feat: Copy over the code from diffpy.srfit.structure to here

.github/workflows/check-news-item.yml

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-      - main  # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
+      - main # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
 
 jobs:
   check-news-item:

LICENSE_DANSE.rst

@@ -0,0 +1,34 @@
+This program is part of the DiffPy and DANSE open-source projects at Columbia
+University and is available subject to the conditions and terms laid out below.
+
+Copyright (c) 2008-2011, The Trustees of Columbia University in
+the City of New York.  All rights reserved.
+
+For more information please visit the diffpy web-page at
+    http://www.diffpy.org
+or email Prof. Simon Billinge at sb2896@columbia.edu.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  * Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+
+  * 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.
+
+  * Neither the names of COLUMBIA UNIVERSITY, MICHIGAN STATE UNIVERSITY nor the
+    names of their 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 OWNER 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.

news/migrate-structure.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 description = "diffpy.cmi package for doing refinements with structure objects"
 keywords = ['diffraction', 'PDF', 'X-ray', 'neutron']
 readme = "README.rst"
-requires-python = ">=3.12, <3.15"
+requires-python = ">=3.11, <3.14"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,9 +25,9 @@ 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',
 ]
@@ -49,7 +49,7 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-cmistructure = "diffpy.cmistructure.app:main"
+diffpy-cmistructure = "diffpy.cmistructure.cmistructure_app:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}

requirements/conda.txt

@@ -1 +1,4 @@
 numpy
+diffpy.srreal
+diffpy.srfit
+diffpy.structure

requirements/pip.txt

@@ -1 +1,4 @@
 numpy
+diffpy.srreal
+diffpy.srfit
+diffpy.structure

requirements/tests.txt

@@ -4,3 +4,4 @@ codecov
 coverage
 pytest-cov
 pytest-env
+pyobjcryst

src/diffpy/__init__.py

@@ -12,3 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)

src/diffpy/cmistructure/__init__.py

@@ -12,11 +12,65 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""diffpy.cmi package for doing refinements with structure objects"""
+"""Modules and classes that adapt structure representations to the
+ParameterSet interface and automatic structure constraint generation
+from space group information."""
+
+from diffpy.cmistructure.sgconstraints import constrain_as_space_group
 
 # package version
 from diffpy.cmistructure.version import __version__  # noqa
 
+__all__ = ["constrain_as_space_group", "structure_to_parameter_set"]
+
+
+def structure_to_parameter_set(name, structure):
+    """Create a ParameterSet adapted to a structure object.
+
+    The adapter is chosen from the type of `structure`. Supported types are
+    diffpy.structure.Structure, pyobjcryst.crystal.Crystal,
+    pyobjcryst.molecule.Molecule and cctbx.crystal.special_position_settings.
+
+    Parameters
+    ----------
+    name : str
+        The name to give the structure.
+    structure : object
+        The structure object to adapt.
+
+    Returns
+    -------
+    BaseStructureParSet
+        The ParameterSet adapting `structure`.
+
+    Raises
+    ------
+    TypeError
+        If `structure` is not one of the supported structure types.
+    """
+    from diffpy.cmistructure.diffpyparset import DiffpyStructureParSet
+
+    if DiffpyStructureParSet.can_adapt(structure):
+        return DiffpyStructureParSet(name, structure)
+
+    from diffpy.cmistructure.objcrystparset import ObjCrystCrystalParSet
+
+    if ObjCrystCrystalParSet.can_adapt(structure):
+        return ObjCrystCrystalParSet(name, structure)
+
+    from diffpy.cmistructure.objcrystparset import ObjCrystMoleculeParSet
+
+    if ObjCrystMoleculeParSet.can_adapt(structure):
+        return ObjCrystMoleculeParSet(name, structure)
+
+    from diffpy.cmistructure.cctbxparset import CCTBXCrystalParSet
+
+    if CCTBXCrystalParSet.can_adapt(structure):
+        return CCTBXCrystalParSet(name, structure)
+
+    raise TypeError("Unadaptable structure format")
+
+
 # silence the pyflakes syntax checker
 assert __version__ or True
 

src/diffpy/cmistructure/basestructureparset.py

@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2009 The Trustees of Columbia University in the City of New York.
+# (c) 2026 Contributors to diffpy.cmistructure.
+# All rights reserved.
+#
+# File coded by: Chris Farrow and members of the diffpy community.
+#
+# Originally developed in diffpy.srfit by the DANSE Diffraction group and
+# Simon J. L. Billinge.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.cmistructure/graphs/contributors
+#
+# See LICENSE.rst and LICENSE_DANSE.rst for license information.
+#
+##############################################################################
+"""Base class for adapting structures to a ParameterSet interface.
+
+The BaseStructureParSet is a ParameterSet with functionality required by
+all structure adapters.
+"""
+
+__all__ = ["BaseStructureParSet"]
+
+from diffpy.srfit.fitbase.parameterset import ParameterSet
+
+
+class BaseStructureParSet(ParameterSet):
+    """Base class for structure adapters.
+
+    BaseStructureParSet derives from ParameterSet and provides methods that
+    help interface the ParameterSet with the space group constraint methods in
+    the sgconstraints module and to ProfileGenerators.
+
+    Attributes
+    ----------
+    structure : object
+        The adapted structure object.
+    """
+
+    @classmethod
+    def can_adapt(self, structure):
+        """Return whether the structure can be adapted by this class.
+
+        Parameters
+        ----------
+        structure : object
+            The structure object to check.
+
+        Returns
+        -------
+        bool
+            The flag indicating if `structure` can be adapted. The base class
+            always returns False.
+        """
+        return False
+
+    def get_lattice(self):
+        """Return the ParameterSet containing the lattice Parameters.
+
+        The returned ParameterSet may contain other Parameters than the
+        lattice Parameters. It is assumed that the lattice parameters
+        are named "a", "b", "c", "alpha", "beta", "gamma".
+
+        The lattice must also have the "angle_units" attribute, which is
+        either "deg" or "rad", to signify degrees or radians.
+
+        Returns
+        -------
+        ParameterSet
+            The ParameterSet holding the lattice Parameters.
+
+        Raises
+        ------
+        NotImplementedError
+            If the subclass does not override this method.
+        """
+        raise NotImplementedError("The must be overloaded")
+
+    def get_scatterers(self):
+        """Return the list of ParameterSets that represent the
+        scatterers.
+
+        The site positions must be accessible from the list entries via
+        the names "x", "y", and "z". The ADPs must be accessible as
+        well, but the name and nature of the ADPs (U-factors, B-factors,
+        isotropic, anisotropic) depends on the adapted structure.
+
+        Returns
+        -------
+        list of ParameterSet
+            The ParameterSets of the scatterers in the structure.
+
+        Raises
+        ------
+        NotImplementedError
+            If the subclass does not override this method.
+        """
+        raise NotImplementedError("The must be overloaded")