diffpy.structure 3.4.0rc0__tar.gz → 3.5.0__tar.gz

{diffpy_structure-3.4.0rc0 → diffpy_structure-3.5.0}/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-3.4.0rc0 → diffpy_structure-3.5.0}/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-3.4.0rc0 → diffpy_structure-3.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.structure
-Version: 3.4.0rc0
+Version: 3.5.0
 Summary: Crystal structure container and parsers for structure formats.
 Author-email: Simon Billinge <sbillinge@ucsb.edu>
 Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
@@ -49,8 +49,8 @@ Dynamic: license-file
 .. |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/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
+.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure

{diffpy_structure-3.4.0rc0 → diffpy_structure-3.5.0}/README.rst

@@ -15,8 +15,8 @@
 .. |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/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
+.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure

{diffpy_structure-3.4.0rc0 → diffpy_structure-3.5.0}/src/diffpy/structure/__init__.py

@@ -33,21 +33,30 @@ Exceptions:
     * SymmetryError
 """
 
-
+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
@@ -72,7 +81,17 @@ 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
@@ -82,10 +101,10 @@ def loadStructure(filename, fmt="auto", **kw):
         Path to the file to be loaded.
     fmt : str, Optional
         Format of the structure file such as 'cif' or 'xyz'. Must be
-        one of the formats listed by the `parsers.inputFormats` function.
+        one of the formats listed by the `parsers.input_formats` function.
         When 'auto', all supported formats are tried in a sequence.
     kw : Optional
-        Extra keyword arguments that are passed to `parsers.getParser`
+        Extra keyword arguments that are passed to `parsers.get_parser`
         function. These configure the dedicated Parser object that
         is used to read content in filename.
 
@@ -96,9 +115,9 @@ 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-3.4.0rc0 → diffpy_structure-3.5.0}/src/diffpy/structure/_legacy_importer.py

@@ -27,7 +27,6 @@ Warning
 This module is deprecated and will be removed in the future.
 """
 
-
 import importlib.abc
 import sys
 from warnings import warn

{diffpy_structure-3.4.0rc0 → diffpy_structure-3.5.0}/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
@@ -123,7 +187,7 @@ def convertStructureFile(pd):
     fmt = pd.get("format", "auto")
     stru = None
     if fmt == "auto":
-        stru, fmt = loadStructureFile(strufile)
+        stru, fmt = load_structure_file(strufile)
         pd["fmt"] = fmt
     # if fmt is recognized by the viewer, use as is
     if fmt in pd["formats"] and pd["formula"] is None:
@@ -134,7 +198,7 @@ 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):
@@ -154,19 +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"]
@@ -176,7 +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)
@@ -197,11 +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:
@@ -231,7 +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)
@@ -255,23 +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-3.4.0rc0 → diffpy_structure-3.5.0}/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
 
@@ -88,14 +88,14 @@ 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:
@@ -109,10 +109,10 @@ def main():
         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)