diffpy.structure 3.2.0__py3-none-any.whl → 3.2.2__py3-none-any.whl

diffpy/structure/atom.py

@@ -536,7 +536,7 @@ class _AtomCartesianCoordinates(numpy.ndarray):
         self._atom.xyz[:] = self._atom.lattice.fractional(self)
         return
 
-    def __array_wrap__(self, out_arr, context=None):
+    def __array_wrap__(self, out_arr, context=None, return_scalar=None):
         """Ensure math operations on this type yield standard numpy array."""
         return out_arr.view(numpy.ndarray)
 

diffpy/structure/structure.py

@@ -711,8 +711,9 @@ class Structure(list):
     element = _linkAtomAttribute(
         "element",
         """Character array of `Atom` types. Assignment updates
-        the element attribute of the respective `Atoms`.""",
-        toarray=numpy.char.array,
+        the element attribute of the respective `Atoms`.
+        Set the maximum length of the element string to 5 characters.""",
+        toarray=lambda items: numpy.char.array(items, itemsize=5),
     )
 
     xyz = _linkAtomAttribute(
@@ -742,8 +743,9 @@ class Structure(list):
     label = _linkAtomAttribute(
         "label",
         """Character array of `Atom` names. Assignment updates
-        the label attribute of all `Atoms`.""",
-        toarray=numpy.char.array,
+        the label attribute of all `Atoms`.
+        Set the maximum length of the label string to 5 characters.""",
+        toarray=lambda items: numpy.char.array(items, itemsize=5),
     )
 
     occupancy = _linkAtomAttribute(

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/AUTHORS.rst

@@ -1,6 +1,7 @@
 Authors
 =======
 
+Billinge Group and community contributors,
 Pavol Juhas,
 Christopher L. Farrow,
 Xiaohao Yang,

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/LICENSE.rst

@@ -15,7 +15,7 @@ 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. 
+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:

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/LICENSE_DANSE.rst

@@ -9,13 +9,13 @@ 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. 
+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

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/LICENSE_pymmlib.rst

@@ -1,5 +1,5 @@
 .. code-block:: text
-        
+
                         The Artistic License 2.0
 
                 Copyright (c) 2000-2006, The Perl Foundation.

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffpy.structure
-Version: 3.2.0
+Version: 3.2.2
 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>
@@ -27,6 +27,8 @@ License-File: LICENSE.rst
 License-File: LICENSE_DANSE.rst
 License-File: LICENSE_pymmlib.rst
 License-File: AUTHORS.rst
+Requires-Dist: numpy
+Requires-Dist: pycifrw
 
 |Icon| |title|_
 ===============
@@ -45,8 +47,8 @@ License-File: AUTHORS.rst
 .. |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
+.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure
@@ -77,6 +79,7 @@ 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
@@ -93,28 +96,6 @@ by citing the following paper in your publication:
    <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
 ------------
 
@@ -138,11 +119,7 @@ Then, to fully install ``diffpy.structure`` in our active environment, run ::
 
 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 ::
+To install using ``pip`` into your ``diffpy.structure_env`` environment, type ::
 
         pip install diffpy.structure
 
@@ -157,7 +134,7 @@ 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>`_. 
+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

