diffpy.mpdf 1.0.4__tar.gz → 1.0.4.2__tar.gz

{diffpy_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/AUTHORS.txt

@@ -1,8 +1,8 @@
-Benjamin Frandsen
-Parker Hamilton
-Jacob Christensen
-Eric Stubben
-Victor Velasco
-Pavol Juhas
-Xiaohao Yang
-Simon J.L. Billinge
+Benjamin Frandsen
+Parker Hamilton
+Jacob Christensen
+Eric Stubben
+Victor Velasco
+Pavol Juhas
+Xiaohao Yang
+Simon J.L. Billinge

{diffpy_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/LICENSE.txt

@@ -1,11 +1,11 @@
-Copyright 2022 BENJAMIN ALLEN FRANDSEN
-
-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.
-
+Copyright 2022 BENJAMIN ALLEN FRANDSEN
+
+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_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include diffpy *
-include AUTHORS.txt LICENSE*.txt README.rst
-include setup.cfg
-recursive-exclude diffpy *.pyc
+recursive-include diffpy *
+include AUTHORS.txt LICENSE*.txt README.rst
+include setup.cfg
+recursive-exclude diffpy *.pyc

{diffpy_mpdf-1.0.4/diffpy.mpdf.egg-info → diffpy_mpdf-1.0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.mpdf
-Version: 1.0.4
+Version: 1.0.4.2
 Summary: Tools for magnetic PDF analysis.
 Author-email: Benjamin Frandsen <benfrandsen@byu.edu>
 License: Copyright 2022 BENJAMIN ALLEN FRANDSEN
@@ -37,44 +37,41 @@ Dynamic: license-file
 
 Framework for comprehensive magnetic PDF analysis.
 
-This package aims to provide a convenient method for computing the magnetic PDF (mPDF) from magnetic structures, performing fits to neutron total scattering data, and generating the experimental mPDF signal from magnetic scattering data. The mPDF is calculated by an MPDFcalculator object, which extracts the spin positions and spin vectors from a MagStructure object that the MPDFcalculator takes as input. The MagStructure object in turn can contain multiple MagSpecies objects, which generate magnetic configurations based on a diffpy.Structure object and a set of propagation vectors and basis vectors either provided by the user or read in directly from an MCIF file. Alternatively, the user can manually define a magnetic unit cell that will be used to generate the magnetic structure, or the magnetic structure can be defined simply as lists of spin positions and spin vectors provided by the user. The MPDFtransformer class is used to generate mPDF data from magnetic scattering data.
+This package aims to provide a convenient method for computing the magnetic PDF (mPDF) from magnetic structures, performing fits to neutron total scattering data, and generating the experimental mPDF signal from magnetic scattering data. The mPDF is calculated by an MPDFcalculator object, which extracts the spin positions and spin vectors from a MagStructure object that the MPDFcalculator takes as input. The MagStructure object in turn can contain multiple MagSpecies objects, which generate magnetic configurations based on a diffpy.Structure object and a set of propagation vectors and basis vectors either provided by the user or read in directly from an MCIF file. Alternatively, the user can manually define a magnetic unit cell that will be used to generate the magnetic structure, or the magnetic structure can be defined simply as lists of spin positions and spin vectors provided by the user. The MPDFtransformer class is used to generate mPDF data from magnetic scattering data. Both one-dimensional (powder) and three-dimensional (single crystal) mPDF patterns can be calculated.
 
