SMACT 3.0__tar.gz → 3.1.0__tar.gz

{smact-3.0/SMACT.egg-info → smact-3.1.0}/PKG-INFO

@@ -1,13 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: SMACT
-Version: 3.0
+Version: 3.1.0
 Summary: Semiconducting Materials by Analogy and Chemical Theory
-Home-page: https://github.com/WMD-group/SMACT
-Author: The SMACT Developers
 Author-email: The SMACT Developers <a.walsh@imperial.ac.uk>
-Maintainer: Anthony O. Onwuli
 Maintainer-email: "Anthony O. Onwuli" <anthony.onwuli16@imperial.ac.uk>
-License: MIT
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/WMD-group/SMACT
 Project-URL: Documentation, https://smact.readthedocs.io/en/latest/
 Project-URL: Repository, https://github.com/WMD-group/SMACT
@@ -16,24 +13,25 @@ Project-URL: Pypi, https://pypi.org/project/SMACT/
 Keywords: python,machine-learning,computational-chemistry,materials-science,materials-informatics,materials-screening,materials-design,materials
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: <3.14,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase
 Requires-Dist: numpy<3
+Requires-Dist: pandarallel[optional]>=1.6.5
 Requires-Dist: pandas
 Requires-Dist: pathos
 Requires-Dist: pymatgen>=2024.2.20
 Requires-Dist: scipy
-Requires-Dist: spglib
+Requires-Dist: spglib>=2.6.0
 Requires-Dist: typing-extensions
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
@@ -50,46 +48,52 @@ Requires-Dist: readthedocs-sphinx-search==0.3.2; extra == "docs"
 Requires-Dist: sphinx-book-theme==1.1.3; extra == "docs"
 Requires-Dist: myst-nb==1.1.2; extra == "docs"
 Provides-Extra: mp
-Requires-Dist: mp-api; extra == "mp"
+Requires-Dist: mp-api>=0.45.3; extra == "mp"
 Provides-Extra: crystal-space
-Requires-Dist: mp-api; extra == "crystal-space"
-Requires-Dist: ElementEmbeddings; extra == "crystal-space"
-Requires-Dist: umap-learn==0.5.3; extra == "crystal-space"
-Requires-Dist: kaleido; extra == "crystal-space"
-Requires-Dist: pydantic<2.10.0; extra == "crystal-space"
+Requires-Dist: smact[mp]; extra == "crystal-space"
+Requires-Dist: ElementEmbeddings>=0.4; extra == "crystal-space"
+Requires-Dist: umap-learn==0.5.7; extra == "crystal-space"
+Requires-Dist: kaleido>=0.2.1; extra == "crystal-space"
 Provides-Extra: featurisers
 Requires-Dist: matminer; extra == "featurisers"
 Requires-Dist: ElementEmbeddings; extra == "featurisers"
 Provides-Extra: visualisation
-Requires-Dist: seaborn; extra == "visualisation"
-Requires-Dist: pymatviz; extra == "visualisation"
-Requires-Dist: dash; extra == "visualisation"
+Requires-Dist: seaborn>=0.13.2; extra == "visualisation"
+Requires-Dist: pymatviz>=0.15; extra == "visualisation"
+Requires-Dist: dash>=2.18.2; extra == "visualisation"
+Provides-Extra: ml
+Requires-Dist: xgboost; extra == "ml"
+Requires-Dist: shap; extra == "ml"
+Requires-Dist: smact[featurisers]; extra == "ml"
 Provides-Extra: optional
 Requires-Dist: pydantic>=2.9.2; extra == "optional"
-Requires-Dist: mp-api>=0.42.2; extra == "optional"
-Requires-Dist: pymatviz>=0.14; extra == "optional"
-Requires-Dist: seaborn>=0.13.2; extra == "optional"
+Requires-Dist: smact[mp]; extra == "optional"
+Requires-Dist: smact[visualisation]; extra == "optional"
 Requires-Dist: pymatgen>=2024.2.20; extra == "optional"
 Requires-Dist: matminer>=0.9.2; extra == "optional"
-Requires-Dist: umap-learn>=0.5.3; extra == "optional"
 Requires-Dist: kaleido>=0.2.1; extra == "optional"
 Requires-Dist: ase>=3.22.0; extra == "optional"
-Requires-Dist: numpy; extra == "optional"
+Requires-Dist: llvmlite>=0.40; extra == "optional"
 Requires-Dist: ElementEmbeddings>=0.4; extra == "optional"
 Requires-Dist: dash>=2.18.2; extra == "optional"
+Requires-Dist: smact[ml]; extra == "optional"
+Requires-Dist: pandarallel>=1.6.5; extra == "optional"
+Requires-Dist: matplotlib-venn[shapely]>=1.1.2; extra == "optional"
 Provides-Extra: strict
 Requires-Dist: pydantic==2.9.2; extra == "strict"
-Requires-Dist: mp-api==0.42.2; extra == "strict"
-Requires-Dist: pymatviz==0.14; extra == "strict"
+Requires-Dist: mp-api==0.45.3; extra == "strict"
+Requires-Dist: pymatviz==0.15.1; extra == "strict"
+Requires-Dist: mp-api==0.45.3; extra == "strict"
 Requires-Dist: seaborn==0.13.2; extra == "strict"
-Requires-Dist: pymatgen==2024.11.13; extra == "strict"
-Requires-Dist: matminer==0.9.2; extra == "strict"
-Requires-Dist: umap-learn==0.5.3; extra == "strict"
+Requires-Dist: pymatgen==2025.3.10; extra == "strict"
+Requires-Dist: matminer==0.9.3; extra == "strict"
+Requires-Dist: umap-learn==0.5.7; extra == "strict"
 Requires-Dist: kaleido==0.2.1; extra == "strict"
-Requires-Dist: ase==3.23.0; extra == "strict"
+Requires-Dist: ase==3.24.0; extra == "strict"
 Requires-Dist: numpy; extra == "strict"
 Requires-Dist: ElementEmbeddings==0.6.1; extra == "strict"
-Requires-Dist: dash==2.18.2; extra == "strict"
+Requires-Dist: dash==3.0.2; extra == "strict"
+Dynamic: license-file
 
