DiffPy and DANSE open-source projects at Columbia
+University and is available subject to the conditions and terms laid out below.
+
+Copyright (c) 2008-2011, The Trustees of Columbia University in
+the City of New York.  All rights reserved.
+
+For more information please visit the diffpy web-page at
+    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 names of COLUMBIA UNIVERSITY, MICHIGAN STATE UNIVERSITY nor the
+    names of their 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 OWNER 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_srfit-3.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+diffpy