structuretoolkit 0.0.45__tar.gz → 0.0.46__tar.gz

structuretoolkit-0.0.46/PKG-INFO

@@ -0,0 +1,167 @@
+Metadata-Version: 2.5
+Name: structuretoolkit
+Version: 0.0.46
+Summary: build, analyse and visualise atomistic structures for materials science
+Project-URL: Homepage, https://github.com/pyiron/structuretoolkit
+Project-URL: Documentation, https://github.com/pyiron/structuretoolkit
+Project-URL: Repository, https://github.com/pyiron/structuretoolkit
+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.
+License-File: LICENSE
+Keywords: pyiron
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: <3.15,>=3.10
+Requires-Dist: ase<=3.29.0,>=3.24.0
+Requires-Dist: numpy<=2.5.3,>=1.23.5
+Requires-Dist: scipy<=1.18.0,>=1.15.0
+Provides-Extra: clusters
+Requires-Dist: scikit-learn==1.8.0; extra == 'clusters'
+Provides-Extra: dscribe
+Requires-Dist: dscribe==2.1.2; extra == 'dscribe'
+Provides-Extra: grainboundary
+Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == 'grainboundary'
+Requires-Dist: pymatgen<=2026.5.4,>=2026.3.23; extra == 'grainboundary'
+Provides-Extra: matplotlib
+Requires-Dist: matplotlib==3.11.1; extra == 'matplotlib'
+Provides-Extra: mp-api
+Requires-Dist: mp-api==0.45.15; extra == 'mp-api'
+Requires-Dist: pymatgen<=2026.5.4,>=2026.3.23; extra == 'mp-api'
+Provides-Extra: nglview
+Requires-Dist: nglview<=4.0.1,>=2.7.7; extra == 'nglview'
+Provides-Extra: phonopy
+Requires-Dist: phonopy<=4.4.0,>=2.21.2; extra == 'phonopy'
+Requires-Dist: spglib==2.7.0; extra == 'phonopy'
+Provides-Extra: plotly
+Requires-Dist: plotly<=7.0.0,>=6.0.0; extra == 'plotly'
+Provides-Extra: pyscal
+Requires-Dist: pyscal3<=3.3.2,>=3.2.5; extra == 'pyscal'
+Provides-Extra: surface
+Requires-Dist: pymatgen<=2026.5.4,>=2026.3.23; extra == 'surface'
+Requires-Dist: spglib==2.7.0; extra == 'surface'
+Provides-Extra: symmetry
+Requires-Dist: spglib==2.7.0; extra == 'symmetry'
+Description-Content-Type: text/markdown
+
+# structuretoolkit 
+
+[![Pipeline](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/structuretoolkit/graph/badge.svg?token=B6I4OACKND)](https://codecov.io/gh/pyiron/structuretoolkit)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/structuretoolkit/HEAD)
+
+`structuretoolkit` extends the [`ase.atoms.Atoms`](https://wiki.fysik.dtu.dk/ase/ase/atoms.html) class from the
+[Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) with a large collection of additional
+functions for **building**, **analysing** and **visualising** atomistic structures in materials science. It does
+not introduce a structure class of its own &ndash; every function takes an `ase.atoms.Atoms` object as input and,
+where applicable, returns one again, so `structuretoolkit` combines freely with the rest of the ASE ecosystem
+(`ase.build`, ASE calculators, ASE I/O, ...). `structuretoolkit` also powers the structure-analysis backend of
+[`pyiron_atomistics`](https://github.com/pyiron/pyiron_atomistics), where the same functions are available as
+methods directly on the structure object.
+
+## 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()` - find the nearest neighbors of every atom, by count or cutoff radius, periodic-boundary-aware
+* `stk.analyse.get_neighborhood()` - find the nearest neighbors of an arbitrary point in space, e.g. an interstitial site
+* `stk.analyse.get_equivalent_atoms()` - label atoms that map onto each other under the structure's symmetry operations
+* `stk.analyse.get_steinhardt_parameters()` - compute rotationally invariant Steinhardt bond-orientational order parameters
+* `stk.analyse.get_centro_symmetry_descriptors()` - compute the centrosymmetry parameter, large for atoms near a defect
+* `stk.analyse.get_diamond_structure_descriptors()` - identify cubic/hexagonal diamond local environments
+* `stk.analyse.get_adaptive_cna_descriptors()` - classify local crystal structure (fcc/hcp/bcc/icosahedral/other) via common neighbor analysis
+* `stk.analyse.get_voronoi_volumes()` - compute the Voronoi cell volume of every atom
+* `stk.analyse.find_solids()` - count how many atoms are "solid" vs. "liquid"-like, e.g. for melting-point calculations
