diffpy.structure 3.3.1rc0__tar.gz → 3.4.0__tar.gz

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/LICENSE-DANSE.rst

@@ -9,14 +9,11 @@ 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
+or email Prof. Simon Billinge at sbillinge@ucsb.edu
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/LICENSE.rst

@@ -18,6 +18,9 @@ Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Labo
 Copyright (c) 2024-2025, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
+Copyright (c) 2026-present, The Contributors to the diffpy.structure project.
+All rights reserved.
+
 The "DiffPy-CMI" is distributed subject to the following license conditions:
 
 .. code-block:: text

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: diffpy.structure
-Version: 3.3.1rc0
+Version: 3.4.0
 Summary: Crystal structure container and parsers for structure formats.
-Author-email: Simon Billinge <sb2896@columbia.edu>
-Maintainer-email: Simon Billinge <sb2896@columbia.edu>
+Author-email: Simon Billinge <sbillinge@ucsb.edu>
+Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
 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
@@ -16,12 +16,12 @@ 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: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: <3.14,>=3.11
+Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE-DANSE.rst
 License-File: LICENSE-pymmlib.rst
@@ -29,6 +29,7 @@ License-File: LICENSE.rst
 License-File: AUTHORS.rst
 Requires-Dist: numpy
 Requires-Dist: pycifrw
+Requires-Dist: diffpy.utils
 Dynamic: license-file
 
 |Icon| |title|_
@@ -58,6 +59,7 @@ Dynamic: license-file
         :target: https://anaconda.org/conda-forge/diffpy.structure
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.structure/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
@@ -132,6 +134,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.structure --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.structure -h
+
 Getting Started
 ---------------
 
@@ -167,8 +182,15 @@ Improvements and fixes are always appreciated.
 
 Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
-Acknowledgement
----------------
+Contact
+-------
+
+For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainer``Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
 
 Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
 originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
@@ -177,8 +199,3 @@ Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
 ``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
-
-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.

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/README.rst

@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.structure
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.structure/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
@@ -99,6 +100,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.structure --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.structure -h
+
 Getting Started
 ---------------
 
@@ -134,8 +148,15 @@ Improvements and fixes are always appreciated.
 
 Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
-Acknowledgement
----------------
+Contact
+-------
+
+For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainer``Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
 
 Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
 originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
@@ -144,8 +165,3 @@ Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
 ``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
-
-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.

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/pyproject.toml

@@ -6,15 +6,15 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.structure"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon Billinge", email="sb2896@columbia.edu" },
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 maintainers = [
-  { name="Simon Billinge", email="sb2896@columbia.edu" },
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 description = "Crystal structure container and parsers for structure formats."
 keywords = ['diffpy', 'crystal structure data storage', 'CIF', 'PDB']
 readme = "README.rst"
-requires-python = ">=3.11, <3.14"
+requires-python = ">=3.12, <3.15"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,16 +25,13 @@ classifiers = [
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
-[project.scripts]
-transtru = "diffpy.structure.apps.transtru:main"
-
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.structure/"
 Issues = "https://github.com/diffpy/diffpy.structure/issues/"
@@ -51,6 +48,9 @@ include = ["*"]  # package names should match these glob patterns (["*"] by defa
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[project.scripts]
+diffpy-structure = "diffpy.structure.app:main"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/requirements/conda.txt

@@ -1,2 +1,3 @@
 numpy
 pycifrw
+diffpy.utils

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/requirements/docs.txt

@@ -2,4 +2,4 @@ sphinx
 sphinx_rtd_theme
 sphinx-copybutton
 doctr
-m2r
+m2r2

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/requirements/pip.txt

@@ -1,2 +1,3 @@
 numpy
 pycifrw
+diffpy.utils

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2026 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/src/diffpy/structure/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2026 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Chris Farrow, Pavol Juhas,  Simon Billinge, Billinge Group members.
@@ -33,22 +33,66 @@ Exceptions:
     * SymmetryError
 """
 