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.01361/status.svg)](https://doi.org/10.21105/joss.01361)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5553202.svg)](https://doi.org/10.5281/zenodo.5553202)
@@ -174,7 +178,7 @@ Use cases are available in our [examples](https://smact.readthedocs.io/en/latest
 
 ## Requirements
 
-The main language is Python 3 and has been tested using Python 3.10+.
+The main language is Python 3 and has been tested using Python 3.10 - 3.13 (Windows is not officially supported for Python 3.13 as of yet).
 Basic requirements are Numpy and Scipy.
 The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE), [spglib](http://atztogo.github.io/spglib), and [pymatgen](https://pymatgen.org) are also required for many components.
 

{smact-3.0 → smact-3.1.0}/README.md

@@ -81,7 +81,7 @@ Use cases are available in our [examples](https://smact.readthedocs.io/en/latest
 
 ## Requirements
 
-The main language is Python 3 and has been tested using Python 3.10+.
+The main language is Python 3 and has been tested using Python 3.10 - 3.13 (Windows is not officially supported for Python 3.13 as of yet).
 Basic requirements are Numpy and Scipy.
 The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE), [spglib](http://atztogo.github.io/spglib), and [pymatgen](https://pymatgen.org) are also required for many components.
 

{smact-3.0 → smact-3.1.0/SMACT.egg-info}/PKG-INFO

@@ -1,13 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: SMACT
-Version: 3.0
+Version: 3.1.0
 Summary: Semiconducting Materials by Analogy and Chemical Theory
-Home-page: https://github.com/WMD-group/SMACT
-Author: The SMACT Developers
 Author-email: The SMACT Developers <a.walsh@imperial.ac.uk>
-Maintainer: Anthony O. Onwuli
 Maintainer-email: "Anthony O. Onwuli" <anthony.onwuli16@imperial.ac.uk>
-License: MIT
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/WMD-group/SMACT
 Project-URL: Documentation, https://smact.readthedocs.io/en/latest/
 Project-URL: Repository, https://github.com/WMD-group/SMACT
@@ -16,24 +13,25 @@ Project-URL: Pypi, https://pypi.org/project/SMACT/
 Keywords: python,machine-learning,computational-chemistry,materials-science,materials-informatics,materials-screening,materials-design,materials
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: <3.14,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase
 Requires-Dist: numpy<3
+Requires-Dist: pandarallel[optional]>=1.6.5
 Requires-Dist: pandas
 Requires-Dist: pathos
 Requires-Dist: pymatgen>=2024.2.20
 Requires-Dist: scipy
-Requires-Dist: spglib
+Requires-Dist: spglib>=2.6.0
 Requires-Dist: typing-extensions
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
@@ -50,46 +48,52 @@ Requires-Dist: readthedocs-sphinx-search==0.3.2; extra == "docs"
 Requires-Dist: sphinx-book-theme==1.1.3; extra == "docs"
 Requires-Dist: myst-nb==1.1.2; extra == "docs"
 Provides-Extra: mp
-Requires-Dist: mp-api; extra == "mp"
+Requires-Dist: mp-api>=0.45.3; extra == "mp"
 Provides-Extra: crystal-space
-Requires-Dist: mp-api; extra == "crystal-space"
-Requires-Dist: ElementEmbeddings; extra == "crystal-space"
