structuretoolkit 0.0.12__tar.gz → 0.0.13__tar.gz

structuretoolkit-0.0.13/PKG-INFO

@@ -0,0 +1,148 @@
+Metadata-Version: 2.1
+Name: structuretoolkit
+Version: 0.0.13
+Summary: build, analyse and visualise atomistic structures for materials science
+Author-email: Jan Janssen <janssen@mpie.de>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2018, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+        All rights reserved.
+        
+        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 name of the copyright holder nor the names of its
+          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 HOLDER 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.
+        
+Project-URL: Homepage, https://github.com/pyiron/structuretoolkit
+Project-URL: Documentation, https://github.com/pyiron/structuretoolkit
+Project-URL: Repository, https://github.com/pyiron/structuretoolkit
+Keywords: pyiron
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ase<=3.22.1,>=3.20.1
+Requires-Dist: matplotlib==3.8.2
+Requires-Dist: numpy<=1.26.2,>=1.23.5
+Requires-Dist: scipy<=1.11.4,>=1.9.3
+Provides-Extra: grainboundary
+Requires-Dist: aimsgb<=1.1.0,>=1.0.2; extra == "grainboundary"
+Requires-Dist: pymatgen<=2023.11.12,>=2022.2.1; extra == "grainboundary"
+Provides-Extra: pyscal
+Requires-Dist: pyscal2==2.10.18; extra == "pyscal"
+Provides-Extra: nglview
+Requires-Dist: nglview<=3.0.8,>=2.7.7; extra == "nglview"
+Provides-Extra: plotly
+Requires-Dist: plotly<=5.18.0,>=4.14.3; extra == "plotly"
+Provides-Extra: clusters
+Requires-Dist: scikit-learn==1.3.2; extra == "clusters"
+Provides-Extra: symmetry
+Requires-Dist: spglib<=2.1.0,>=1.16.5; extra == "symmetry"
+Provides-Extra: surface
+Requires-Dist: spglib<=2.1.0,>=1.16.5; extra == "surface"
+Requires-Dist: pymatgen<=2023.11.12,>=2022.2.1; extra == "surface"
+Provides-Extra: phonopy
+Requires-Dist: phonopy<=2.20.0,>=2.16.2; extra == "phonopy"
+Requires-Dist: spglib<=2.1.0,>=1.16.5; extra == "phonopy"
+Provides-Extra: pyxtal
+Requires-Dist: pyxtal<=0.6.1,>=0.5.5; extra == "pyxtal"
+
+# structuretoolkit 
+
+[![Unittests](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml)
+[![Coverage Status](https://coveralls.io/repos/github/pyiron/structuretoolkit/badge.svg?branch=main)](https://coveralls.io/github/pyiron/structuretoolkit?branch=main)
+
+Originally developed as part of the `pyiron_atomistics` module the `structuretoolkit` was release as standalone library
+for analysing, building and visualising atomistic structures. Internally it uses the `ase.atoms.Atoms` class to 
+represent atomistic structures in python. The `structuretoolkit` is integrated inside `pyiron_atomistics`.
+
+## Disclaimer 
+The `structuretoolkit` is currently under development. 
+
+## Example
+
+```python
+import structuretoolkit as stk
+from ase.build import bulk
+
+structure = bulk("Al", cubic=True)
+stk.analyse.get_adaptive_cna_descriptors(structure)
+stk.plot3d(structure)
+```
+
+## Features 
+### Analysis
+* `stk.analyse.get_neighbors()`
+* `stk.analyse.get_neighborhood()`
+* `stk.analyse.get_equivalent_atoms()`
+* `stk.analyse.get_steinhardt_parameters()`
+* `stk.analyse.get_centro_symmetry_descriptors()` 
+* `stk.analyse.get_diamond_structure_descriptors()` 
+* `stk.analyse.get_adaptive_cna_descriptors()` 
+* `stk.analyse.get_voronoi_volumes()` 
+* `stk.analyse.find_solids()`
+* `stk.analyse.get_mean_positions()`
+* `stk.analyse.get_average_of_unique_labels()`
+* `stk.analyse.get_interstitials()`
+* `stk.analyse.get_layers()`
+* `stk.analyse.get_voronoi_vertices()`
+* `stk.analyse.get_voronoi_neighbors()`
+* `stk.analyse.get_delaunay_neighbors()`
+* `stk.analyse.get_cluster_positions()`
+* `stk.analyse.get_strain()`
+
+### Build
+* `stk.build.get_grainboundary_info()`
+* `stk.build.grainboundary()`
+* `stk.build.high_index_surface()`
+* `stk.build.get_high_index_surface_info()`
+* `stk.build.sqs_structures()`
+* `stk.build.pyxtal()`
+* `stk.build.B2()`
+* `stk.build.C14()`
+* `stk.build.C15()`
+* `stk.build.C36()`
+* `stk.build.D03()`
+
+### Visualize 
+* `stk.visualize.plot3d()`
+
+### Common 
+* `stk.common.ase_to_pymatgen()`
+* `stk.common.pymatgen_to_ase()`
+* `stk.common.pymatgen_read_from_file()`
+* `stk.common.ase_to_pyscal()`
+* `stk.common.apply_strain()`
+* `stk.common.center_coordinates_in_unit_cell()`
+* `stk.common.get_extended_positions()`
+* `stk.common.get_vertical_length()`
+* `stk.common.get_wrapped_coordinates()`
+* `stk.common.select_index()`