-# Interface definitions ------------------------------------------------------
 
+import os
+import sys
+
+import diffpy.structure as _structure
 from diffpy.structure.atom import Atom
 from diffpy.structure.lattice import Lattice
-from diffpy.structure.parsers import getParser
+from diffpy.structure.parsers import get_parser
 from diffpy.structure.pdffitstructure import PDFFitStructure
 from diffpy.structure.structure import Structure
 from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
 
 # package version
 from diffpy.structure.version import __version__
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+# Deprecations -------------------------------------------------------
+base = "diffpy.structure"
+removal_version = "4.0.0"
+loadStructure_deprecation_msg = build_deprecation_message(
+    base,
+    "loadStructure",
+    "load_structure",
+    removal_version,
+)
+
+
+# @deprecated
+# custom deprecator for diffpy.Structure module
+class DeprecatedStructureModule:
+    """Proxy for backward compatibility of diffpy.Structure."""
+
+    def __getattr__(self, name):
+        import warnings
+
+        warnings.warn(
+            "Module 'diffpy.Structure' is deprecated and will be removed in version 4.0. "
+            "Use 'diffpy.structure' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return getattr(_structure, name)
+
+
+sys.modules["diffpy.Structure"] = DeprecatedStructureModule()
 
 # top level routines
 
 
+@deprecated(loadStructure_deprecation_msg)
 def loadStructure(filename, fmt="auto", **kw):
+    """This function has been deprecated and will be removed in version
+    4.0.0.
+
+    Please use diffpy.structure.load_structure instead.
+    """
+    return load_structure(filename, fmt, **kw)
+
+
+def load_structure(filename, fmt="auto", **kw):
     """Load new structure object from the specified file.
 
     Parameters
@@ -72,9 +116,9 @@ def loadStructure(filename, fmt="auto", **kw):
         Return a more specific PDFFitStructure type for 'pdffit'
         and 'discus' formats.
     """
-
-    p = getParser(fmt, **kw)
-    rv = p.parseFile(filename)
+    filename = os.fspath(filename)
+    p = get_parser(fmt, **kw)
+    rv = p.parse_file(filename)
     return rv
 
 

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/src/diffpy/structure/_legacy_importer.py

@@ -80,7 +80,11 @@ class MapRenamedStructureModule(importlib.abc.Loader):
 # ----------------------------------------------------------------------------
 
 # show deprecation warning for diffpy.Structure
-warn(WMSG.format("diffpy.Structure", "diffpy.structure"), DeprecationWarning, stacklevel=2)
+warn(
+    WMSG.format("diffpy.Structure", "diffpy.structure"),
+    DeprecationWarning,
+    stacklevel=2,
+)
 
 # install meta path finder for diffpy.Structure submodules
 sys.meta_path.append(FindRenamedStructureModule())

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/src/diffpy/structure/apps/anyeye.py

@@ -52,6 +52,46 @@ import signal
 import sys
 
 from diffpy.structure.structureerrors import StructureFormatError
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+base = "diffpy.structure"
+removal_version = "4.0.0"
+loadStructureFile_deprecation_msg = build_deprecation_message(
+    base,
+    "loadStructureFile",
+    "load_structure_file",
+    removal_version,
+)
+convertStructureFile_deprecation_msg = build_deprecation_message(
+    base,
+    "loadStructureFile",
+    "load_structure_file",
+    removal_version,
+)
+watchStructureFile_deprecation_msg = build_deprecation_message(
+    base,
+    "watchStructureFile",
+    "watch_structure_file",
+    removal_version,
+)
+cleanUp_deprecation_msg = build_deprecation_message(
+    base,
+    "cleanUp",
+    "clean_up",
+    removal_version,
+)
+parseFormula_deprecation_msg = build_deprecation_message(
+    base,
+    "parseFormula",
+    "parse_formula",
+    removal_version,
+)
+signalHandler_deprecation_msg = build_deprecation_message(
+    base,
+    "signalHandler",
+    "signal_handler",
+    removal_version,
+)
 
 # parameter dictionary
 pd = {
@@ -72,9 +112,9 @@ def usage(style=None):
     if style == "brief":
         msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
     else:
-        from diffpy.structure.parsers import inputFormats
+        from diffpy.structure.parsers import input_formats
 
-        fmts = [f for f in inputFormats() if f != "auto"]
+        fmts = [f for f in input_formats() if f != "auto"]
         msg = msg.replace("inputFormats", " ".join(fmts))
     print(msg)
     return
@@ -87,9 +127,28 @@ def version():
     return
 
 
+@deprecated(loadStructureFile_deprecation_msg)
 def loadStructureFile(filename, format="auto"):
     """Load structure from specified file.
 