-Requires-Dist: umap-learn==0.5.3; extra == "crystal-space"
-Requires-Dist: kaleido; extra == "crystal-space"
-Requires-Dist: pydantic<2.10.0; extra == "crystal-space"
+Requires-Dist: smact[mp]; extra == "crystal-space"
+Requires-Dist: ElementEmbeddings>=0.4; extra == "crystal-space"
+Requires-Dist: umap-learn==0.5.7; extra == "crystal-space"
+Requires-Dist: kaleido>=0.2.1; extra == "crystal-space"
 Provides-Extra: featurisers
 Requires-Dist: matminer; extra == "featurisers"
 Requires-Dist: ElementEmbeddings; extra == "featurisers"
 Provides-Extra: visualisation
-Requires-Dist: seaborn; extra == "visualisation"
-Requires-Dist: pymatviz; extra == "visualisation"
-Requires-Dist: dash; extra == "visualisation"
+Requires-Dist: seaborn>=0.13.2; extra == "visualisation"
+Requires-Dist: pymatviz>=0.15; extra == "visualisation"
+Requires-Dist: dash>=2.18.2; extra == "visualisation"
+Provides-Extra: ml
+Requires-Dist: xgboost; extra == "ml"
+Requires-Dist: shap; extra == "ml"
+Requires-Dist: smact[featurisers]; extra == "ml"
 Provides-Extra: optional
 Requires-Dist: pydantic>=2.9.2; extra == "optional"
-Requires-Dist: mp-api>=0.42.2; extra == "optional"
-Requires-Dist: pymatviz>=0.14; extra == "optional"
-Requires-Dist: seaborn>=0.13.2; extra == "optional"
+Requires-Dist: smact[mp]; extra == "optional"
+Requires-Dist: smact[visualisation]; extra == "optional"
 Requires-Dist: pymatgen>=2024.2.20; extra == "optional"
 Requires-Dist: matminer>=0.9.2; extra == "optional"
-Requires-Dist: umap-learn>=0.5.3; extra == "optional"
 Requires-Dist: kaleido>=0.2.1; extra == "optional"
 Requires-Dist: ase>=3.22.0; extra == "optional"
-Requires-Dist: numpy; extra == "optional"
+Requires-Dist: llvmlite>=0.40; extra == "optional"
 Requires-Dist: ElementEmbeddings>=0.4; extra == "optional"
 Requires-Dist: dash>=2.18.2; extra == "optional"
+Requires-Dist: smact[ml]; extra == "optional"
+Requires-Dist: pandarallel>=1.6.5; extra == "optional"
+Requires-Dist: matplotlib-venn[shapely]>=1.1.2; extra == "optional"
 Provides-Extra: strict
 Requires-Dist: pydantic==2.9.2; extra == "strict"
-Requires-Dist: mp-api==0.42.2; extra == "strict"
-Requires-Dist: pymatviz==0.14; extra == "strict"
+Requires-Dist: mp-api==0.45.3; extra == "strict"
+Requires-Dist: pymatviz==0.15.1; extra == "strict"
+Requires-Dist: mp-api==0.45.3; extra == "strict"
 Requires-Dist: seaborn==0.13.2; extra == "strict"
-Requires-Dist: pymatgen==2024.11.13; extra == "strict"
-Requires-Dist: matminer==0.9.2; extra == "strict"
-Requires-Dist: umap-learn==0.5.3; extra == "strict"
+Requires-Dist: pymatgen==2025.3.10; extra == "strict"
+Requires-Dist: matminer==0.9.3; extra == "strict"
+Requires-Dist: umap-learn==0.5.7; extra == "strict"
 Requires-Dist: kaleido==0.2.1; extra == "strict"
-Requires-Dist: ase==3.23.0; extra == "strict"
+Requires-Dist: ase==3.24.0; extra == "strict"
 Requires-Dist: numpy; extra == "strict"
 Requires-Dist: ElementEmbeddings==0.6.1; extra == "strict"
-Requires-Dist: dash==2.18.2; extra == "strict"
+Requires-Dist: dash==3.0.2; extra == "strict"
+Dynamic: license-file
 