 Please cite: Frandsen _et al._, "diffpy.mpdf: open-source software for magnetic pair distribution function analysis", _J. Appl. Cryst._ (2022) __55__, 1377-1382. https://doi.org/10.1107/S1600576722007257
 
 
 ## Requirements
 
-This package requires Python 3.7 and the following software:
+This package requires Python 3.11 or greater and the following software:
 
-numpy, matplotlib, scipy, diffpy.Structure, diffpy.srreal
+numpy, matplotlib, scipy, diffpy.structure, diffpy.srreal
 
 Recommended software:
 
-Full diffpy-cmi suite.
+Full diffpy.cmi suite, jupyter notebook
 
-Current supported platforms are Linux (64- and 32-bit) and MacOS (64-bit). With some effort, it may also be possible to run the program on Windows using the Linux Subsystem available for Windows 10. Perhaps a better option if you have a Windows PC is to install a virtual machine with a Linux distribution. Here's a useful guide on how to do that for Ubuntu using VirtualBox: https://ubuntu.com/tutorials/how-to-run-ubuntu-desktop-on-a-virtual-machine-using-virtualbox#1-overview . 
+Current supported platforms are Linux, Unix, macOS, and Windows.
 
-## Installation
+## Recommended Installation Procedure
 
-The recommended way to install this package is first to install diffpy-cmi through conda using the Anaconda python distribution, then install diffpy.mpdf using pip. See https://www.anaconda.com/distribution for instructions about installing the Anaconda python distribution. See also https://www.diffpy.org/products/diffpycmi/index.html for the diffpy-cmi installation instructions (reproduced here for convenience).
+#### Step 1: Install diffpy.cmi
+Follow the instructions at https://github.com/diffpy/diffpy.cmi. 
 
-#### Step 1 (recommended): Create and activate a conda environment for diffpy + diffpy.mpdf.
-    >>> conda create --name diffpy python=3.7
-    >>> conda activate diffpy
-Note that you can name the environment anything you choose by passing it a different name after the --name flag in the first command.
+#### Step 2: Install diffpy.mpdf with pip
+Making sure you are in the correct python environment, run the command:
 
-#### Step 2: Install diffpy-cmi through conda.
-    >>> conda install -c diffpy diffpy-cmi
-Make sure you are installing this in the environment you created in the previous step.
+    >>> pip install diffpy.mpdf
 
-#### Step 3: Install diffpy.mpdf with pip
-Making sure you have activated your diffpy environment, run the command:
+Alternatively, you can install from source by installing diffpy.structure and diffpy.srreal following the instructions on their respective github pages, then cloning or downloading the github repository https://github.com/FrandsenGroup/diffpy.mpdf on your local machine, navigating to the downloaded repository, and running the following command (making sure that you are in the correct python environment):
 
-    >>> pip install diffpy.mpdf
+    >>> pip install .
 
-Alternatively, you can install from source by cloning or downloading the github repository https://github.com/FrandsenGroup/diffpy.mpdf on your local machine, navigating to the downloaded repository, and running the following command (making sure that you are in the environment you created in Step 1):
+#### Step 3 (recommended): Install jupyter notebook and interactive plotting tools
+To use the jupyter notebook tutorials mentioned below, install the notebook and ipympl packages as follows:
 
-    >>> python setup.py install
+    >>> pip install notebook ipympl
 
 ## Documentation and Helpful Examples
 Complete documentation is available  at [https://frandsengroup.github.io/diffpy.mpdf/index.html](https://frandsengroup.github.io/diffpy.mpdf/index.html).

{diffpy_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/README.md

@@ -2,44 +2,41 @@
 
 Framework for comprehensive magnetic PDF analysis.
 
