diffpy.structure 3.0.2__tar.gz → 3.2.0__tar.gz

diffpy.structure-3.0.2/AUTHORS.txt → diffpy_structure-3.2.0/AUTHORS.rst

@@ -1,10 +1,13 @@
-Authors:
+Authors
+=======
 
 Pavol Juhas,
 Christopher L. Farrow,
 Xiaohao Yang,
 Simon J.L. Billinge
 
-Contributors:
+Contributors
+------------
 
+For a list of contributors, visit
 https://github.com/diffpy/diffpy.structure/graphs/contributors

diffpy_structure-3.2.0/LICENSE.rst

@@ -0,0 +1,141 @@
+OPEN SOURCE LICENSE AGREEMENT
+=============================
+
+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) 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) 2009-2011, University of Tennessee
+
+Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
+
+Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
+
+Copyright (c) 2024, The Trustees of Columbia University in the City of New York. 
+All rights reserved.
+
+The "DiffPy-CMI" is distributed subject to the following license conditions:
+
+.. code-block:: text
+
+    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:
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+        (a) Copies in source code must include the copyright notice and this
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+Brookhaven National Laboratory Notice
+=====================================
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+Acknowledgment of sponsorship
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+Government disclaimer of liability
+----------------------------------
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+Maintenance of notice
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+
+END OF LICENSE

diffpy.structure-3.0.2/LICENSE_DANSE.txt → diffpy_structure-3.2.0/LICENSE_DANSE.rst

@@ -1,26 +1,35 @@
+LICENSE
+=======
+
 This program is part of the DiffPy and DANSE open-source projects
 and is available subject to the conditions and terms laid out below.
 
 Copyright 2006-2007, Board of Trustees of Michigan State University,
+
 Copyright 2008-2012, The Trustees of Columbia University in the
 City of New York.  (Copyright holder indicated in each source file).
 
+Copyright (c) 2024, The Trustees of Columbia University in the City of New York. 
+All rights reserved.
+
 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
+- 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
+- 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
+- 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.
 

diffpy_structure-3.2.0/LICENSE_pymmlib.rst

@@ -0,0 +1,203 @@
+.. code-block:: text
+        
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diffpy_structure-3.2.0/MANIFEST.in

@@ -0,0 +1,14 @@
+include AUTHORS.rst
+include LICENSE
+include README.rst
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat
+
+include diffpy.structure/version.py
+
+# If including data files in the package, add them like:
+# include path/to/data_file

diffpy_structure-3.2.0/PKG-INFO

@@ -0,0 +1,197 @@
+Metadata-Version: 2.1
+Name: diffpy.structure
+Version: 3.2.0
+Summary: Crystal structure container and parsers for structure formats.
+Author-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Maintainer-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Project-URL: Homepage, https://github.com/diffpy/diffpy.structure/
+Project-URL: Issues, https://github.com/diffpy/diffpy.structure/issues/
+Keywords: diffpy,crystal structure data storage CIF PDB
+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 :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+License-File: LICENSE_DANSE.rst
+License-File: LICENSE_pymmlib.rst
+License-File: AUTHORS.rst
+
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.structure
+.. _title: https://diffpy.github.io/diffpy.structure
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.structure
+        :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.structure/actions/workflows/main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.structure
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.structure
+        :target: https://anaconda.org/conda-forge/diffpy.structure
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.structure
+        :target: https://pypi.org/project/diffpy.structure/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.structure
+        :target: https://pypi.org/project/diffpy.structure/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.structure/issues
+
+Crystal structure container and parsers for structure formats.
+
+The diffpy.structure package provides objects for storing atomic
+coordinates, displacement parameters and other crystal structure data.
+diffpy.structure supports import and export of structure data in several
+structure formats such as CIF, PDB, and xyz.  It provides conversion
+between fractional and absolute Cartesian coordinates, functions for
+symmetry expansion of atom sites in the asymmetric unit and generation
+of symmetry constraints for atom positions and displacement parameters.
+diffpy.structure includes definitions of all space groups in over 500
+symmetry settings.
+
+For more information about the diffpy.structure library, please consult our `online documentation <https://diffpy.github.io/diffpy.structure>`_.
+
+Citation
+--------
+
+If you use this program for a scientific research that leads
+to publication, we ask that you acknowledge use of the program
+by citing the following paper in your publication:
+
+   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).
+
+Requirements
+------------------------------------------------------------------------
+
+The diffpy.structure package requires Python 3.7 or later and
+the following software:
+
+* ``setuptools`` - software distribution tools for Python
+* ``NumPy`` - numerical mathematics and fast array operations for Python
+
+We recommend to use `Anaconda Python <https://www.anaconda.com/download>`_
+as it allows to install all software dependencies together with
+diffpy.structure.  For other Python distributions it is necessary to
+install the required software separately.  As an example on Ubuntu
+Linux the required software can be installed with ::
+
+   sudo aptitude install python3-setuptools python3-numpy
+
+diffpy.structure also uses the
+`PyCifRW <https://bitbucket.org/jamesrhester/pycifrw>`_
+library, which is automatically deployed during the
+installation process.
+
+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.structure_env`` ::
+
+        conda create -n diffpy.structure_env python=3
+        conda activate diffpy.structure_env
+
+Then, to fully install ``diffpy.structure`` in our active environment, run ::
+
+        conda install diffpy.structure
+
+Another option is to use ``pip`` to download and install the latest release from
+`Python Package Index <https://pypi.python.org>`_.
+To install using ``pip`` into your ``diffpy.structure_env`` environment, we will also have to install dependencies ::
+
+        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.structure/main/requirements/run.txt
+
+and then install the package ::
+
+        pip install diffpy.structure
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.structure/>`_. Once installed, ``cd`` into your ``diffpy.structure`` directory
+and run the following ::
+
+        pip install .
+
+Support and Contribute
+----------------------
+
+`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.structure. Please join the diffpy.structure users community by joining the Google group. The diffpy.structure project welcomes your expertise and enthusiasm!
+
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.structure/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.structure/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_. 
+
+Feel free to fork the project and contribute. To install diffpy.structure
+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 contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE_OF_CONDUCT.rst>`_.
+
+Acknowledgement
+---------------
+
+Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
+originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
+
+Less common settings of space groups were generating using the
+`Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
+
+Contact
+-------
+
+For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.