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.01361/status.svg)](https://doi.org/10.21105/joss.01361)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5553202.svg)](https://doi.org/10.5281/zenodo.5553202)
@@ -174,7 +178,7 @@ Use cases are available in our [examples](https://smact.readthedocs.io/en/latest
 
 ## Requirements
 
-The main language is Python 3 and has been tested using Python 3.10+.
+The main language is Python 3 and has been tested using Python 3.10 - 3.13 (Windows is not officially supported for Python 3.13 as of yet).
 Basic requirements are Numpy and Scipy.
 The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE), [spglib](http://atztogo.github.io/spglib), and [pymatgen](https://pymatgen.org) are also required for many components.
 

{smact-3.0 → smact-3.1.0}/SMACT.egg-info/SOURCES.txt

@@ -2,11 +2,9 @@ LICENSE
 MANIFEST.in
 README.md
 pyproject.toml
-setup.py
 SMACT.egg-info/PKG-INFO
 SMACT.egg-info/SOURCES.txt
 SMACT.egg-info/dependency_links.txt
-SMACT.egg-info/not-zip-safe
 SMACT.egg-info/requires.txt
 SMACT.egg-info/top_level.txt
 smact/__init__.py
@@ -16,9 +14,14 @@ smact/distorter.py
 smact/lattice.py
 smact/lattice_parameters.py
 smact/mainpage.py
+smact/metallicity.py
 smact/oxidation_states.py
 smact/properties.py
 smact/screening.py
+smact/benchmarking/__init__.py
+smact/benchmarking/pymatgen_benchmark.py
+smact/benchmarking/smact_benchmark.py
+smact/benchmarking/utilities.py
 smact/data/Covalent_radii.csv
 smact/data/SSE.csv
 smact/data/SSE_2015.csv
@@ -43,6 +46,8 @@ smact/data/shannon_radii.csv
 smact/data/shannon_radii_ML_extended.csv
 smact/data/solid_properties.txt
 smact/data/solid_properties.xlsx
+smact/data/species_rep/ion_embedding_M3GNet-MP-2023.11.1-oxi-Eform_cosine_similarity.json
+smact/data/species_rep/ion_embedding_M3GNet-MP-2023.11.1-oxi-band_gap_cosine_similarity.json
 smact/data/species_rep/skipspecies_20221028_319ion_dim200_cosine_similarity.json
 smact/dopant_prediction/__init__.py
 smact/dopant_prediction/doper.py
@@ -56,9 +61,14 @@ smact/structure_prediction/utilities.py
 smact/tests/__init__.py
 smact/tests/test_core.py
 smact/tests/test_doper.py
+smact/tests/test_metallicity.py
 smact/tests/test_structure.py
 smact/tests/test_utils.py
 smact/utils/__init__.py
 smact/utils/band_gap_simple.py
 smact/utils/composition.py
-smact/utils/oxidation.py
+smact/utils/oxidation.py
+smact/utils/crystal_space/__init__.py
+smact/utils/crystal_space/download_compounds_with_mp_api.py
+smact/utils/crystal_space/generate_composition_with_smact.py
+smact/utils/crystal_space/plot_embedding.py

