diffpy.structure 3.2.2__tar.gz → 3.2.2rc0__tar.gz

{diffpy_structure-3.2.2 → diffpy_structure-3.2.2rc0}/AUTHORS.rst

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

{diffpy_structure-3.2.2 → diffpy_structure-3.2.2rc0}/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-3.2.2 → diffpy_structure-3.2.2rc0}/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-3.2.2 → diffpy_structure-3.2.2rc0}/LICENSE_pymmlib.rst

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

diffpy_structure-3.2.2rc0/MANIFEST.in

@@ -0,0 +1,14 @@
+include AUTHORS.rst
+include LICENSE
+include README.rst
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat
+
+include diffpy.structure/version.py
+
+# If including data files in the package, add them like:
+# include path/to/data_file

{diffpy_structure-3.2.2 → diffpy_structure-3.2.2rc0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffpy.structure
-Version: 3.2.2
+Version: 3.2.2rc0
 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>
@@ -47,8 +47,8 @@ Requires-Dist: pycifrw
 .. |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/main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure
@@ -79,7 +79,6 @@ 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
@@ -119,7 +118,11 @@ 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, type ::
+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 ::
 
         pip install diffpy.structure
 
@@ -134,7 +137,7 @@ 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-3.2.2 → diffpy_structure-3.2.2rc0}/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/main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure
@@ -47,7 +47,6 @@ 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
@@ -87,7 +86,11 @@ 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, type ::
+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 ::
 
         pip install diffpy.structure
 
@@ -102,7 +105,7 @@ 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-3.2.2 → diffpy_structure-3.2.2rc0}/pyproject.toml

@@ -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)
 
 [tool.setuptools.dynamic]
-dependencies = {file = ["requirements/pip.txt"]}
+dependencies = {file = ["requirements/run.txt"]}
 
 [tool.black]
 line-length = 115

diffpy_structure-3.2.2/requirements/conda.txt → diffpy_structure-3.2.2rc0/requirements/run.txt

@@ -1,2 +1,2 @@
-numpy
-pycifrw
+numpy
+pycifrw

diffpy_structure-3.2.2rc0/src/diffpy/Structure.py

@@ -0,0 +1,35 @@
+#!/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

{diffpy_structure-3.2.2 → diffpy_structure-3.2.2rc0}/src/diffpy.structure.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffpy.structure
-Version: 3.2.2
+Version: 3.2.2rc0
 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>
@@ -47,8 +47,8 @@ Requires-Dist: pycifrw
 .. |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/main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure
@@ -79,7 +79,6 @@ 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
@@ -119,7 +118,11 @@ 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, type ::
+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 ::
 
         pip install diffpy.structure
 
@@ -134,7 +137,7 @@ 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-3.2.2 → diffpy_structure-3.2.2rc0}/src/diffpy.structure.egg-info/SOURCES.txt

@@ -5,11 +5,8 @@ LICENSE_pymmlib.rst
 MANIFEST.in
 README.rst
 pyproject.toml
-requirements/build.txt
-requirements/conda.txt
-requirements/docs.txt
-requirements/pip.txt
-requirements/test.txt
+requirements/run.txt
+src/diffpy/Structure.py
 src/diffpy/__init__.py
 src/diffpy.structure.egg-info/PKG-INFO
 src/diffpy.structure.egg-info/SOURCES.txt
@@ -48,10 +45,10 @@ src/diffpy/structure/parsers/p_xcfg.py
 src/diffpy/structure/parsers/p_xyz.py
 src/diffpy/structure/parsers/parser_index_mod.py
 src/diffpy/structure/parsers/structureparser.py
-tests/conftest.py
 tests/test_atom.py
 tests/test_lattice.py
 tests/test_loadstructure.py
+tests/test_oldimports.py
 tests/test_p_cif.py
 tests/test_p_discus.py
 tests/test_p_pdffit.py
@@ -60,31 +57,4 @@ tests/test_spacegroups.py
 tests/test_structure.py
 tests/test_supercell.py
 tests/test_symmetryutilities.py
-tests/test_version.py
-tests/testdata/BubbleRaftShort.xcfg
-tests/testdata/CdSe_bulk.stru
-tests/testdata/LiCl-bad.cif
-tests/testdata/Ni-bad.stru
-tests/testdata/Ni-discus.stru
-tests/testdata/Ni.stru
-tests/testdata/Ni_prim123.stru
-tests/testdata/Ni_ref.cif
-tests/testdata/PbTe.cif
-tests/testdata/TeI-unkocc.cif
-tests/testdata/TeI.cif
-tests/testdata/ZnSb_RT_Q28X_VM_20_fxiso.rstr
-tests/testdata/arginine.pdb
-tests/testdata/badspacegroup.cif
-tests/testdata/bucky-bad1.xyz
-tests/testdata/bucky-bad2.xyz
-tests/testdata/bucky-plain-bad.xyz
-tests/testdata/bucky-plain.xyz
-tests/testdata/bucky-raw.xyz
-tests/testdata/bucky.xyz
-tests/testdata/curlybrackets.cif
-tests/testdata/customsg.cif
-tests/testdata/graphite.cif
-tests/testdata/hexagon-raw-bad.xyz
-tests/testdata/hexagon-raw.xy
-tests/testdata/hexagon-raw.xyz
-tests/testdata/nosites.cif
+tests/test_version.py

