PyPI - SMACT - Versions diffs - 2.5.4__tar.gz → 2.6__tar.gz - Mend

SMACT 2.5.4tar.gz → 2.6tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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{SMACT-2.5.4/SMACT.egg-info → smact-2.6}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SMACT
-Version: 2.5.4
+Version: 2.6
 Summary: Semiconducting Materials by Analogy and Chemical Theory
 Home-page: https://github.com/WMD-group/SMACT
 Author: Daniel W. Davies
@@ -9,26 +9,27 @@ Maintainer: Anthony O. Onwuli
 Maintainer-email: anthony.onwuli16@imperial.ac.uk
 License: MIT
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: scipy
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: spglib
-Requires-Dist: pymatgen
+Requires-Dist: pymatgen>=2024.2.20
 Requires-Dist: ase
 Requires-Dist: pandas
 Requires-Dist: pathos
+Requires-Dist: typing-extensions
 [![DOI](http://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)
@@ -47,10 +48,10 @@ Requires-Dist: pathos
 SMACT
 =====
-**Semiconducting Materials from Analogy and Chemical Theory** (SMACT) is a collection of rapid screening tools that uses data about chemical elements.
+**Semiconducting Materials from Analogy and Chemical Theory** (SMACT) is a collection of rapid screening and informatics tools that uses data about chemical elements.
 - **Documentation:** https://smact.readthedocs.io/en/latest/
-- **Examples folder:** https://github.com/WMD-group/SMACT/tree/master/examples
+- **Examples:** https://github.com/WMD-group/SMACT/tree/master/examples
 ![](SMACT.png)
@@ -58,18 +59,13 @@ SMACT
 Statement of need
 --------
-There is a strong demand for functional materials across a wide range of technologies. The motivation can include cost reduction, performance enhancement, or to enable a new application. Data collections such as the [Materials Project](https://www.materialsproject.org), [NREL Materials Database](http://materials.nrel.gov) and the [Open Quantum Materials Database](http://oqmd.org) are valuable resources, but they largely cover the properties of *known* compounds as calculated using high-level quantum mechanical theories.
-We have developed low-cost procedures for screening hypothetical materials in SMACT. This framework can be used for simple calculations on your own computer. SMACT follows a top-down approach where a set of element combinations is generated and then screened using rapid chemical filters. It can be used as part of a multi-technique workflow or to feed machine learning models for materials.
+There is a strong demand for functional materials across a wide range of technologies. The motivation can include cost reduction, performance enhancement, or to enable a new application. We have developed low-cost procedures for screening hypothetical materials. This framework can be used for simple calculations on your own computer. SMACT follows a top-down approach where a set of element combinations is generated and then screened using rapid chemical filters. It can be used as part of a multi-technique workflow or to feed machine learning models for materials.
 ![](smact_simple.gif)
 Getting started
 -----
-SMACT's features are accessed through Python scripts, importing classes and functions as needed.
+Features are accessed through Python scripts, importing classes and functions as needed.
 The best place to start is looking at [the docs](https://smact.readthedocs.io/en/latest/), which highlight some simple examples of how these classes and functions can be used.
 Extended examples are available in [our examples folder](https://github.com/WMD-group/SMACT/tree/master/examples).
@@ -77,9 +73,9 @@ Code features
 --------
 - At the core of SMACT are [Element](https://smact.readthedocs.io/en/latest/smact.html#smact.Element) and [Species](https://smact.readthedocs.io/en/latest/smact.html#smact.Species) (element in a given oxidation state) classes that have various properties associated with them.
-- The various oxidation states that are accessible to each element are included in their properties.
+- Oxidation states that are accessible to each element are included in their properties.
-- Element compositions can be screened through based on the heuristic filters of charge neutrality and electronegativity order. This is handled using the [screening module](https://smact.readthedocs.io/en/latest/smact.screening.html) and [this publication](https://www.cell.com/chem/fulltext/S2451-9294(16)30155-3) describes the underlying theory. An example procedure is [outlined in the docs](https://smact.readthedocs.io/en/latest/examples.html#neutral-combinations) and further examples can be found in the [counting examples subfolder](https://github.com/WMD-group/SMACT/tree/master/examples/Counting).
+- Element compositions can be screened through based on the heuristic filters of charge neutrality and electronegativity order. This is handled using the [screening module](https://smact.readthedocs.io/en/latest/smact.screening.html) and [this publication](https://www.cell.com/chem/fulltext/S2451-9294(16)30155-3) describes the underlying theory. An example procedure is [outlined in the docs](https://smact.readthedocs.io/en/latest/examples.html#neutral-combinations) and more examples can be found in the [counting examples subfolder](https://github.com/WMD-group/SMACT/tree/master/examples/Counting).