{smact-3.0 → smact-3.1.0}/SMACT.egg-info/requires.txt

@@ -1,18 +1,18 @@
 ase
 numpy<3
+pandarallel[optional]>=1.6.5
 pandas
 pathos
 pymatgen>=2024.2.20
 scipy
-spglib
+spglib>=2.6.0
 typing-extensions
 
 [crystal_space]
-mp-api
-ElementEmbeddings
-umap-learn==0.5.3
-kaleido
-pydantic<2.10.0
+smact[mp]
+ElementEmbeddings>=0.4
+umap-learn==0.5.7
+kaleido>=0.2.1
 
 [dev]
 pytest
@@ -34,38 +34,44 @@ myst-nb==1.1.2
 matminer
 ElementEmbeddings
 
+[ml]
+xgboost
+shap
+smact[featurisers]
+
 [mp]
-mp-api
+mp-api>=0.45.3
 
 [optional]
 pydantic>=2.9.2
-mp-api>=0.42.2
-pymatviz>=0.14
-seaborn>=0.13.2
+smact[mp]
+smact[visualisation]
 pymatgen>=2024.2.20
 matminer>=0.9.2
-umap-learn>=0.5.3
 kaleido>=0.2.1
 ase>=3.22.0
-numpy
+llvmlite>=0.40
 ElementEmbeddings>=0.4
 dash>=2.18.2
+smact[ml]
+pandarallel>=1.6.5
+matplotlib-venn[shapely]>=1.1.2
 
 [strict]
 pydantic==2.9.2
-mp-api==0.42.2
-pymatviz==0.14
+mp-api==0.45.3
+pymatviz==0.15.1
 seaborn==0.13.2
-pymatgen==2024.11.13
-matminer==0.9.2
-umap-learn==0.5.3
+pymatgen==2025.3.10
+matminer==0.9.3
+umap-learn==0.5.7
 kaleido==0.2.1
-ase==3.23.0
+ase==3.24.0
 numpy
 ElementEmbeddings==0.6.1
-dash==2.18.2
+dash==3.0.2
 
 [visualisation]
-seaborn
-pymatviz
-dash
+seaborn>=0.13.2
+pymatviz>=0.15
+dash>=2.18.2

{smact-3.0 → smact-3.1.0}/pyproject.toml

@@ -1,11 +1,12 @@
 [build-system]
 # Minimum requirements for the build system to execute.
-requires = ["setuptools>=65.0.0"]  # PEP 508 specifications.
+requires = ["setuptools>=77.0.0",
+"oldest-supported-numpy"]  # PEP 508 specifications.
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "SMACT"
-version = "3.0"
+version = "3.1.0"
 description = "Semiconducting Materials by Analogy and Chemical Theory"
 readme = "README.md"
 authors = [
@@ -17,16 +18,16 @@ maintainers = [
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Chemistry",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 keywords = [
     "python",
     "machine-learning",
@@ -40,14 +41,16 @@ keywords = [
 dependencies = [
     "ase",
     "numpy<3",
+    "pandarallel[optional]>=1.6.5",
     "pandas",
     "pathos",
     "pymatgen>=2024.2.20",
     "scipy",
-    "spglib",
+    "spglib>=2.6.0",
     "typing-extensions",
 ]
-license = {text = "MIT"}
+license = "MIT"
+license-files = ["LICENSE"]
 
