diffpy.utils 3.4.0__tar.gz → 3.4.2__tar.gz

diffpy_utils-3.4.2/AUTHORS.rst

@@ -0,0 +1,10 @@
+Authors
+=======
+
+Billinge Group and community contibutors.
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.utils/graphs/contributors

diffpy_utils-3.4.2/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) 2019-2024, 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:
+
+        (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.
+
+
+    (4) You may modify a copy or copies of the Software or any portion of it, thus
+    forming a work based on the Software, and distribute copies of such work
+    outside your organization, if you meet all of 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;
+
+        (c) Modified copies and works based on the Software must carry prominent
+            notices stating that you changed specified portions of the Software.
+
+        (d) Neither the name of Brookhaven Science Associates or Brookhaven
+            National Laboratory nor the names of its contributors may be used to
+            endorse or promote products derived from this software without specific
+            written permission.
+
+
+    (5) Portions of the Software resulted from work developed under a U.S.
+    Government contract and are subject to the following license:
+    The Government is granted for itself and others acting on its behalf a
+    paid-up, nonexclusive, irrevocable worldwide license in this computer software
+    to reproduce, prepare derivative works, and perform publicly and display
+    publicly.
+
+
+    (6) WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT
+    WARRANTY OF ANY KIND. THE COPYRIGHT HOLDERS, THEIR THIRD PARTY
+    LICENSORS, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND
+    THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING
+    BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+    PARTICULAR PURPOSE, TITLE OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL
+    LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF
+    THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF THE SOFTWARE WOULD NOT INFRINGE
+    PRIVATELY OWNED RIGHTS, (4) DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION
+    UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL BE CORRECTED.
+
+
+    (7) LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT HOLDERS, THEIR
+    THIRD PARTY LICENSORS, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF
+    ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR  ANY INDIRECT, INCIDENTAL,
+    CONSEQUENTIAL, SPECIAL OR PUNITIVE  DAMAGES OF ANY KIND OR NATURE, INCLUDING
+    BUT NOT LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER,
+    WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT (INCLUDING
+    NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, EVEN IF ANY OF SAID PARTIES HAS
+    BEEN WARNED OF THE POSSIBILITY OF SUCH LOSS OR DAMAGES.
+
+
+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
+----------------------------------
+
+Neither the United States nor the United States Department of Energy, nor
+any of their employees, makes any warranty, express or implied, or assumes
+any legal liability or responsibility for the accuracy, completeness, or
+usefulness of any data, apparatus, product, or process disclosed, or
+represents that its use would not infringe privately owned rights.
+
+
+Brookhaven disclaimer of liability
+----------------------------------
+
+Brookhaven National Laboratory makes no representations or warranties,
+express or implied, nor assumes any liability for the use of this software.
+
+
+Maintenance of notice
+---------------------
+
+In the interest of clarity regarding the origin and status of this
+software, Brookhaven National Laboratory requests that any recipient of it
+maintain this notice affixed to any distribution by the recipient that
+contains a copy or derivative of this software.
+
+END OF LICENSE

diffpy_utils-3.4.2/MANIFEST.in

@@ -0,0 +1,12 @@
+graft src
+graft tests
+graft requirements
+
+include AUTHORS.rst LICENSE*.rst README.rst
+
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.

diffpy_utils-3.4.2/PKG-INFO

@@ -0,0 +1,157 @@
+Metadata-Version: 2.1
+Name: diffpy.utils
+Version: 3.4.2
+Summary: Shared utilities for diffpy packages
+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.utils/
+Project-URL: Issues, https://github.com/diffpy/diffpy.utils/issues/
+Keywords: "text data parsers" "wx grid" "diffraction objects"
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: Free To Use But Restricted
+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.txt
+License-File: AUTHORS.rst
+Requires-Dist: numpy
+
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.utils
+.. _title: https://diffpy.github.io/diffpy.utils
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.utils
+        :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.utils/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.utils/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.utils/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.utils
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.utils
+        :target: https://anaconda.org/conda-forge/diffpy.utils
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.utils
+        :target: https://pypi.org/project/diffpy.utils/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.utils
+        :target: https://pypi.org/project/diffpy.utils/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.utils/issues
+
+diffpy.utils Package
+========================================================================
+
+General purpose shared utilities for the diffpy libraries.
+
+The diffpy.utils package provides functions for extracting array data from
+variously formatted text files and wx GUI utilities used by the PDFgui
+program.  The package also includes an interpolation function based on the
+Whittaker-Shannon formula that can be used to resample a PDF or other profile
+function over a new grid.
+
+Citation
+--------
+
+If you use diffpy.utils in a scientific publication, we would like you to cite this package as
+
+        diffpy.utils Package, https://github.com/diffpy/diffpy.utils
+
+Documentation
+-------------
+
+Documentation may be found at, https://diffpy.github.io/diffpy.utils
+
+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.utils_env`` ::
+
+        conda create -n diffpy.utils_env python=3
+        conda activate diffpy.utils_env
+
+Then, to fully install ``diffpy.utils`` in our active environment, run ::
+
+        conda install diffpy.utils
+
+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.utils_env`` environment type ::
+
+        pip install diffpy.utils
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.utils/>`_. Once installed, ``cd`` into your ``diffpy.utils`` 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.utils. Please join the diffpy.utils users community by joining the Google group. The diffpy.utils 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.utils/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.utils/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.utils
+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.utils/blob/main/CODE_OF_CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on diffpy.utils please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