 - Further filters can be applied to generated lists of compositions in order to screen for particular properties. These properties are either intrinsic properties of elements or are calculated for compositions using the [properties module](https://smact.readthedocs.io/en/latest/smact.properties.html). For example:
   - A use case is shown in [this publication](https://pubs.rsc.org/en/content/articlehtml/2018/sc/c7sc03961a), in which 160,000 chemical compositions are screened based on optical band gap calculated using the [solid-state energy scale](https://www.sciencedirect.com/science/article/pii/S0022459615300888).
@@ -87,18 +83,17 @@ Code features
 - Compositions can also be filtered based on sustainability via the abundance of elements in the Earth's crust or via the [HHI scale](https://pubs.acs.org/doi/10.1021/cm400893e).
-- Compositions can easily be converted for use in Pymatgen or for representation to machine learning algorithms ([see "next steps" in this example](https://github.com/WMD-group/SMACT/blob/master/examples/Counting/Generate_compositions_lists.ipynb)).
+- Compositions can be converted for use in Pymatgen or for representation to machine learning algorithms ([see "next steps" in this example](https://github.com/WMD-group/SMACT/blob/master/examples/Counting/Generate_compositions_lists.ipynb)) and the related [ElementEmbeddings](https://github.com/WMD-group/ElementEmbeddings) package.
-- The code also has some tools for manipulating common crystal lattice types:
- - Common crystal structure types can be built using the [builder module](https://smact.readthedocs.io/en/latest/smact.builder.html)
- - Lattice parameters can be quickly estimated using ionic radii of the elements for various common crystal structure types using the [lattice_parameters module](https://smact.readthedocs.io/en/latest/smact.lattice_parameters.html).
- - The [lattice module](https://smact.readthedocs.io/en/latest/smact.lattice.html) and [distorter module](https://smact.readthedocs.io/en/latest/smact.distorter.html) rely on the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) and can be used to generate unique atomic substitutions on a given crystal structure.
- - The [structure  prediction](https://smact.readthedocs.io/en/latest/smact.structure_prediction.html) module can be used to predict the structure of hypothetical compositions using species similarity measures.
- - The [dopant prediction](https://smact.readthedocs.io/en/latest/smact.dopant_prediction.html) module can be used to facilitate high-throughput predictions of p-type and n-type dopants of multicomponent solids.
+- The code also has tools for manipulating common crystal lattice types:
+  - Certain structure types can be built using the [builder module](https://smact.readthedocs.io/en/latest/smact.builder.html)
+  - Lattice parameters can be estimated using ionic radii of the elements for various common crystal structure types using the [lattice_parameters module](https://smact.readthedocs.io/en/latest/smact.lattice_parameters.html).
+  - The [lattice module](https://smact.readthedocs.io/en/latest/smact.lattice.html) and [distorter module](https://smact.readthedocs.io/en/latest/smact.distorter.html) rely on the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) and can be used to generate unique atomic substitutions on a given crystal structure.
+  - The [structure  prediction](https://smact.readthedocs.io/en/latest/smact.structure_prediction.html) module can be used to predict the structure of hypothetical compositions using species similarity measures.
+  - The [dopant prediction](https://smact.readthedocs.io/en/latest/smact.dopant_prediction.html) module can be used to facilitate high-throughput predictions of p-type and n-type dopants of multicomponent solids.
 List of modules
 -------
 * **smact** library containing:
   * **\_\_init\_\_.py** Contains the core `Element` and `Species` classes.
   *  **data_loader.py** Handles the loading of external data used to initialise the core `smact.Element` and `smact.Species` classes.
@@ -106,7 +101,7 @@ List of modules
   *  **properties.py** A collection of tools for estimating useful properties based on composition.
   * **lattice.py** Given the sites, multiplicities and possible oxidation states
     at those sites, this reads from the database and generates all possible
-    stoichiometeries.
+    stoichiometries.
   * **builder.py** Builds some common lattice structures, given the chemical
     composition.
   * **lattice_parameters.py** Estimation of lattice parameters for various lattice types using covalent/ionic radii.
@@ -114,18 +109,17 @@ List of modules
     substituting on inequivalent sites of a sub-lattice.
   * **oxidation_states.py**: Used for predicting the likelihood of species coexisting in a compound based on a statistical model.
   * **structure_prediction**: A submodule which contains a collection of tools for facilitating crystal structure predictions via ionic substitutions
-  * **dopant_prediction**: A submodule which contains a collections of tools for predicting n-type and p-type dopants.
+  * **dopant_prediction**: A submodule which contains a collections of tools for predicting dopants.
 Requirements
 ------------
-The main language is Python 3 and has been tested using Python 3.8+.
+The main language is Python 3 and has been tested using Python 3.9+.
 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](www.pymatgen.org) are also required for many components.
+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.
 Installation
 ------------
-The latest stable release of SMACT can be installed via pip which will automatically setup other Python packages as required:
+The latest stable release can be installed via pip which will automatically set up other Python packages as required:
     pip install smact
@@ -137,12 +131,12 @@ conda install -c conda-forge smact
 Alternatively, the very latest version can be installed using:
-    pip install git+git://github.com/WMD-group/SMACT.git
+    pip install git+https://github.com/WMD-group/SMACT.git
 For developer installation SMACT can be installed from a copy of the source
 repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches.