+* `stk.analyse.get_mean_positions()` - average atomic positions across periodic boundary conditions
+* `stk.analyse.get_average_of_unique_labels()` - average values that share the same (possibly repeated) integer label
+* `stk.analyse.get_interstitials()` - locate interstitial sites of a given coordination number (e.g. tetrahedral, octahedral)
+* `stk.analyse.get_layers()` - group atoms into layers along the cell directions or arbitrary planes
+* `stk.analyse.get_voronoi_vertices()` - compute the Voronoi vertices of the (periodic) structure
+* `stk.analyse.get_voronoi_neighbors()` - find pairs of atoms sharing a Voronoi facet
+* `stk.analyse.get_delaunay_neighbors()` - find pairs of atoms sharing a Delaunay tetrahedron
+* `stk.analyse.get_cluster_positions()` - cluster nearby positions together via DBSCAN
+* `stk.analyse.get_strain()` - compute the per-atom Lagrangian strain tensor relative to a reference structure
+
+### Build
+* `stk.build.get_grainboundary_info()` - list the geometrically possible grain boundaries (by CSL sigma value) for a rotation axis
+* `stk.build.grainboundary()` - build a bicrystal grain-boundary structure for a chosen sigma value and plane
+* `stk.build.high_index_surface()` - build a stepped/kinked high-index surface slab
+* `stk.build.get_high_index_surface_info()` - derive the Miller index for a given terrace/step/kink orientation
+* `stk.build.sqs_structures()` - generate special quasirandom structures (SQS) for disordered alloys
+* `stk.build.B2()` - build a cubic AB B2 (CsCl-type) intermetallic structure
+* `stk.build.C14()` - build a hexagonal AB2 C14 Laves phase structure
+* `stk.build.C15()` - build a cubic AB2 C15 Laves phase structure
+* `stk.build.C36()` - build a hexagonal AB2 C36 Laves phase structure
+* `stk.build.D03()` - build a cubic AB3 D03 structure
+
+### Visualize 
+* `stk.visualize.plot3d()` - render an `Atoms` object in 3d, via NGLView or plotly
+
+### Common 
+* `stk.common.ase_to_pymatgen()` - convert an `ase.atoms.Atoms` object to a `pymatgen.core.Structure`
+* `stk.common.pymatgen_to_ase()` - convert a `pymatgen.core.Structure` back to an `ase.atoms.Atoms` object
+* `stk.common.pymatgen_read_from_file()` - read a structure file directly into an `ase.atoms.Atoms` object via pymatgen
+* `stk.common.ase_to_pyscal()` - convert an `ase.atoms.Atoms` object to a `pyscal3.core.System`
+* `stk.common.apply_strain()` - apply a homogeneous strain to a structure's cell, and its atoms
+* `stk.common.center_coordinates_in_unit_cell()` - wrap atomic coordinates back into the unit cell
+* `stk.common.get_extended_positions()` - repeat atoms across the periodic boundary to include neighbor images
+* `stk.common.get_vertical_length()` - get the height of the cell perpendicular to each face
+* `stk.common.get_wrapped_coordinates()` - wrap arbitrary Cartesian coordinates into the periodic cell
+* `stk.common.select_index()` - get the indices of atoms of a given chemical element
+
+## Documentation 
+
+* [structuretoolkit](https://structuretoolkit.readthedocs.io/en/latest/README.html)
+  * [Example](https://structuretoolkit.readthedocs.io/en/latest/README.html#example)
+  * [Features](https://structuretoolkit.readthedocs.io/en/latest/README.html#features)
+* [Introduction](https://structuretoolkit.readthedocs.io/en/latest/introduction.html)
+  * [How the package is organised](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#how-the-package-is-organised)
+  * [Helpers and converters](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-common-helpers-and-converters)
+  * [Analysing existing structures](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-analyse-analysing-existing-structures)
+  * [Constructing new structures](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-build-constructing-new-structures)
+  * [Looking at structures](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-visualize-looking-at-structures)
+  * [Where to go from here](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#where-to-go-from-here)
+* [Interface](https://structuretoolkit.readthedocs.io/en/latest/api.html)