diffpy_utils-3.4.2/README.rst

@@ -0,0 +1,127 @@
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.utils
+.. _title: https://diffpy.github.io/diffpy.utils
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.utils
+        :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.utils/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.utils/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.utils/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.utils
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.utils
+        :target: https://anaconda.org/conda-forge/diffpy.utils
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.utils
+        :target: https://pypi.org/project/diffpy.utils/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.utils
+        :target: https://pypi.org/project/diffpy.utils/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.utils/issues
+
+diffpy.utils Package
+========================================================================
+
+General purpose shared utilities for the diffpy libraries.
+
+The diffpy.utils package provides functions for extracting array data from
+variously formatted text files and wx GUI utilities used by the PDFgui
+program.  The package also includes an interpolation function based on the
+Whittaker-Shannon formula that can be used to resample a PDF or other profile
+function over a new grid.
+
+Citation
+--------
+
+If you use diffpy.utils in a scientific publication, we would like you to cite this package as
+
+        diffpy.utils Package, https://github.com/diffpy/diffpy.utils
+
+Documentation
+-------------
+
+Documentation may be found at, https://diffpy.github.io/diffpy.utils
+
+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.utils_env`` ::
+
+        conda create -n diffpy.utils_env python=3
+        conda activate diffpy.utils_env
+
+Then, to fully install ``diffpy.utils`` in our active environment, run ::
+
+        conda install diffpy.utils
+
+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.utils_env`` environment type ::
+
+        pip install diffpy.utils
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.utils/>`_. Once installed, ``cd`` into your ``diffpy.utils`` 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.utils. Please join the diffpy.utils users community by joining the Google group. The diffpy.utils 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.utils/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.utils/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.utils
+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.utils/blob/main/CODE_OF_CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on diffpy.utils please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

{diffpy_utils-3.4.0 → diffpy_utils-3.4.2}/pyproject.toml

@@ -4,38 +4,37 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "diffpy.utils"
-dynamic=['version']
+dynamic=['version', 'dependencies']
 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 = "Shared utilities for diffpy packages."
-keywords = ["text data parsers", "wx grid", "diffraction objects"]
+description = "Shared utilities for diffpy packages"
+keywords = ['"text data parsers" "wx grid" "diffraction objects"']
 readme = "README.rst"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
+        'License :: Free To Use But Restricted',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.utils/"
-Issues = "https://github.com/diffpy/diffpy.utils/issues"
+Issues = "https://github.com/diffpy/diffpy.utils/issues/"
 
 [tool.setuptools-git-versioning]
 enabled = true
@@ -45,10 +44,13 @@ dirty_template = "{tag}"
 
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
-include = ["diffpy*"]  # package names should match these glob patterns (["*"] by default)
-exclude = ["diffpy.utils.tests*"]  # exclude packages matching these glob patterns (empty by default)
+include = ["*"]  # package names should match these glob patterns (["*"] by default)
+exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements/run.txt"]}
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

diffpy_utils-3.4.2/requirements/build.txt

@@ -0,0 +1,2 @@
+python
+setuptools

diffpy_utils-3.4.2/requirements/docs.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx_rtd_theme
+doctr
+m2r

diffpy_utils-3.4.2/requirements/run.txt

@@ -0,0 +1 @@
+numpy

diffpy_utils-3.4.2/requirements/test.txt

@@ -0,0 +1,8 @@
+flake8
+pytest
+codecov
+coverage
+pytest-env
+pytest-mock
+pytest-cov
+freezegun

{diffpy_utils-3.4.0 → diffpy_utils-3.4.2}/src/diffpy/__init__.py

@@ -5,11 +5,15 @@
 #                   Simon J. L. Billinge
 #                   (c) 2010 The Trustees of Columbia University
 #                   in the City of New York.  All rights reserved.
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
 #
-# File coded by:    Pavol Juhas
+# File coded by: Billinge Group members and community contributors.
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE_DANSE.txt for license information.
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.utils/graphs/contributors
+#
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 
@@ -23,5 +27,4 @@ from pkgutil import extend_path
 
 __path__ = extend_path(__path__, __name__)
 
-
 # End of file

diffpy_utils-3.4.2/src/diffpy/utils/__init__.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.utils/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Shared utilities for diffpy packages"""
+
+# package version
+from diffpy.utils.version import __version__
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file