diffpy.structure 3.2.2rc0__tar.gz → 3.2.3__tar.gz

{diffpy_structure-3.2.2rc0 → diffpy_structure-3.2.3}/AUTHORS.rst

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

{diffpy_structure-3.2.2rc0 → diffpy_structure-3.2.3}/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-3.2.2rc0 → diffpy_structure-3.2.3}/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-3.2.2rc0 → diffpy_structure-3.2.3}/LICENSE_pymmlib.rst

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

diffpy_structure-3.2.3/MANIFEST.in

@@ -0,0 +1,12 @@
+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-3.2.2rc0 → diffpy_structure-3.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffpy.structure
-Version: 3.2.2rc0
+Version: 3.2.3
 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>
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 License-File: LICENSE_DANSE.rst
@@ -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/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
@@ -79,6 +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
@@ -109,20 +110,18 @@ To add "conda-forge" to the conda channels, run the following in a terminal. ::
 We want to install our packages in a suitable conda environment.
 The following creates and activates a new environment named ``diffpy.structure_env`` ::
 
-        conda create -n diffpy.structure_env python=3
+        conda create -n diffpy.structure_env diffpy.structure
         conda activate diffpy.structure_env
 
-Then, to fully install ``diffpy.structure`` in our active environment, run ::
-
-        conda install diffpy.structure
+To confirm that the installation was successful, type ::
 
-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 ::
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
 
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.structure/main/requirements/run.txt
+The output should print the latest version displayed on the badges above.
 
-and then install the package ::
+If the above does not work, you can 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 ::
 
         pip install diffpy.structure
 
@@ -132,12 +131,17 @@ and run the following ::
 
         pip install .
 
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.structure>`_ for tutorials and API references.
+
 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-3.2.2rc0 → diffpy_structure-3.2.3}/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/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
@@ -47,6 +47,7 @@ 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
@@ -77,20 +78,18 @@ To add "conda-forge" to the conda channels, run the following in a terminal. ::
 We want to install our packages in a suitable conda environment.
 The following creates and activates a new environment named ``diffpy.structure_env`` ::
 
-        conda create -n diffpy.structure_env python=3
+        conda create -n diffpy.structure_env diffpy.structure
         conda activate diffpy.structure_env
 
-Then, to fully install ``diffpy.structure`` in our active environment, run ::
-
-        conda install diffpy.structure
+To confirm that the installation was successful, type ::
 
-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 ::
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
 
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.structure/main/requirements/run.txt
+The output should print the latest version displayed on the badges above.
 
-and then install the package ::
+If the above does not work, you can 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 ::
 
         pip install diffpy.structure
 
@@ -100,12 +99,17 @@ and run the following ::
 
         pip install .
 
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.structure>`_ for tutorials and API references.
+
 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-3.2.2rc0 → diffpy_structure-3.2.3}/pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 description = "Crystal structure container and parsers for structure formats."
 keywords = ['diffpy', 'crystal structure data storage CIF PDB']
 readme = "README.rst"
-requires-python = ">=3.10"
+requires-python = ">=3.10, <3.13"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -36,6 +36,9 @@ classifiers = [
 Homepage = "https://github.com/diffpy/diffpy.structure/"
 Issues = "https://github.com/diffpy/diffpy.structure/issues/"
 
+[project.scripts]
+transtru = "diffpy.structure.apps.transtru:main"
+
 [tool.setuptools-git-versioning]
 enabled = true
 template = "{tag}"
@@ -49,7 +52,7 @@ 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/run.txt"]}
+dependencies = {file = ["requirements/pip.txt"]}
 
 [tool.black]
 line-length = 115

diffpy_structure-3.2.3/requirements/docs.txt

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

diffpy_structure-3.2.2rc0/requirements/run.txt → diffpy_structure-3.2.3/requirements/pip.txt

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

diffpy_structure-3.2.3/requirements/test.txt

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

{diffpy_structure-3.2.2rc0 → diffpy_structure-3.2.3}/src/diffpy/structure/apps/anyeye.py

@@ -265,7 +265,7 @@ def main():
         spawnargs = (pd["viewer"], pd["viewer"], pd["tmpfile"], env)
         # load strufile in atomeye
         if pd["watch"]:
-            signal.signal(signal.SIGCLD, signalHandler)
+            signal.signal(signal.SIGCHLD, signalHandler)
             os.spawnlpe(os.P_NOWAIT, *spawnargs)
             watchStructureFile(pd)
         else:

{diffpy_structure-3.2.2rc0 → diffpy_structure-3.2.3}/src/diffpy.structure.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffpy.structure
-Version: 3.2.2rc0
+Version: 3.2.3
 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>
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 License-File: LICENSE_DANSE.rst
@@ -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/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
@@ -79,6 +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
@@ -109,20 +110,18 @@ To add "conda-forge" to the conda channels, run the following in a terminal. ::
 We want to install our packages in a suitable conda environment.
 The following creates and activates a new environment named ``diffpy.structure_env`` ::
 
-        conda create -n diffpy.structure_env python=3
+        conda create -n diffpy.structure_env diffpy.structure
         conda activate diffpy.structure_env
 
-Then, to fully install ``diffpy.structure`` in our active environment, run ::
-
-        conda install diffpy.structure
+To confirm that the installation was successful, type ::
 
-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 ::
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
 
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.structure/main/requirements/run.txt
+The output should print the latest version displayed on the badges above.
 
-and then install the package ::
+If the above does not work, you can 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 ::
 
         pip install diffpy.structure
 
@@ -132,12 +131,17 @@ and run the following ::
 
         pip install .
 
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.structure>`_ for tutorials and API references.
+
 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-3.2.2rc0 → diffpy_structure-3.2.3}/src/diffpy.structure.egg-info/SOURCES.txt

@@ -5,12 +5,16 @@ LICENSE_pymmlib.rst
 MANIFEST.in
 README.rst
 pyproject.toml
-requirements/run.txt
-src/diffpy/Structure.py
+requirements/build.txt
+requirements/conda.txt
+requirements/docs.txt
+requirements/pip.txt
+requirements/test.txt
 src/diffpy/__init__.py
 src/diffpy.structure.egg-info/PKG-INFO
 src/diffpy.structure.egg-info/SOURCES.txt
 src/diffpy.structure.egg-info/dependency_links.txt
+src/diffpy.structure.egg-info/entry_points.txt
 src/diffpy.structure.egg-info/requires.txt
 src/diffpy.structure.egg-info/top_level.txt
 src/diffpy/structure/__init__.py
@@ -45,10 +49,10 @@ 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
@@ -57,4 +61,31 @@ tests/test_spacegroups.py
 tests/test_structure.py
 tests/test_supercell.py
 tests/test_symmetryutilities.py
-tests/test_version.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

diffpy_structure-3.2.3/src/diffpy.structure.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+transtru = diffpy.structure.apps.transtru:main

diffpy_structure-3.2.3/src/diffpy.structure.egg-info/requires.txt

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

diffpy_structure-3.2.3/tests/conftest.py

@@ -0,0 +1,29 @@
+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