structuretoolkit-0.0.46/README.md

@@ -0,0 +1,87 @@
+# structuretoolkit 
+
+[![Pipeline](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/structuretoolkit/graph/badge.svg?token=B6I4OACKND)](https://codecov.io/gh/pyiron/structuretoolkit)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/structuretoolkit/HEAD)
+
+`structuretoolkit` extends the [`ase.atoms.Atoms`](https://wiki.fysik.dtu.dk/ase/ase/atoms.html) class from the
+[Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) with a large collection of additional
+functions for **building**, **analysing** and **visualising** atomistic structures in materials science. It does
+not introduce a structure class of its own – every function takes an `ase.atoms.Atoms` object as input and,
+where applicable, returns one again, so `structuretoolkit` combines freely with the rest of the ASE ecosystem
+(`ase.build`, ASE calculators, ASE I/O, ...). `structuretoolkit` also powers the structure-analysis backend of
+[`pyiron_atomistics`](https://github.com/pyiron/pyiron_atomistics), where the same functions are available as
+methods directly on the structure object.
+
+## 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()` - find the nearest neighbors of every atom, by count or cutoff radius, periodic-boundary-aware
+* `stk.analyse.get_neighborhood()` - find the nearest neighbors of an arbitrary point in space, e.g. an interstitial site
+* `stk.analyse.get_equivalent_atoms()` - label atoms that map onto each other under the structure's symmetry operations
+* `stk.analyse.get_steinhardt_parameters()` - compute rotationally invariant Steinhardt bond-orientational order parameters
+* `stk.analyse.get_centro_symmetry_descriptors()` - compute the centrosymmetry parameter, large for atoms near a defect
+* `stk.analyse.get_diamond_structure_descriptors()` - identify cubic/hexagonal diamond local environments
+* `stk.analyse.get_adaptive_cna_descriptors()` - classify local crystal structure (fcc/hcp/bcc/icosahedral/other) via common neighbor analysis
+* `stk.analyse.get_voronoi_volumes()` - compute the Voronoi cell volume of every atom
+* `stk.analyse.find_solids()` - count how many atoms are "solid" vs. "liquid"-like, e.g. for melting-point calculations
+* `stk.analyse.get_mean_positions()` - average atomic positions across periodic boundary conditions
+* `stk.analyse.get_average_of_unique_labels()` - average values that share the same (possibly repeated) integer label
+* `stk.analyse.get_interstitials()` - locate interstitial sites of a given coordination number (e.g. tetrahedral, octahedral)
+* `stk.analyse.get_layers()` - group atoms into layers along the cell directions or arbitrary planes
+* `stk.analyse.get_voronoi_vertices()` - compute the Voronoi vertices of the (periodic) structure
+* `stk.analyse.get_voronoi_neighbors()` - find pairs of atoms sharing a Voronoi facet
+* `stk.analyse.get_delaunay_neighbors()` - find pairs of atoms sharing a Delaunay tetrahedron
+* `stk.analyse.get_cluster_positions()` - cluster nearby positions together via DBSCAN
+* `stk.analyse.get_strain()` - compute the per-atom Lagrangian strain tensor relative to a reference structure
+
+### Build
+* `stk.build.get_grainboundary_info()` - list the geometrically possible grain boundaries (by CSL sigma value) for a rotation axis
+* `stk.build.grainboundary()` - build a bicrystal grain-boundary structure for a chosen sigma value and plane
+* `stk.build.high_index_surface()` - build a stepped/kinked high-index surface slab
+* `stk.build.get_high_index_surface_info()` - derive the Miller index for a given terrace/step/kink orientation
+* `stk.build.sqs_structures()` - generate special quasirandom structures (SQS) for disordered alloys
+* `stk.build.B2()` - build a cubic AB B2 (CsCl-type) intermetallic structure
+* `stk.build.C14()` - build a hexagonal AB2 C14 Laves phase structure
+* `stk.build.C15()` - build a cubic AB2 C15 Laves phase structure
+* `stk.build.C36()` - build a hexagonal AB2 C36 Laves phase structure
+* `stk.build.D03()` - build a cubic AB3 D03 structure
+
+### Visualize 
+* `stk.visualize.plot3d()` - render an `Atoms` object in 3d, via NGLView or plotly
+
+### Common 
+* `stk.common.ase_to_pymatgen()` - convert an `ase.atoms.Atoms` object to a `pymatgen.core.Structure`
+* `stk.common.pymatgen_to_ase()` - convert a `pymatgen.core.Structure` back to an `ase.atoms.Atoms` object
+* `stk.common.pymatgen_read_from_file()` - read a structure file directly into an `ase.atoms.Atoms` object via pymatgen
+* `stk.common.ase_to_pyscal()` - convert an `ase.atoms.Atoms` object to a `pyscal3.core.System`
+* `stk.common.apply_strain()` - apply a homogeneous strain to a structure's cell, and its atoms
+* `stk.common.center_coordinates_in_unit_cell()` - wrap atomic coordinates back into the unit cell
+* `stk.common.get_extended_positions()` - repeat atoms across the periodic boundary to include neighbor images
+* `stk.common.get_vertical_length()` - get the height of the cell perpendicular to each face
+* `stk.common.get_wrapped_coordinates()` - wrap arbitrary Cartesian coordinates into the periodic cell
+* `stk.common.select_index()` - get the indices of atoms of a given chemical element
+
+## Documentation 
+
+* [structuretoolkit](https://structuretoolkit.readthedocs.io/en/latest/README.html)
+  * [Example](https://structuretoolkit.readthedocs.io/en/latest/README.html#example)
+  * [Features](https://structuretoolkit.readthedocs.io/en/latest/README.html#features)
+* [Introduction](https://structuretoolkit.readthedocs.io/en/latest/introduction.html)
+  * [How the package is organised](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#how-the-package-is-organised)
+  * [Helpers and converters](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-common-helpers-and-converters)
+  * [Analysing existing structures](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-analyse-analysing-existing-structures)
+  * [Constructing new structures](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-build-constructing-new-structures)
+  * [Looking at structures](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#structuretoolkit-visualize-looking-at-structures)
+  * [Where to go from here](https://structuretoolkit.readthedocs.io/en/latest/introduction.html#where-to-go-from-here)
+* [Interface](https://structuretoolkit.readthedocs.io/en/latest/api.html)