+    Parameters
+    ----------
+    filename : str
+        Path to the structure file.
+    format : str, Optional
+        File format, by default "auto".
+
+    Returns
+    -------
+    tuple
+        A tuple of (Structure, fileformat).
+    """
+    return load_structure_file(filename, format)
+
+
+def load_structure_file(filename, format="auto"):
+    """Load structure from specified file.
+
     Parameters
     ----------
     filename : str
@@ -110,7 +169,12 @@ def loadStructureFile(filename, format="auto"):
     return (stru, fileformat)
 
 
+@deprecated(convertStructureFile_deprecation_msg)
 def convertStructureFile(pd):
+    return convert_structure_file(pd)
+
+
+def convert_structure_file(pd):
     # make temporary directory on the first pass
     if "tmpdir" not in pd:
         from tempfile import mkdtemp
@@ -134,11 +198,14 @@ def convertStructureFile(pd):
         return
     # otherwise convert to the first recognized viewer format
     if stru is None:
-        stru = loadStructureFile(strufile, fmt)[0]
+        stru = load_structure_file(strufile, fmt)[0]
     if pd["formula"]:
         formula = pd["formula"]
         if len(formula) != len(stru):
-            emsg = "Formula has %i atoms while structure %i" % (len(formula), len(stru))
+            emsg = "Formula has %i atoms while structure %i" % (
+                len(formula),
+                len(stru),
+            )
             raise RuntimeError(emsg)
         for a, el in zip(stru, formula):
             a.element = el
@@ -151,19 +218,29 @@ def convertStructureFile(pd):
     return
 
 
+@deprecated(watchStructureFile_deprecation_msg)
 def watchStructureFile(pd):
+    return watch_structure_file(pd)
+
+
+def watch_structure_file(pd):
     from time import sleep
 
     strufile = pd["strufile"]
     tmpfile = pd["tmpfile"]
     while pd["watch"]:
         if os.path.getmtime(tmpfile) < os.path.getmtime(strufile):
-            convertStructureFile(pd)
+            convert_structure_file(pd)
         sleep(1)
     return
 
 
+@deprecated(cleanUp_deprecation_msg)
 def cleanUp(pd):
+    return clean_up(pd)
+
+
+def clean_up(pd):
     if "tmpfile" in pd:
         os.remove(pd["tmpfile"])
         del pd["tmpfile"]
@@ -173,7 +250,14 @@ def cleanUp(pd):
     return
 
 
+@deprecated(parseFormula_deprecation_msg)
 def parseFormula(formula):
+    """Parse chemical formula and return a list of elements."""
+    # remove all blanks
+    return parse_formula(formula)
+
+
+def parse_formula(formula):
     """Parse chemical formula and return a list of elements."""
     # remove all blanks
     formula = re.sub(r"\s", "", formula)
@@ -194,11 +278,17 @@ def parseFormula(formula):
 
 
 def die(exit_status=0, pd={}):
-    cleanUp(pd)
+    clean_up(pd)
     sys.exit(exit_status)
 