-To clone the project from Github and make a local installation:
+To clone the project from GitHub and make a local installation:
     git clone https://github.com/wmd-group/smact.git
     cd smact
@@ -164,10 +158,9 @@ Development notes
 Please use the [Issue Tracker](https://github.com/WMD-group/smact/issues) to report bugs or request features in the first instance. While we hope that most questions can be answered by searching [the docs](https://smact.readthedocs.io/en/latest/), we welcome new questions on the issue tracker, especially if they helps us improve the docs! For other queries about any aspect of the code, please contact either Dan Davies (author) or Anthony Onwuli (maintainer) by e-mail: d.w.davies@imperial.ac.uk or anthony.onwuli16@imperial.ac.uk respectively.
 ### Code contributions
-We are always looking for ways to make SMACT better and more useful to the wider community; contributions are very welcome. Please use the ["Fork and Pull"](https://guides.github.com/activities/forking/) workflow to make contributions and stick as closely as possible to the following:
+We are always looking for ways to make SMACT better and more useful to the wider community; contributions are welcome. Please use the ["Fork and Pull"](https://guides.github.com/activities/forking/) workflow to make contributions and stick as closely as possible to the following:
-- Code style should comply with [PEP8](http://www.python.org/dev/peps/pep-0008) where possible. [Google's house style](https://google.github.io/styleguide/pyguide.html)
-is also helpful, including a good model for docstrings.
+- Code style should comply with [PEP8](http://www.python.org/dev/peps/pep-0008) where possible. [Google's house style](https://google.github.io/styleguide/pyguide.html) is also helpful, including a good model for docstrings.
 - Please use comments liberally when adding nontrivial features, and take the chance to clean up other people's code while looking at it.
 - Add tests wherever possible, and use the test suite to check if you broke anything.
@@ -176,24 +169,21 @@ Testing modules should be pass/fail and wrapped into **tests/test_core.py** or a
 Run the tests using `python -m pytest -v`.
 (The final `-v` is optional and adds more detail to the output.)
-We also use integrated testing on Github via [GitHub Actions](hhttps://github.com/features/actions).
+We also use integrated testing on GitHub via [GitHub Actions](hhttps://github.com/features/actions).
 References
 ----------
-[D. W. Davies et al,
-"SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
+[H. Park et al.,
+"Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
-[D. W. Davies et al,
-"Data-driven discovery of photoactive quaternary oxides using first-principles machine learning" *Chem. Mater.* **31**, 7221 (2019)](https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.9b01519)
+[D. W. Davies et al.,
+"SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Materials discovery by chemical analogy: role of oxidation states in structure prediction" *Faraday Discuss.* **211**, 553 (2018)](https://pubs.rsc.org/en/Content/ArticleLanding/2018/FD/C8FD00032H)
-[D. W. Davies et al,
-"Computer-aided design of metal chalcohalide semiconductors: from chemical composition to crystal structure" *Chem. Sci.* **9**, 1022 (2018)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Computational screening of all stoichiometric inorganic materials" *Chem* **1**, 617 (2016)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
 [B. R. Pamplin, "A systematic method of deriving new semiconducting

{SMACT-2.5.4 → smact-2.6}/README.md RENAMED Viewed

@@ -15,10 +15,10 @@
 SMACT
 =====
-**Semiconducting Materials from Analogy and Chemical Theory** (SMACT) is a collection of rapid screening tools that uses data about chemical elements.
+**Semiconducting Materials from Analogy and Chemical Theory** (SMACT) is a collection of rapid screening and informatics tools that uses data about chemical elements.
 - **Documentation:** https://smact.readthedocs.io/en/latest/
-- **Examples folder:** https://github.com/WMD-group/SMACT/tree/master/examples
+- **Examples:** https://github.com/WMD-group/SMACT/tree/master/examples
 ![](SMACT.png)
@@ -26,18 +26,13 @@ SMACT
 Statement of need
 --------
-There is a strong demand for functional materials across a wide range of technologies. The motivation can include cost reduction, performance enhancement, or to enable a new application. Data collections such as the [Materials Project](https://www.materialsproject.org), [NREL Materials Database](http://materials.nrel.gov) and the [Open Quantum Materials Database](http://oqmd.org) are valuable resources, but they largely cover the properties of *known* compounds as calculated using high-level quantum mechanical theories.
-We have developed low-cost procedures for screening hypothetical materials in SMACT. This framework can be used for simple calculations on your own computer. SMACT follows a top-down approach where a set of element combinations is generated and then screened using rapid chemical filters. It can be used as part of a multi-technique workflow or to feed machine learning models for materials.
