ElementEmbeddings 0.4__tar.gz → 0.5__tar.gz

{ElementEmbeddings-0.4 → elementembeddings-0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ElementEmbeddings
-Version: 0.4
+Version: 0.5
 Summary: Element Embeddings
 Author: Anthony O. Onwuli
 Author-email: anthony.onwuli16@imperial.ac.uk
@@ -15,9 +15,35 @@ Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: License :: OSI Approved :: MIT License
 Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy<2,>=1.23.3
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: pymatgen>2022.9.21
+Requires-Dist: seaborn>=0.13.0
+Requires-Dist: matplotlib>=3.7.1
+Requires-Dist: scikit-learn>=1.3.0
+Requires-Dist: umap-learn>=0.5.3
+Requires-Dist: adjustText>=0.8
+Requires-Dist: openTSNE>=1.0.0
+Requires-Dist: typing-extensions
 Provides-Extra: dev
+Requires-Dist: pre-commit==3.6.0; extra == "dev"
+Requires-Dist: black==24.3.0; extra == "dev"
+Requires-Dist: isort==5.13.2; extra == "dev"
+Requires-Dist: pytest==8.0.2; extra == "dev"
+Requires-Dist: pytest-subtests==0.10.0; extra == "dev"
+Requires-Dist: nbqa==1.7.1; extra == "dev"
+Requires-Dist: flake8==7.0.0; extra == "dev"
+Requires-Dist: pyupgrade==3.13.0; extra == "dev"
+Requires-Dist: autopep8==2.0.2; extra == "dev"
+Requires-Dist: pytest-cov==5.0.0; extra == "dev"
+Requires-Dist: pytest-mpl==0.16.1; extra == "dev"
 Provides-Extra: docs
-License-File: LICENSE.md
+Requires-Dist: mkdocs==1.6.0; extra == "docs"
+Requires-Dist: mkdocs-material==9.5.16; extra == "docs"
+Requires-Dist: mkdocstrings==0.25.1; extra == "docs"
+Requires-Dist: mkdocstrings-python==1.9.0; extra == "docs"
+Requires-Dist: mike==2.0.0; extra == "docs"
 
 # ElementEmbeddings
 
@@ -187,6 +213,20 @@ Please use the [issue tracker](https://github.com/WMD-group/ElementEmbeddings/is
 
 We welcome new contributions to this project. See [the contributing guide](contributing.md) for detailed instructions on how to contribute to our project.
 
+### Add an embedding scheme
+
+The steps required to add a new representation scheme are:
+1. Add data file to [data/element_representations](src/elementembeddings/data/element_representations).
+2. Edit docstring table in [core.py](src/elementembeddings/core.py).
+3. Edit [utils/config.py](src/elementembeddings/utils/config.py) to include the representation in `DEFAULT_ELEMENT_EMBEDDINGS` and `CITATIONS`.
+4. Add the represention to the documentation in the [reference.md](docs/reference.md) file.
+
 ### Developer
 
 * [Anthony Onwuli](https://github.com/AntObi) (Department of Materials, Imperial College London)
+
+
+## References
+[H. Park et al, "Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
+
+[A. Onwuli et al, "Element similarity in high-dimensional materials representations" *Digital Discovery* **2**, 1558 (2023)](https://pubs.rsc.org/en/content/articlelanding/2023/dd/d3dd00121k)

ElementEmbeddings-0.4/src/ElementEmbeddings.egg-info/PKG-INFO → elementembeddings-0.5/README.md

@@ -1,24 +1,3 @@
-Metadata-Version: 2.1
-Name: ElementEmbeddings
-Version: 0.4
-Summary: Element Embeddings
-Author: Anthony O. Onwuli
-Author-email: anthony.onwuli16@imperial.ac.uk
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Science/Research
-Classifier: Operating System :: OS Independent
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: License :: OSI Approved :: MIT License
-Description-Content-Type: text/markdown
-Provides-Extra: dev
-Provides-Extra: docs
-License-File: LICENSE.md
-
 # ElementEmbeddings
 
 [![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
@@ -187,6 +166,20 @@ Please use the [issue tracker](https://github.com/WMD-group/ElementEmbeddings/is
 
 We welcome new contributions to this project. See [the contributing guide](contributing.md) for detailed instructions on how to contribute to our project.
 