-This package aims to provide a convenient method for computing the magnetic PDF (mPDF) from magnetic structures, performing fits to neutron total scattering data, and generating the experimental mPDF signal from magnetic scattering data. The mPDF is calculated by an MPDFcalculator object, which extracts the spin positions and spin vectors from a MagStructure object that the MPDFcalculator takes as input. The MagStructure object in turn can contain multiple MagSpecies objects, which generate magnetic configurations based on a diffpy.Structure object and a set of propagation vectors and basis vectors either provided by the user or read in directly from an MCIF file. Alternatively, the user can manually define a magnetic unit cell that will be used to generate the magnetic structure, or the magnetic structure can be defined simply as lists of spin positions and spin vectors provided by the user. The MPDFtransformer class is used to generate mPDF data from magnetic scattering data.
+This package aims to provide a convenient method for computing the magnetic PDF (mPDF) from magnetic structures, performing fits to neutron total scattering data, and generating the experimental mPDF signal from magnetic scattering data. The mPDF is calculated by an MPDFcalculator object, which extracts the spin positions and spin vectors from a MagStructure object that the MPDFcalculator takes as input. The MagStructure object in turn can contain multiple MagSpecies objects, which generate magnetic configurations based on a diffpy.Structure object and a set of propagation vectors and basis vectors either provided by the user or read in directly from an MCIF file. Alternatively, the user can manually define a magnetic unit cell that will be used to generate the magnetic structure, or the magnetic structure can be defined simply as lists of spin positions and spin vectors provided by the user. The MPDFtransformer class is used to generate mPDF data from magnetic scattering data. Both one-dimensional (powder) and three-dimensional (single crystal) mPDF patterns can be calculated.
 
 Please cite: Frandsen _et al._, "diffpy.mpdf: open-source software for magnetic pair distribution function analysis", _J. Appl. Cryst._ (2022) __55__, 1377-1382. https://doi.org/10.1107/S1600576722007257
 
 
 ## Requirements
 
-This package requires Python 3.7 and the following software:
+This package requires Python 3.11 or greater and the following software:
 
-numpy, matplotlib, scipy, diffpy.Structure, diffpy.srreal
+numpy, matplotlib, scipy, diffpy.structure, diffpy.srreal
 
 Recommended software:
 
-Full diffpy-cmi suite.
+Full diffpy.cmi suite, jupyter notebook
 
-Current supported platforms are Linux (64- and 32-bit) and MacOS (64-bit). With some effort, it may also be possible to run the program on Windows using the Linux Subsystem available for Windows 10. Perhaps a better option if you have a Windows PC is to install a virtual machine with a Linux distribution. Here's a useful guide on how to do that for Ubuntu using VirtualBox: https://ubuntu.com/tutorials/how-to-run-ubuntu-desktop-on-a-virtual-machine-using-virtualbox#1-overview . 
+Current supported platforms are Linux, Unix, macOS, and Windows.
 
-## Installation
+## Recommended Installation Procedure
 
-The recommended way to install this package is first to install diffpy-cmi through conda using the Anaconda python distribution, then install diffpy.mpdf using pip. See https://www.anaconda.com/distribution for instructions about installing the Anaconda python distribution. See also https://www.diffpy.org/products/diffpycmi/index.html for the diffpy-cmi installation instructions (reproduced here for convenience).
+#### Step 1: Install diffpy.cmi
+Follow the instructions at https://github.com/diffpy/diffpy.cmi. 
 
-#### Step 1 (recommended): Create and activate a conda environment for diffpy + diffpy.mpdf.
-    >>> conda create --name diffpy python=3.7
-    >>> conda activate diffpy
-Note that you can name the environment anything you choose by passing it a different name after the --name flag in the first command.
+#### Step 2: Install diffpy.mpdf with pip
+Making sure you are in the correct python environment, run the command:
 
-#### Step 2: Install diffpy-cmi through conda.
-    >>> conda install -c diffpy diffpy-cmi
-Make sure you are installing this in the environment you created in the previous step.
+    >>> pip install diffpy.mpdf
 
-#### Step 3: Install diffpy.mpdf with pip
-Making sure you have activated your diffpy environment, run the command:
+Alternatively, you can install from source by installing diffpy.structure and diffpy.srreal following the instructions on their respective github pages, then cloning or downloading the github repository https://github.com/FrandsenGroup/diffpy.mpdf on your local machine, navigating to the downloaded repository, and running the following command (making sure that you are in the correct python environment):
 
-    >>> pip install diffpy.mpdf
+    >>> pip install .
 