+There is a strong demand for functional materials across a wide range of technologies. The motivation can include cost reduction, performance enhancement, or to enable a new application. We have developed low-cost procedures for screening hypothetical materials. This framework can be used for simple calculations on your own computer. SMACT follows a top-down approach where a set of element combinations is generated and then screened using rapid chemical filters. It can be used as part of a multi-technique workflow or to feed machine learning models for materials.
 ![](smact_simple.gif)
 Getting started
 -----
-SMACT's features are accessed through Python scripts, importing classes and functions as needed.
+Features are accessed through Python scripts, importing classes and functions as needed.
 The best place to start is looking at [the docs](https://smact.readthedocs.io/en/latest/), which highlight some simple examples of how these classes and functions can be used.
 Extended examples are available in [our examples folder](https://github.com/WMD-group/SMACT/tree/master/examples).
@@ -45,9 +40,9 @@ Code features
 --------
 - At the core of SMACT are [Element](https://smact.readthedocs.io/en/latest/smact.html#smact.Element) and [Species](https://smact.readthedocs.io/en/latest/smact.html#smact.Species) (element in a given oxidation state) classes that have various properties associated with them.
-- The various oxidation states that are accessible to each element are included in their properties.
+- Oxidation states that are accessible to each element are included in their properties.
-- Element compositions can be screened through based on the heuristic filters of charge neutrality and electronegativity order. This is handled using the [screening module](https://smact.readthedocs.io/en/latest/smact.screening.html) and [this publication](https://www.cell.com/chem/fulltext/S2451-9294(16)30155-3) describes the underlying theory. An example procedure is [outlined in the docs](https://smact.readthedocs.io/en/latest/examples.html#neutral-combinations) and further examples can be found in the [counting examples subfolder](https://github.com/WMD-group/SMACT/tree/master/examples/Counting).
+- Element compositions can be screened through based on the heuristic filters of charge neutrality and electronegativity order. This is handled using the [screening module](https://smact.readthedocs.io/en/latest/smact.screening.html) and [this publication](https://www.cell.com/chem/fulltext/S2451-9294(16)30155-3) describes the underlying theory. An example procedure is [outlined in the docs](https://smact.readthedocs.io/en/latest/examples.html#neutral-combinations) and more examples can be found in the [counting examples subfolder](https://github.com/WMD-group/SMACT/tree/master/examples/Counting).
 - Further filters can be applied to generated lists of compositions in order to screen for particular properties. These properties are either intrinsic properties of elements or are calculated for compositions using the [properties module](https://smact.readthedocs.io/en/latest/smact.properties.html). For example:
   - A use case is shown in [this publication](https://pubs.rsc.org/en/content/articlehtml/2018/sc/c7sc03961a), in which 160,000 chemical compositions are screened based on optical band gap calculated using the [solid-state energy scale](https://www.sciencedirect.com/science/article/pii/S0022459615300888).
@@ -55,18 +50,17 @@ Code features
 - Compositions can also be filtered based on sustainability via the abundance of elements in the Earth's crust or via the [HHI scale](https://pubs.acs.org/doi/10.1021/cm400893e).
-- Compositions can easily be converted for use in Pymatgen or for representation to machine learning algorithms ([see "next steps" in this example](https://github.com/WMD-group/SMACT/blob/master/examples/Counting/Generate_compositions_lists.ipynb)).
+- Compositions can be converted for use in Pymatgen or for representation to machine learning algorithms ([see "next steps" in this example](https://github.com/WMD-group/SMACT/blob/master/examples/Counting/Generate_compositions_lists.ipynb)) and the related [ElementEmbeddings](https://github.com/WMD-group/ElementEmbeddings) package.
-- The code also has some tools for manipulating common crystal lattice types:
- - Common crystal structure types can be built using the [builder module](https://smact.readthedocs.io/en/latest/smact.builder.html)
- - Lattice parameters can be quickly estimated using ionic radii of the elements for various common crystal structure types using the [lattice_parameters module](https://smact.readthedocs.io/en/latest/smact.lattice_parameters.html).
- - The [lattice module](https://smact.readthedocs.io/en/latest/smact.lattice.html) and [distorter module](https://smact.readthedocs.io/en/latest/smact.distorter.html) rely on the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) and can be used to generate unique atomic substitutions on a given crystal structure.
- - The [structure  prediction](https://smact.readthedocs.io/en/latest/smact.structure_prediction.html) module can be used to predict the structure of hypothetical compositions using species similarity measures.
- - The [dopant prediction](https://smact.readthedocs.io/en/latest/smact.dopant_prediction.html) module can be used to facilitate high-throughput predictions of p-type and n-type dopants of multicomponent solids.
+- The code also has tools for manipulating common crystal lattice types:
+  - Certain structure types can be built using the [builder module](https://smact.readthedocs.io/en/latest/smact.builder.html)
+  - Lattice parameters can be estimated using ionic radii of the elements for various common crystal structure types using the [lattice_parameters module](https://smact.readthedocs.io/en/latest/smact.lattice_parameters.html).