 
+@deprecated(signalHandler_deprecation_msg)
 def signalHandler(signum, stackframe):
+    # revert to default handler
+    return signal_handler(signum, stackframe)
+
+
+def signal_handler(signum, stackframe):
     # revert to default handler
     signal.signal(signum, signal.SIG_DFL)
     if signum == signal.SIGCHLD:
@@ -217,7 +307,9 @@ def main():
     pd["watch"] = False
     try:
         opts, args = getopt.getopt(
-            sys.argv[1:], "f:whV", ["formula=", "watch", "viewer=", "formats=", "help", "version"]
+            sys.argv[1:],
+            "f:whV",
+            ["formula=", "watch", "viewer=", "formats=", "help", "version"],
         )
     except getopt.GetoptError as errmsg:
         print(errmsg, file=sys.stderr)
@@ -226,7 +318,7 @@ def main():
     for o, a in opts:
         if o in ("-f", "--formula"):
             try:
-                pd["formula"] = parseFormula(a)
+                pd["formula"] = parse_formula(a)
             except RuntimeError as msg:
                 print(msg, file=sys.stderr)
                 die(2)
@@ -250,23 +342,23 @@ def main():
         die(2)
     pd["strufile"] = args[0]
     # trap the following signals
-    signal.signal(signal.SIGHUP, signalHandler)
-    signal.signal(signal.SIGQUIT, signalHandler)
-    signal.signal(signal.SIGSEGV, signalHandler)
-    signal.signal(signal.SIGTERM, signalHandler)
-    signal.signal(signal.SIGINT, signalHandler)
+    signal.signal(signal.SIGHUP, signal_handler)
+    signal.signal(signal.SIGQUIT, signal_handler)
+    signal.signal(signal.SIGSEGV, signal_handler)
+    signal.signal(signal.SIGTERM, signal_handler)
+    signal.signal(signal.SIGINT, signal_handler)
     env = os.environ.copy()
     if os.path.basename(pd["viewer"]).startswith("atomeye"):
         env["XLIB_SKIP_ARGB_VISUALS"] = "1"
     # try to run the thing:
     try:
-        convertStructureFile(pd)
+        convert_structure_file(pd)
         spawnargs = (pd["viewer"], pd["viewer"], pd["tmpfile"], env)
         # load strufile in atomeye
         if pd["watch"]:
-            signal.signal(signal.SIGCHLD, signalHandler)
+            signal.signal(signal.SIGCHLD, signal_handler)
             os.spawnlpe(os.P_NOWAIT, *spawnargs)
-            watchStructureFile(pd)
+            watch_structure_file(pd)
         else:
             status = os.spawnlpe(os.P_WAIT, *spawnargs)
             die(status, pd)

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0}/src/diffpy/structure/apps/transtru.py

@@ -52,10 +52,10 @@ def usage(style=None):
     if style == "brief":
         msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
     else:
-        from diffpy.structure.parsers import inputFormats, outputFormats
+        from diffpy.structure.parsers import input_formats, output_formats
 
-        msg = msg.replace("inputFormats", " ".join(inputFormats()))
-        msg = msg.replace("outputFormats", " ".join(outputFormats()))
+        msg = msg.replace("inputFormats", " ".join(input_formats()))
+        msg = msg.replace("outputFormats", " ".join(output_formats()))
     print(msg)
     return
 
@@ -88,28 +88,31 @@ def main():
         usage("brief")
         sys.exit()
     # process arguments
-    from diffpy.structure.parsers import inputFormats, outputFormats
+    from diffpy.structure.parsers import input_formats, output_formats
 
     try:
         infmt, outfmt = args[0].split("..", 1)
-        if infmt not in inputFormats():
+        if infmt not in input_formats():
             print("'%s' is not valid input format" % infmt, file=sys.stderr)
             sys.exit(2)
-        if outfmt not in outputFormats():
+        if outfmt not in output_formats():
             print("'%s' is not valid output format" % outfmt, file=sys.stderr)
             sys.exit(2)
     except ValueError:
-        print("invalid format specification '%s' does not contain .." % args[0], file=sys.stderr)
+        print(
+            "invalid format specification '%s' does not contain .." % args[0],
+            file=sys.stderr,
+        )
         sys.exit(2)
     # ready to do some real work
     try:
         strufile = args[1]
         stru = Structure()
         if args[1] == "-":
-            stru.readStr(sys.stdin.read(), infmt)
+            stru.read_structure(sys.stdin.read(), infmt)
         else:
             stru.read(strufile, infmt)
-        sys.stdout.write(stru.writeStr(outfmt))
+        sys.stdout.write(stru.write_structure(outfmt))
     except IndexError:
         print("strufile not specified", file=sys.stderr)
         sys.exit(2)