{structuretoolkit-0.0.45 → structuretoolkit-0.0.46}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["ase", "numpy", "scipy", "hatchling==1.30.1", "hatch-vcs==0.5.0"]
+requires = ["ase", "numpy", "scipy", "hatchling==1.32.0", "hatch-vcs==0.5.0"]
 build-backend = "hatchling.build"
 
 [project]
@@ -21,11 +21,12 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
     "ase>=3.24.0,<=3.29.0",
-    "numpy>=1.23.5,<=2.4.6",
-    "scipy>=1.15.0,<=1.17.1",
+    "numpy>=1.23.5,<=2.5.3",
+    "scipy>=1.15.0,<=1.18.0",
 ]
 dynamic = ["version"]
 
@@ -38,25 +39,25 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.2"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen==2026.3.23",
+    "pymatgen>=2026.3.23,<=2026.5.4",
 ]
 pyscal = ["pyscal3>=3.2.5,<=3.3.2"]
 nglview = ["nglview>=2.7.7,<=4.0.1"]
-matplotlib = ["matplotlib==3.10.9"]
-plotly = ["plotly>=6.0.0,<=6.8.0"]
+matplotlib = ["matplotlib==3.11.1"]
+plotly = ["plotly>=6.0.0,<=7.0.0"]
 clusters = ["scikit-learn==1.8.0"]
 symmetry = ["spglib==2.7.0"]
 surface = [
     "spglib==2.7.0",
-    "pymatgen==2026.3.23",
+    "pymatgen>=2026.3.23,<=2026.5.4",
 ]
 phonopy = [
-    "phonopy>=2.21.2,<=4.0.1",
+    "phonopy>=2.21.2,<=4.4.0",
     "spglib==2.7.0",
 ]
 mp-api = [
     "mp-api==0.45.15",
-    "pymatgen==2026.3.23",
+    "pymatgen>=2026.3.23,<=2026.5.4",
 ]
 