+  - The [lattice module](https://smact.readthedocs.io/en/latest/smact.lattice.html) and [distorter module](https://smact.readthedocs.io/en/latest/smact.distorter.html) rely on the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) and can be used to generate unique atomic substitutions on a given crystal structure.
+  - The [structure  prediction](https://smact.readthedocs.io/en/latest/smact.structure_prediction.html) module can be used to predict the structure of hypothetical compositions using species similarity measures.
+  - The [dopant prediction](https://smact.readthedocs.io/en/latest/smact.dopant_prediction.html) module can be used to facilitate high-throughput predictions of p-type and n-type dopants of multicomponent solids.
 List of modules
 -------
 * **smact** library containing:
   * **\_\_init\_\_.py** Contains the core `Element` and `Species` classes.
   *  **data_loader.py** Handles the loading of external data used to initialise the core `smact.Element` and `smact.Species` classes.
@@ -74,7 +68,7 @@ List of modules
   *  **properties.py** A collection of tools for estimating useful properties based on composition.
   * **lattice.py** Given the sites, multiplicities and possible oxidation states
     at those sites, this reads from the database and generates all possible
-    stoichiometeries.
+    stoichiometries.
   * **builder.py** Builds some common lattice structures, given the chemical
     composition.
   * **lattice_parameters.py** Estimation of lattice parameters for various lattice types using covalent/ionic radii.
@@ -82,18 +76,17 @@ List of modules
     substituting on inequivalent sites of a sub-lattice.
   * **oxidation_states.py**: Used for predicting the likelihood of species coexisting in a compound based on a statistical model.
   * **structure_prediction**: A submodule which contains a collection of tools for facilitating crystal structure predictions via ionic substitutions
-  * **dopant_prediction**: A submodule which contains a collections of tools for predicting n-type and p-type dopants.
+  * **dopant_prediction**: A submodule which contains a collections of tools for predicting dopants.
 Requirements
 ------------
-The main language is Python 3 and has been tested using Python 3.8+.
+The main language is Python 3 and has been tested using Python 3.9+.
 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](www.pymatgen.org) are also required for many components.
+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.
 Installation
 ------------
-The latest stable release of SMACT can be installed via pip which will automatically setup other Python packages as required:
+The latest stable release can be installed via pip which will automatically set up other Python packages as required:
     pip install smact
@@ -105,12 +98,12 @@ conda install -c conda-forge smact
 Alternatively, the very latest version can be installed using:
-    pip install git+git://github.com/WMD-group/SMACT.git
+    pip install git+https://github.com/WMD-group/SMACT.git
 For developer installation SMACT can be installed from a copy of the source
 repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches.
-To clone the project from Github and make a local installation:
+To clone the project from GitHub and make a local installation:
     git clone https://github.com/wmd-group/smact.git
     cd smact
@@ -132,10 +125,9 @@ Development notes
 Please use the [Issue Tracker](https://github.com/WMD-group/smact/issues) to report bugs or request features in the first instance. While we hope that most questions can be answered by searching [the docs](https://smact.readthedocs.io/en/latest/), we welcome new questions on the issue tracker, especially if they helps us improve the docs! For other queries about any aspect of the code, please contact either Dan Davies (author) or Anthony Onwuli (maintainer) by e-mail: d.w.davies@imperial.ac.uk or anthony.onwuli16@imperial.ac.uk respectively.
 ### Code contributions
-We are always looking for ways to make SMACT better and more useful to the wider community; contributions are very welcome. Please use the ["Fork and Pull"](https://guides.github.com/activities/forking/) workflow to make contributions and stick as closely as possible to the following:
+We are always looking for ways to make SMACT better and more useful to the wider community; contributions are welcome. Please use the ["Fork and Pull"](https://guides.github.com/activities/forking/) workflow to make contributions and stick as closely as possible to the following:
-- Code style should comply with [PEP8](http://www.python.org/dev/peps/pep-0008) where possible. [Google's house style](https://google.github.io/styleguide/pyguide.html)
-is also helpful, including a good model for docstrings.
+- Code style should comply with [PEP8](http://www.python.org/dev/peps/pep-0008) where possible. [Google's house style](https://google.github.io/styleguide/pyguide.html) is also helpful, including a good model for docstrings.
 - Please use comments liberally when adding nontrivial features, and take the chance to clean up other people's code while looking at it.
 - Add tests wherever possible, and use the test suite to check if you broke anything.
@@ -144,26 +136,23 @@ Testing modules should be pass/fail and wrapped into **tests/test_core.py** or a
 Run the tests using `python -m pytest -v`.
 (The final `-v` is optional and adds more detail to the output.)
-We also use integrated testing on Github via [GitHub Actions](hhttps://github.com/features/actions).
+We also use integrated testing on GitHub via [GitHub Actions](hhttps://github.com/features/actions).