 [project.urls]
 Homepage = "https://github.com/WMD-group/SMACT"
@@ -73,58 +76,65 @@ docs = [
     "sphinx-book-theme==1.1.3",
     "myst-nb==1.1.2"
 ]
-mp = ["mp-api"]
-
-crystal_space = ["mp-api",
-"ElementEmbeddings",
-"umap-learn==0.5.3",
-"kaleido",
-"pydantic<2.10.0"]
-
+mp = ["mp-api>=0.45.3"]
+crystal_space = ["smact[mp]",
+"ElementEmbeddings>=0.4",
+"umap-learn==0.5.7",
+"kaleido>=0.2.1",]
 featurisers = [
     "matminer",
     "ElementEmbeddings",
 ]
-
 visualisation = [
-    "seaborn",
-    "pymatviz",
-    "dash",
+    "seaborn>=0.13.2",
+    "pymatviz>=0.15",
+    "dash>=2.18.2",
 ]
-
+ml = ["xgboost","shap","smact[featurisers]"]
 optional = [
     "pydantic>=2.9.2",
-    "mp-api>=0.42.2",
-    "pymatviz>=0.14",
-    "seaborn>=0.13.2",
+    "smact[mp]",
+    "smact[visualisation]",
     "pymatgen>=2024.2.20",
     "matminer>=0.9.2",
-    "umap-learn>=0.5.3",
     "kaleido>=0.2.1",
     "ase>=3.22.0",
-    "numpy",
+    "llvmlite>=0.40",
     "ElementEmbeddings>=0.4",
     "dash>=2.18.2",
-
+    "smact[ml]",
+    "pandarallel>=1.6.5",
+    "matplotlib-venn[shapely]>=1.1.2",
 ]
 strict = [
     "pydantic==2.9.2",
-    "mp-api==0.42.2",
-    "pymatviz==0.14",
+    "mp-api==0.45.3",
+    "pymatviz==0.15.1",
+    "mp-api==0.45.3",
     "seaborn==0.13.2",
-    "pymatgen==2024.11.13",
-    "matminer==0.9.2",
-    "umap-learn==0.5.3",
+    "pymatgen==2025.3.10",
+    "matminer==0.9.3",
+    "umap-learn==0.5.7",
     "kaleido==0.2.1",
-    "ase==3.23.0",
+    "ase==3.24.0",
     "numpy",
     "ElementEmbeddings==0.6.1",
-    "dash==2.18.2",
+    "dash==3.0.2",
 ]
 
-[tool.semantic_release]
-version_variable = "setup.py:__version__"
-version_source = "tag"
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["smact","smact.*"]
+
+[tool.setuptools.package-data]
+"smact" = ["data/*.txt", "data/*.csv", "data/*.data", "data/*.xlsx", "data/*.json", "data/species_rep/*.json"]
+
+[tool.pytest.ini_options]
+minversion = 6.0
+testpaths = ["smact/tests"]
 
 [tool.ruff]
 target-version = "py310"
@@ -214,7 +224,7 @@ reportPossiblyUnboundVariable = true
 reportUnboundVariable = true
 
 [tool.codespell]
-skip = "*.csv,*/site/*,*/docs/_build/*,paper.md,*dev_docs/*,paper.bib,*.txt,*examples/Structure_Prediction/Li-Garnets_SP-Pym-new.ipynb"
+skip = "*.csv,*/site/*,*/docs/_build/*,docs/tutorials/data/*,paper.md,*dev_docs/*,paper.bib,*.txt,*examples/Structure_Prediction/Li-Garnets_SP-Pym-new.ipynb"
 check-filenames = true
 ignore-regex = "[A-Za-z0-9+/]{100,}"
 