-Alternatively, you can install from source by cloning or downloading the github repository https://github.com/FrandsenGroup/diffpy.mpdf on your local machine, navigating to the downloaded repository, and running the following command (making sure that you are in the environment you created in Step 1):
+#### Step 3 (recommended): Install jupyter notebook and interactive plotting tools
+To use the jupyter notebook tutorials mentioned below, install the notebook and ipympl packages as follows:
 
-    >>> python setup.py install
+    >>> pip install notebook ipympl
 
 ## Documentation and Helpful Examples
 Complete documentation is available  at [https://frandsengroup.github.io/diffpy.mpdf/index.html](https://frandsengroup.github.io/diffpy.mpdf/index.html).

{diffpy_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/diffpy/__init__.py

@@ -1,17 +1,16 @@
-#!/usr/bin/env python
-##############################################################################
-#
-# diffpy.mpdf         by Frandsen Group
-#                     Benjamin A. Frandsen benfrandsen@byu.edu
-#                     (c) 2022 Benjamin Allen Frandsen
-#                      All rights reserved
-#
-# File coded by:    Benjamin Frandsen
-#
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
-#
-##############################################################################
-
-__import__('pkg_resources').declare_namespace(__name__)
-
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.mpdf         by Frandsen Group
+#                     Benjamin A. Frandsen benfrandsen@byu.edu
+#                     (c) 2022 Benjamin Allen Frandsen
+#                      All rights reserved
+#
+# File coded by:    Benjamin Frandsen
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)

{diffpy_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/diffpy/mpdf/__init__.py

@@ -1,32 +1,32 @@
-#!/usr/bin/env python
-##############################################################################
-#
-# diffpy.mpdf         by Frandsen Group
-#                     Benjamin A. Frandsen benfrandsen@byu.edu
-#                     (c) 2022 Benjamin Allen Frandsen
-#                      All rights reserved
-#
-# File coded by:    Benjamin Frandsen
-#
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
-#
-##############################################################################
-
-"""Tools for magnetic pair distribution function analysis
-"""
-
-# package version
-from diffpy.mpdf.version import __version__
-
-# convenience imports
-from diffpy.mpdf.magstructure import *
-from diffpy.mpdf.mpdfcalculator import *
-from diffpy.mpdf.magutils import *
-from diffpy.mpdf.mpdf3Dcalculator import *
-from diffpy.mpdf.visualize3D import *
-from diffpy.mpdf.mciftools import *
-from diffpy.mpdf.simpleparser import *
-from diffpy.mpdf.mpdftransformer import *
-
-# End of file
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.mpdf         by Frandsen Group
+#                     Benjamin A. Frandsen benfrandsen@byu.edu
+#                     (c) 2022 Benjamin Allen Frandsen
+#                      All rights reserved
+#
+# File coded by:    Benjamin Frandsen
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""Tools for magnetic pair distribution function analysis
+"""
+
+# package version
+from diffpy.mpdf.version import __version__
+
+# convenience imports
+from diffpy.mpdf.magstructure import *
+from diffpy.mpdf.mpdfcalculator import *
+from diffpy.mpdf.magutils import *
+from diffpy.mpdf.mpdf3Dcalculator import *
+from diffpy.mpdf.visualize3D import *
+from diffpy.mpdf.mciftools import *
+from diffpy.mpdf.simpleparser import *
+from diffpy.mpdf.mpdftransformer import *
+
+# End of file

{diffpy_mpdf-1.0.4 → diffpy_mpdf-1.0.4.2}/diffpy/mpdf/gitarchive.cfg

@@ -1,5 +1,5 @@
-[DEFAULT]
-commit = $Format:%H$
-date = $Format:%ai$
-timestamp = $Format:%at$
-refnames = $Format:%D$
+[DEFAULT]
+commit = $Format:%H$
+date = $Format:%ai$
+timestamp = $Format:%at$
+refnames = $Format:%D$