 References
 ----------
-[D. W. Davies et al,
-"SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
+[H. Park et al.,
+"Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
-[D. W. Davies et al,
-"Data-driven discovery of photoactive quaternary oxides using first-principles machine learning" *Chem. Mater.* **31**, 7221 (2019)](https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.9b01519)
+[D. W. Davies et al.,
+"SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Materials discovery by chemical analogy: role of oxidation states in structure prediction" *Faraday Discuss.* **211**, 553 (2018)](https://pubs.rsc.org/en/Content/ArticleLanding/2018/FD/C8FD00032H)
-[D. W. Davies et al,
-"Computer-aided design of metal chalcohalide semiconductors: from chemical composition to crystal structure" *Chem. Sci.* **9**, 1022 (2018)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Computational screening of all stoichiometric inorganic materials" *Chem* **1**, 617 (2016)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
 [B. R. Pamplin, "A systematic method of deriving new semiconducting
 compounds by structural analogy", *J. Phys. Chem. Solids*
-**25**, 675 (1964)](http://www.sciencedirect.com/science/article/pii/0022369764901763)
+**25**, 675 (1964)](http://www.sciencedirect.com/science/article/pii/0022369764901763)

{SMACT-2.5.4 → smact-2.6/SMACT.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SMACT
-Version: 2.5.4
+Version: 2.6
 Summary: Semiconducting Materials by Analogy and Chemical Theory
 Home-page: https://github.com/WMD-group/SMACT
 Author: Daniel W. Davies
@@ -9,26 +9,27 @@ Maintainer: Anthony O. Onwuli
 Maintainer-email: anthony.onwuli16@imperial.ac.uk
 License: MIT
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: scipy
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: spglib
-Requires-Dist: pymatgen
+Requires-Dist: pymatgen>=2024.2.20
 Requires-Dist: ase
 Requires-Dist: pandas
 Requires-Dist: pathos
+Requires-Dist: typing-extensions
 [![DOI](http://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)
@@ -47,10 +48,10 @@ Requires-Dist: pathos
 SMACT
 =====
-**Semiconducting Materials from Analogy and Chemical Theory** (SMACT) is a collection of rapid screening tools that uses data about chemical elements.
+**Semiconducting Materials from Analogy and Chemical Theory** (SMACT) is a collection of rapid screening and informatics tools that uses data about chemical elements.
 - **Documentation:** https://smact.readthedocs.io/en/latest/
-- **Examples folder:** https://github.com/WMD-group/SMACT/tree/master/examples
+- **Examples:** https://github.com/WMD-group/SMACT/tree/master/examples
 ![](SMACT.png)
@@ -58,18 +59,13 @@ SMACT
 Statement of need
 --------
-There is a strong demand for functional materials across a wide range of technologies. The motivation can include cost reduction, performance enhancement, or to enable a new application. Data collections such as the [Materials Project](https://www.materialsproject.org), [NREL Materials Database](http://materials.nrel.gov) and the [Open Quantum Materials Database](http://oqmd.org) are valuable resources, but they largely cover the properties of *known* compounds as calculated using high-level quantum mechanical theories.
-We have developed low-cost procedures for screening hypothetical materials in SMACT. This framework can be used for simple calculations on your own computer. SMACT follows a top-down approach where a set of element combinations is generated and then screened using rapid chemical filters. It can be used as part of a multi-technique workflow or to feed machine learning models for materials.
+There is a strong demand for functional materials across a wide range of technologies. The motivation can include cost reduction, performance enhancement, or to enable a new application. We have developed low-cost procedures for screening hypothetical materials. This framework can be used for simple calculations on your own computer. SMACT follows a top-down approach where a set of element combinations is generated and then screened using rapid chemical filters. It can be used as part of a multi-technique workflow or to feed machine learning models for materials.
 ![](smact_simple.gif)
 Getting started
 -----
-SMACT's features are accessed through Python scripts, importing classes and functions as needed.
+Features are accessed through Python scripts, importing classes and functions as needed.
 The best place to start is looking at [the docs](https://smact.readthedocs.io/en/latest/), which highlight some simple examples of how these classes and functions can be used.
 Extended examples are available in [our examples folder](https://github.com/WMD-group/SMACT/tree/master/examples).
@@ -77,9 +73,9 @@ Code features
 --------
 - At the core of SMACT are [Element](https://smact.readthedocs.io/en/latest/smact.html#smact.Element) and [Species](https://smact.readthedocs.io/en/latest/smact.html#smact.Species) (element in a given oxidation state) classes that have various properties associated with them.
-- The various oxidation states that are accessible to each element are included in their properties.
+- Oxidation states that are accessible to each element are included in their properties.
-- Element compositions can be screened through based on the heuristic filters of charge neutrality and electronegativity order. This is handled using the [screening module](https://smact.readthedocs.io/en/latest/smact.screening.html) and [this publication](https://www.cell.com/chem/fulltext/S2451-9294(16)30155-3) describes the underlying theory. An example procedure is [outlined in the docs](https://smact.readthedocs.io/en/latest/examples.html#neutral-combinations) and further examples can be found in the [counting examples subfolder](https://github.com/WMD-group/SMACT/tree/master/examples/Counting).