@@ -320,3 +330,37 @@ ignore-words-list = [
             "assertIn",
             "Mater",
         ]
+[tool.coverage.report]
+exclude_also = [
+    'def __repr__',
+    'if self.debug:',
+    'if settings.DEBUG',
+    'raise AssertionError',
+    'raise NotImplementedError',
+    'if 0:',
+    'if __name__ == .__main__.:',
+    'if TYPE_CHECKING:',
+    'class .*\bProtocol\):',
+    '@(abc\.)?abstractmethod',
+    ]
+
+[dependency-groups]
+dev = [
+    "jupyter>=1.1.1",
+    "jupyter-client>=8.6.3",
+    "notebook>=7.3.3",
+    "blacken-docs>=1.19.1",
+    "codespell>=2.4.1",
+    "ipykernel>=6.29.5",
+    "myst-nb==1.1.2",
+    "nbstripout>=0.8.1",
+    "pre-commit>=4.2.0",
+    "pyright>=1.1.398",
+    "pytest>=8.3.5",
+    "pytest-cov>=6.1.0",
+    "readthedocs-sphinx-search==0.3.2",
+    "ruff>=0.11.2",
+    "sphinx==8.1.3",
+    "sphinx-book-theme==1.1.3",
+    "sphinx-rtd-theme==3.0.2",
+]

smact-3.1.0/smact/benchmarking/__init__.py

@@ -0,0 +1 @@
+"""SMACT benchmarking."""

smact-3.1.0/smact/benchmarking/pymatgen_benchmark.py

@@ -0,0 +1,40 @@
+"""Benchmarking functions for pymatgen."""
+
+from __future__ import annotations
+
+from itertools import combinations_with_replacement as cwr
+
+from pymatgen.analysis.structure_prediction.substitution_probability import (
+    SubstitutionProbability,
+)
+
+from .utilities import timeit
+
+
+class ProbabilityBenchmarker:
+    """Benchmarking tests for pymatgen SubstitutionProbability."""
+
+    @timeit
+    def run_tests(self):
+        """Run all tests."""
+        self.__sp_setup()
+        self.__pair_corr()
+
+    @timeit
+    def __sp_setup(self):
+        """Set up SubstitutionProbability."""
+        self.sp = SubstitutionProbability()
+
+    @timeit
+    def __pair_corr(self):
+        """Get pair correlation."""
+        pairs = cwr(self.sp.species, 2)
+
+        for s1, s2 in pairs:
+            self.sp.pair_corr(s1, s2)
+
+
+@timeit(delim=True, n=100)
+def probability_test_run():
+    """Run all tests."""
+    ProbabilityBenchmarker().run_tests()

smact-3.1.0/smact/benchmarking/smact_benchmark.py

@@ -0,0 +1,33 @@
+"""SMACT benchmarking."""
+
+from __future__ import annotations
+
+from smact.structure_prediction.mutation import CationMutator
+
+from .utilities import timeit
+
+
+class MutatorBenchmarker:
+    """Benchmarking tests for CationMutator."""
+
+    @timeit
+    def run_tests(self):
+        """Initialize Mutator and perform tests."""
+        self.__cm_setup()
+        self.__pair_corr()
+
+    @timeit
+    def __cm_setup(self) -> CationMutator:
+        """Create a CationMutator."""
+        self.cm = CationMutator.from_json()
+
+    @timeit
+    def __pair_corr(self):
+        """Get pair correlations."""
+        self.cm.complete_pair_corrs()
+
+
+@timeit(delim=True, n=100)
+def mutator_test_run():
+    """Run benchmark tests for CationMutator."""
+    MutatorBenchmarker().run_tests()