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/RECORD

@@ -1,15 +1,14 @@
-diffpy/Structure.py,sha256=qBWWvx2GV65SJqgS6qK933SDfZc1yUQCBtJpW_wFqj8,1005
 diffpy/__init__.py,sha256=WntnKrzS4hxw7YDYxwU-2hCJYNSFBf3gvjbPOrci0dk,673
 diffpy/structure/__init__.py,sha256=EPy-CMdt1GkwzPmFs6vBPFjxygb-xMCsrxZMEEnrODo,2600
 diffpy/structure/_legacy_importer.py,sha256=IXoPovMWIEY7tQTp1prTjICudfiVsR_Blmae-zDcHKA,2574
-diffpy/structure/atom.py,sha256=njq7vUr2yop9Rw8lgW2DX63cpTO0r4rToIcjAfQdIf0,17702
+diffpy/structure/atom.py,sha256=hB7ZbJgSe2RvHeu7HcnPGeJpopSs17xXLHdv-G93kE4,17722
 diffpy/structure/lattice.py,sha256=NhSYxFMyfPRJYwiLCyObEPC7vlZBAsP0x9PYSzJ1O7U,22499
 diffpy/structure/mmlibspacegroups.py,sha256=J4F8nbcZ2OmjhzxtOnFVKLQpzXgyQ-S8wh3EnNxqz-w,245608
 diffpy/structure/pdffitstructure.py,sha256=lzARAIDN-FiuMnQJIeFbfRMdRXCGgv2J2qPmOctkN_I,3202
 diffpy/structure/sgtbxspacegroups.py,sha256=9Mz_vVfC3CYpKBYFeYc2Un0VdsqNIx8e9KdZ-Szhw3Y,135078
 diffpy/structure/spacegroupmod.py,sha256=xMeWjiODk21koPQo7aQnwdWf4wzZ82PnVl3MmlTj5yU,15176
 diffpy/structure/spacegroups.py,sha256=BPKW75UNGqDlfi6lkntrjAJiqyxcKmIAeaUScrKA7LA,23359
-diffpy/structure/structure.py,sha256=wYIIdZpjXE4h-8gv5mv0dfFYlLJ-AAxmmwc-NdNPHP0,27337
+diffpy/structure/structure.py,sha256=r8_Z3MyevqlU5EEsQ5G4Xzji_8AwLAUOp6_M3hwq-K8,27541
 diffpy/structure/structureerrors.py,sha256=9T4Fwy-_dafyiMRGeK0qAmZ6TXBpRqlhSnOxIfV5mxM,880
 diffpy/structure/symmetryutilities.py,sha256=jxR8Sxp7Fw8seSX_8y8GgrbfpVadj4_leXFukTkDPKQ,37377
 diffpy/structure/utils.py,sha256=IMgzeIPg0WOIVeACpg2YZX4wL0NZhu_tZRuGctSmLuM,3320
@@ -32,11 +31,11 @@ diffpy/structure/parsers/p_xcfg.py,sha256=QIaaq30FoRnZwYIlAsLUMVRWGPoQaivRwMPWqX
 diffpy/structure/parsers/p_xyz.py,sha256=PDmkc_MyHRP5wqJsHxxa7W4bce60YHhkurUrmrhU8Ks,5017
 diffpy/structure/parsers/parser_index_mod.py,sha256=QWwV0tPpbIlk2i-gwR6MlKkUF0H05lGzO0yBq5nPOxk,3045
 diffpy/structure/parsers/structureparser.py,sha256=p6eXkziF0sBOR6p9tyfvs8O6D9oRqETrr_v54h3C5mg,2254
-diffpy.structure-3.2.0.dist-info/AUTHORS.rst,sha256=-15SGTrM2oMYIlTjqw81R2YKVMvWepQGgrG00jJWK44,212
-diffpy.structure-3.2.0.dist-info/LICENSE.rst,sha256=nXbHfaJU5pWBgoiK0ed_aJDs1icKfjV7bJwOZl-BaV0,6007
-diffpy.structure-3.2.0.dist-info/LICENSE_DANSE.rst,sha256=BC6IAe60b_BSdb-hI0GulJ5uPAu-RvuYdI8GKYtNL4U,2282
-diffpy.structure-3.2.0.dist-info/LICENSE_pymmlib.rst,sha256=eLh3rsGOgX3byYIbQlJ2jeGbpvjYK_7p25Dn6W7Gw_M,9599
-diffpy.structure-3.2.0.dist-info/METADATA,sha256=7x_IOt_u5518l1BujfJ82RufthvZp-U0VwzhOu1zotQ,8598
-diffpy.structure-3.2.0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-diffpy.structure-3.2.0.dist-info/top_level.txt,sha256=34qLZyi9mxikpHepVDTMHrrNbe8VoOuz3ShYeiWA7KA,7
-diffpy.structure-3.2.0.dist-info/RECORD,,
+diffpy.structure-3.2.2.dist-info/AUTHORS.rst,sha256=PH7xKOE6eZ60_LSn4IugF1w-9O2TWHJBBBC6WuiBXIg,255
+diffpy.structure-3.2.2.dist-info/LICENSE.rst,sha256=cewTuMX5-lzPdcCj6s5_YeJvPbc3ZyUHZJg5FB7nlIs,6006
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+diffpy.structure-3.2.2.dist-info/LICENSE_pymmlib.rst,sha256=9RJGn2ZWB4NaWRh8AE8nefdlKDEENs0EBFBk3D2YAas,9591
+diffpy.structure-3.2.2.dist-info/METADATA,sha256=WMTIbLk4KdhtEYBaBgCrBWWw38pwXlqHIdGDOGJl2c0,7670
+diffpy.structure-3.2.2.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+diffpy.structure-3.2.2.dist-info/top_level.txt,sha256=34qLZyi9mxikpHepVDTMHrrNbe8VoOuz3ShYeiWA7KA,7
+diffpy.structure-3.2.2.dist-info/RECORD,,

{diffpy.structure-3.2.0.dist-info → diffpy.structure-3.2.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.1.0)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

diffpy/Structure.py

@@ -1,35 +0,0 @@
-#!/usr/bin/env python
-##############################################################################
-#
-# diffpy.structure  Complex Modeling Initiative
-#                   (c) 2017 Brookhaven Science Associates,
-#                   Brookhaven National Laboratory.
-#                   All rights reserved.
-#
-# File coded by:    Pavol Juhas
-#
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
-#
-##############################################################################
-
-"""Support import of old camel-case module names with `DeprecationWarning`.
-
-The imported camel-case modules are aliases for the current module
-instances. Their `__name__` attributes are thus all in lower-case.
-
-Warning
--------
-This module is deprecated and will be removed in the future.
-"""
-
-
-import sys
-
-# install legacy import hooks
-import diffpy.structure._legacy_importer
-
-# replace this module with the new one
-sys.modules["diffpy.Structure"] = diffpy.structure
-
-# End of file