+- Element compositions can be screened through based on the heuristic filters of charge neutrality and electronegativity order. This is handled using the [screening module](https://smact.readthedocs.io/en/latest/smact.screening.html) and [this publication](https://www.cell.com/chem/fulltext/S2451-9294(16)30155-3) describes the underlying theory. An example procedure is [outlined in the docs](https://smact.readthedocs.io/en/latest/examples.html#neutral-combinations) and more examples can be found in the [counting examples subfolder](https://github.com/WMD-group/SMACT/tree/master/examples/Counting).
 - Further filters can be applied to generated lists of compositions in order to screen for particular properties. These properties are either intrinsic properties of elements or are calculated for compositions using the [properties module](https://smact.readthedocs.io/en/latest/smact.properties.html). For example:
   - A use case is shown in [this publication](https://pubs.rsc.org/en/content/articlehtml/2018/sc/c7sc03961a), in which 160,000 chemical compositions are screened based on optical band gap calculated using the [solid-state energy scale](https://www.sciencedirect.com/science/article/pii/S0022459615300888).
@@ -87,18 +83,17 @@ Code features
 - Compositions can also be filtered based on sustainability via the abundance of elements in the Earth's crust or via the [HHI scale](https://pubs.acs.org/doi/10.1021/cm400893e).
-- Compositions can easily be converted for use in Pymatgen or for representation to machine learning algorithms ([see "next steps" in this example](https://github.com/WMD-group/SMACT/blob/master/examples/Counting/Generate_compositions_lists.ipynb)).
+- Compositions can be converted for use in Pymatgen or for representation to machine learning algorithms ([see "next steps" in this example](https://github.com/WMD-group/SMACT/blob/master/examples/Counting/Generate_compositions_lists.ipynb)) and the related [ElementEmbeddings](https://github.com/WMD-group/ElementEmbeddings) package.
-- The code also has some tools for manipulating common crystal lattice types:
- - Common crystal structure types can be built using the [builder module](https://smact.readthedocs.io/en/latest/smact.builder.html)
- - Lattice parameters can be quickly estimated using ionic radii of the elements for various common crystal structure types using the [lattice_parameters module](https://smact.readthedocs.io/en/latest/smact.lattice_parameters.html).
- - The [lattice module](https://smact.readthedocs.io/en/latest/smact.lattice.html) and [distorter module](https://smact.readthedocs.io/en/latest/smact.distorter.html) rely on the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) and can be used to generate unique atomic substitutions on a given crystal structure.
- - The [structure  prediction](https://smact.readthedocs.io/en/latest/smact.structure_prediction.html) module can be used to predict the structure of hypothetical compositions using species similarity measures.
- - The [dopant prediction](https://smact.readthedocs.io/en/latest/smact.dopant_prediction.html) module can be used to facilitate high-throughput predictions of p-type and n-type dopants of multicomponent solids.
+- The code also has tools for manipulating common crystal lattice types:
+  - Certain structure types can be built using the [builder module](https://smact.readthedocs.io/en/latest/smact.builder.html)
+  - Lattice parameters can be estimated using ionic radii of the elements for various common crystal structure types using the [lattice_parameters module](https://smact.readthedocs.io/en/latest/smact.lattice_parameters.html).
+  - The [lattice module](https://smact.readthedocs.io/en/latest/smact.lattice.html) and [distorter module](https://smact.readthedocs.io/en/latest/smact.distorter.html) rely on the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) and can be used to generate unique atomic substitutions on a given crystal structure.
+  - The [structure  prediction](https://smact.readthedocs.io/en/latest/smact.structure_prediction.html) module can be used to predict the structure of hypothetical compositions using species similarity measures.
+  - The [dopant prediction](https://smact.readthedocs.io/en/latest/smact.dopant_prediction.html) module can be used to facilitate high-throughput predictions of p-type and n-type dopants of multicomponent solids.
 List of modules
 -------
 * **smact** library containing:
   * **\_\_init\_\_.py** Contains the core `Element` and `Species` classes.
   *  **data_loader.py** Handles the loading of external data used to initialise the core `smact.Element` and `smact.Species` classes.
@@ -106,7 +101,7 @@ List of modules
   *  **properties.py** A collection of tools for estimating useful properties based on composition.
   * **lattice.py** Given the sites, multiplicities and possible oxidation states
     at those sites, this reads from the database and generates all possible
-    stoichiometeries.
+    stoichiometries.
   * **builder.py** Builds some common lattice structures, given the chemical
     composition.
   * **lattice_parameters.py** Estimation of lattice parameters for various lattice types using covalent/ionic radii.
@@ -114,18 +109,17 @@ List of modules
     substituting on inequivalent sites of a sub-lattice.
   * **oxidation_states.py**: Used for predicting the likelihood of species coexisting in a compound based on a statistical model.