structuretoolkit-0.0.13/pyproject.toml

@@ -0,0 +1,70 @@
+[build-system]
+requires = ["ase", "matplotlib", "numpy", "setuptools", "scipy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "structuretoolkit"
+description = "build, analyse and visualise atomistic structures for materials science"
+authors = [
+    { name = "Jan Janssen", email = "janssen@mpie.de" },
+]
+readme = "README.md"
+license = { file = "LICENSE" }
+keywords = ["pyiron"]
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: BSD License",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+dependencies = [
+    "ase>=3.20.1,<=3.22.1",
+    "matplotlib==3.8.2",
+    "numpy>=1.23.5,<=1.26.2",
+    "scipy>=1.9.3,<=1.11.4",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/pyiron/structuretoolkit"
+Documentation = "https://github.com/pyiron/structuretoolkit"
+Repository = "https://github.com/pyiron/structuretoolkit"
+
+[project.optional-dependencies]
+grainboundary = [
+    "aimsgb>=1.0.2,<=1.1.0",
+    "pymatgen>=2022.2.1,<=2023.11.12",
+]
+pyscal = ["pyscal2==2.10.18"]
+nglview = ["nglview>=2.7.7,<=3.0.8"]
+plotly = ["plotly>=4.14.3,<=5.18.0"]
+clusters = ["scikit-learn==1.3.2"]
+symmetry = ["spglib>=1.16.5,<=2.1.0"]
+surface = [
+    "spglib>=1.16.5,<=2.1.0",
+    "pymatgen>=2022.2.1,<=2023.11.12",
+]
+phonopy = [
+    "phonopy>=2.16.2,<=2.20.0",
+    "spglib>=1.16.5,<=2.1.0",
+]
+pyxtal = ["pyxtal>=0.5.5,<=0.6.1"]
+
+[tool.setuptools]
+packages = ["structuretoolkit"]
+
+[tool.setuptools.dynamic]
+version = {attr = "structuretoolkit.__version__"}
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440-pre"
+versionfile_source = "structuretoolkit/_version.py"
+parentdir_prefix = "structuretoolkit"
+tag_prefix = "structuretoolkit-"

structuretoolkit-0.0.13/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

structuretoolkit-0.0.13/setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()

{structuretoolkit-0.0.12 → structuretoolkit-0.0.13}/structuretoolkit/__init__.py

@@ -1,3 +1,5 @@
+from . import _version
+
 # Analyse
 from structuretoolkit.analyse import (
     find_mic,
@@ -73,3 +75,5 @@ from structuretoolkit.build import (
     grainboundary as grainboundary_build,
     sqs_structures as get_sqs_structures,
 )
+
+__version__ = _version.get_versions()["version"]