diffpy_structure-3.2.2rc0/tests/test_oldimports.py

@@ -0,0 +1,77 @@
+#!/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.
+#
+##############################################################################
+
+"""
+Unit tests for imports of old camel-case names.
+"""
+
+
+import importlib
+import sys
+import unittest
+import warnings
+
+import diffpy
+
+# ----------------------------------------------------------------------------
+
+
+class TestOldImports(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        "Uncache any already-imported old modules."
+        for modname in tuple(sys.modules):
+            if modname.startswith("diffpy.Structure"):
+                del sys.modules[modname]  # pragma: no cover
+        return
+
+    def test_00TopImport(self):
+        """check import of diffpy.Structure"""
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=DeprecationWarning)
+            import diffpy.Structure as m0
+        self.assertIs(diffpy.structure, m0)
+        # second import should raise no warning
+        with warnings.catch_warnings():
+            warnings.simplefilter("error")
+            import diffpy.Structure as m1
+        self.assertIs(diffpy.structure, m1)
+        return
+
+    def test_O1SubmoduleImport(self):
+        """check import of diffpy.Structure submodules."""
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter("always", category=DeprecationWarning)
+            import diffpy.Structure.SymmetryUtilities as symutil
+
+            self.assertIs(DeprecationWarning, w[0].category)
+        self.assertIs(diffpy.structure.symmetryutilities, symutil)
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter("always", category=DeprecationWarning)
+            import diffpy.Structure.Parsers.P_cif as pcif
+
+            self.assertIs(DeprecationWarning, w[0].category)
+        self.assertIs(diffpy.structure.parsers.p_cif, pcif)
+        self.assertRaises(ImportError, importlib.import_module, "diffpy.Structure.SSpaceGroups")
+        return
+
+
+# End of class TestOldImports
+
+# ----------------------------------------------------------------------------
+
+if __name__ == "__main__":
+    unittest.main()

diffpy_structure-3.2.2/MANIFEST.in

@@ -1,12 +0,0 @@
-graft src
-graft tests
-graft requirements
-
-include AUTHORS.rst LICENSE*.rst README.rst
-
-# Exclude all bytecode files and __pycache__ directories
-global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
-global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
-global-exclude __pycache__  # Exclude Python cache directories.
-global-exclude .git*  # Exclude git files and directories.
-global-exclude .idea  # Exclude PyCharm project settings.

diffpy_structure-3.2.2/requirements/docs.txt

@@ -1,4 +0,0 @@
-sphinx
-sphinx_rtd_theme
-doctr
-m2r

diffpy_structure-3.2.2/requirements/pip.txt

@@ -1,2 +0,0 @@
-numpy
-pycifrw

diffpy_structure-3.2.2/requirements/test.txt

@@ -1,6 +0,0 @@
-flake8
-pytest
-codecov
-coverage
-pytest-cov
-pytest-env

diffpy_structure-3.2.2/tests/conftest.py

@@ -1,29 +0,0 @@
-import json
-from pathlib import Path
-
-import pytest
-
-
-@pytest.fixture
-def user_filesystem(tmp_path):
-    base_dir = Path(tmp_path)
-    home_dir = base_dir / "home_dir"
-    home_dir.mkdir(parents=True, exist_ok=True)
-    cwd_dir = base_dir / "cwd_dir"
-    cwd_dir.mkdir(parents=True, exist_ok=True)
-
-    home_config_data = {"username": "home_username", "email": "home@email.com"}
-    with open(home_dir / "diffpyconfig.json", "w") as f:
-        json.dump(home_config_data, f)
-
-    yield tmp_path
-
-
-@pytest.fixture
-def datafile():
-    """Fixture to dynamically load any test file."""
-
-    def _load(filename):
-        return "tests/testdata/" + filename
-
-    return _load