   * **structure_prediction**: A submodule which contains a collection of tools for facilitating crystal structure predictions via ionic substitutions
-  * **dopant_prediction**: A submodule which contains a collections of tools for predicting n-type and p-type dopants.
+  * **dopant_prediction**: A submodule which contains a collections of tools for predicting dopants.
 Requirements
 ------------
-The main language is Python 3 and has been tested using Python 3.8+.
+The main language is Python 3 and has been tested using Python 3.9+.
 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](www.pymatgen.org) are also required for many components.
+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.
 Installation
 ------------
-The latest stable release of SMACT can be installed via pip which will automatically setup other Python packages as required:
+The latest stable release can be installed via pip which will automatically set up other Python packages as required:
     pip install smact
@@ -137,12 +131,12 @@ conda install -c conda-forge smact
 Alternatively, the very latest version can be installed using:
-    pip install git+git://github.com/WMD-group/SMACT.git
+    pip install git+https://github.com/WMD-group/SMACT.git
 For developer installation SMACT can be installed from a copy of the source
 repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches.
-To clone the project from Github and make a local installation:
+To clone the project from GitHub and make a local installation:
     git clone https://github.com/wmd-group/smact.git
     cd smact
@@ -164,10 +158,9 @@ Development notes
 Please use the [Issue Tracker](https://github.com/WMD-group/smact/issues) to report bugs or request features in the first instance. While we hope that most questions can be answered by searching [the docs](https://smact.readthedocs.io/en/latest/), we welcome new questions on the issue tracker, especially if they helps us improve the docs! For other queries about any aspect of the code, please contact either Dan Davies (author) or Anthony Onwuli (maintainer) by e-mail: d.w.davies@imperial.ac.uk or anthony.onwuli16@imperial.ac.uk respectively.
 ### Code contributions
-We are always looking for ways to make SMACT better and more useful to the wider community; contributions are very welcome. Please use the ["Fork and Pull"](https://guides.github.com/activities/forking/) workflow to make contributions and stick as closely as possible to the following:
+We are always looking for ways to make SMACT better and more useful to the wider community; contributions are welcome. Please use the ["Fork and Pull"](https://guides.github.com/activities/forking/) workflow to make contributions and stick as closely as possible to the following:
-- Code style should comply with [PEP8](http://www.python.org/dev/peps/pep-0008) where possible. [Google's house style](https://google.github.io/styleguide/pyguide.html)
-is also helpful, including a good model for docstrings.
+- Code style should comply with [PEP8](http://www.python.org/dev/peps/pep-0008) where possible. [Google's house style](https://google.github.io/styleguide/pyguide.html) is also helpful, including a good model for docstrings.
 - Please use comments liberally when adding nontrivial features, and take the chance to clean up other people's code while looking at it.
 - Add tests wherever possible, and use the test suite to check if you broke anything.
@@ -176,24 +169,21 @@ Testing modules should be pass/fail and wrapped into **tests/test_core.py** or a
 Run the tests using `python -m pytest -v`.
 (The final `-v` is optional and adds more detail to the output.)
-We also use integrated testing on Github via [GitHub Actions](hhttps://github.com/features/actions).
+We also use integrated testing on GitHub via [GitHub Actions](hhttps://github.com/features/actions).
 References
 ----------
-[D. W. Davies et al,
-"SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
+[H. Park et al.,
+"Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
-[D. W. Davies et al,
-"Data-driven discovery of photoactive quaternary oxides using first-principles machine learning" *Chem. Mater.* **31**, 7221 (2019)](https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.9b01519)
+[D. W. Davies et al.,
+"SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Materials discovery by chemical analogy: role of oxidation states in structure prediction" *Faraday Discuss.* **211**, 553 (2018)](https://pubs.rsc.org/en/Content/ArticleLanding/2018/FD/C8FD00032H)
-[D. W. Davies et al,
-"Computer-aided design of metal chalcohalide semiconductors: from chemical composition to crystal structure" *Chem. Sci.* **9**, 1022 (2018)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Computational screening of all stoichiometric inorganic materials" *Chem* **1**, 617 (2016)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
 [B. R. Pamplin, "A systematic method of deriving new semiconducting

{SMACT-2.5.4 → smact-2.6}/SMACT.egg-info/SOURCES.txt RENAMED Viewed

@@ -38,6 +38,7 @@ 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/skipspecies_20221028_319ion_dim200_cosine_similarity.json
 smact/dopant_prediction/__init__.py
 smact/dopant_prediction/doper.py
 smact/structure_prediction/__init__.py

smact-2.6/SMACT.egg-info/requires.txt ADDED Viewed

@@ -0,0 +1,8 @@
+scipy
+numpy<2
+spglib
+pymatgen>=2024.2.20
+ase
+pandas
+pathos
+typing-extensions

SMACT 2.5.4__tar.gz → 2.6__tar.gz

SMACT 2.5.4tar.gz → 2.6tar.gz