 [tool.ruff]
@@ -100,6 +101,8 @@ ignore = [
     "PLC0415",
     # Too many arguments in function definition
     "PLR0913",
+    # Too many not-keyword-only arguments,
+    "PLR0917",
     # Magic value used in comparison
     "PLR2004",
     # Too many branches

{structuretoolkit-0.0.45 → structuretoolkit-0.0.46}/src/structuretoolkit/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.45'
-__version_tuple__ = version_tuple = (0, 0, 45)
+__version__ = version = '0.0.46'
+__version_tuple__ = version_tuple = (0, 0, 46)
 
 __commit_id__ = commit_id = None

structuretoolkit-0.0.45/PKG-INFO

@@ -1,149 +0,0 @@
-Metadata-Version: 2.4
-Name: structuretoolkit
-Version: 0.0.45
-Summary: build, analyse and visualise atomistic structures for materials science
-Project-URL: Homepage, https://github.com/pyiron/structuretoolkit
-Project-URL: Documentation, https://github.com/pyiron/structuretoolkit
-Project-URL: Repository, https://github.com/pyiron/structuretoolkit
-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.
-License-File: LICENSE
-Keywords: pyiron
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: <3.15,>=3.10
-Requires-Dist: ase<=3.29.0,>=3.24.0
-Requires-Dist: numpy<=2.4.6,>=1.23.5
-Requires-Dist: scipy<=1.17.1,>=1.15.0
-Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.8.0; extra == 'clusters'
-Provides-Extra: dscribe
-Requires-Dist: dscribe==2.1.2; extra == 'dscribe'
-Provides-Extra: grainboundary
-Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == 'grainboundary'
-Requires-Dist: pymatgen==2026.3.23; extra == 'grainboundary'
-Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.10.9; extra == 'matplotlib'
-Provides-Extra: mp-api
-Requires-Dist: mp-api==0.45.15; extra == 'mp-api'
-Requires-Dist: pymatgen==2026.3.23; extra == 'mp-api'
-Provides-Extra: nglview
-Requires-Dist: nglview<=4.0.1,>=2.7.7; extra == 'nglview'
-Provides-Extra: phonopy
-Requires-Dist: phonopy<=4.0.1,>=2.21.2; extra == 'phonopy'
-Requires-Dist: spglib==2.7.0; extra == 'phonopy'
-Provides-Extra: plotly
-Requires-Dist: plotly<=6.8.0,>=6.0.0; extra == 'plotly'
-Provides-Extra: pyscal
-Requires-Dist: pyscal3<=3.3.2,>=3.2.5; extra == 'pyscal'
-Provides-Extra: surface
-Requires-Dist: pymatgen==2026.3.23; extra == 'surface'
-Requires-Dist: spglib==2.7.0; extra == 'surface'
-Provides-Extra: symmetry
-Requires-Dist: spglib==2.7.0; extra == 'symmetry'
-Description-Content-Type: text/markdown
-
-# structuretoolkit 
-
-[![Pipeline](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml)
-[![codecov](https://codecov.io/gh/pyiron/structuretoolkit/graph/badge.svg?token=B6I4OACKND)](https://codecov.io/gh/pyiron/structuretoolkit)
-
-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.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-0.0.45/README.md

@@ -1,70 +0,0 @@
-# structuretoolkit 
-
-[![Pipeline](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml)
-[![codecov](https://codecov.io/gh/pyiron/structuretoolkit/graph/badge.svg?token=B6I4OACKND)](https://codecov.io/gh/pyiron/structuretoolkit)
-
-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.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()`