+### Add an embedding scheme
+
+The steps required to add a new representation scheme are:
+1. Add data file to [data/element_representations](src/elementembeddings/data/element_representations).
+2. Edit docstring table in [core.py](src/elementembeddings/core.py).
+3. Edit [utils/config.py](src/elementembeddings/utils/config.py) to include the representation in `DEFAULT_ELEMENT_EMBEDDINGS` and `CITATIONS`.
+4. Add the represention to the documentation in the [reference.md](docs/reference.md) file.
+
 ### Developer
 
 * [Anthony Onwuli](https://github.com/AntObi) (Department of Materials, Imperial College London)
+
+
+## References
+[H. Park et al, "Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
+
+[A. Onwuli et al, "Element similarity in high-dimensional materials representations" *Digital Discovery* **2**, 1558 (2023)](https://pubs.rsc.org/en/content/articlelanding/2023/dd/d3dd00121k)

{ElementEmbeddings-0.4 → elementembeddings-0.5}/setup.py

@@ -5,7 +5,7 @@ from setuptools import find_namespace_packages, setup
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
 
-VERSION = "0.4"
+VERSION = "0.5"
 DESCRIPTION = "Element Embeddings"
 with open(os.path.join(module_dir, "README.md"), encoding="utf-8") as f:
     LONG_DESCRIPTION = f.read()
@@ -28,34 +28,37 @@ setup(
     },
     test_suite="elementembeddings.tests.test",
     install_requires=[
-        "numpy==1.23.3",
-        "scipy==1.10.1",
+        "numpy>=1.23.3,<2",
+        "scipy>=1.10.1",
         "pymatgen>2022.9.21",
-        "seaborn==0.12.2",
-        "matplotlib==3.7.1",
-        "scikit-learn==1.3.0",
-        "umap-learn==0.5.3",
-        "adjustText==0.8",
+        "seaborn>=0.13.0",
+        "matplotlib>=3.7.1",
+        "scikit-learn>=1.3.0",
+        "umap-learn>=0.5.3",
+        "adjustText>=0.8",
+        "openTSNE>=1.0.0",
+        "typing-extensions",
     ],
     extras_require={
         "dev": [
-            "pre-commit==3.3.3",
-            "black==23.3.0",
-            "isort==5.12.0",
-            "pytest==7.2.1",
+            "pre-commit==3.6.0",
+            "black==24.3.0",
+            "isort==5.13.2",
+            "pytest==8.0.2",
             "pytest-subtests==0.10.0",
-            "nbqa==1.5.3",
-            "pyupgrade==3.3.1",
-            "flake8==6.0.0",
+            "nbqa==1.7.1",
+            "flake8==7.0.0",
+            "pyupgrade==3.13.0",
             "autopep8==2.0.2",
-            "pytest-cov==4.1.0",
+            "pytest-cov==5.0.0",
+            "pytest-mpl==0.16.1",
         ],
         "docs": [
-            "mkdocs==1.4.3",
-            "mkdocs-material==9.1.17",
-            "mkdocstrings ==0.21.2",
-            "mkdocstrings-python == 1.2.1",
-            "mike ==1.1.2",
+            "mkdocs==1.6.0",
+            "mkdocs-material==9.5.16",
+            "mkdocstrings ==0.25.1",
+            "mkdocstrings-python == 1.9.0",
+            "mike ==2.0.0",
         ],
     },
     classifiers=[

ElementEmbeddings-0.4/README.md → elementembeddings-0.5/src/ElementEmbeddings.egg-info/PKG-INFO

@@ -1,3 +1,50 @@
+Metadata-Version: 2.1
+Name: ElementEmbeddings
+Version: 0.5
+Summary: Element Embeddings
+Author: Anthony O. Onwuli
+Author-email: anthony.onwuli16@imperial.ac.uk
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: License :: OSI Approved :: MIT License
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy<2,>=1.23.3
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: pymatgen>2022.9.21
+Requires-Dist: seaborn>=0.13.0
+Requires-Dist: matplotlib>=3.7.1
+Requires-Dist: scikit-learn>=1.3.0
+Requires-Dist: umap-learn>=0.5.3
+Requires-Dist: adjustText>=0.8
+Requires-Dist: openTSNE>=1.0.0
+Requires-Dist: typing-extensions
+Provides-Extra: dev
+Requires-Dist: pre-commit==3.6.0; extra == "dev"
+Requires-Dist: black==24.3.0; extra == "dev"
+Requires-Dist: isort==5.13.2; extra == "dev"
+Requires-Dist: pytest==8.0.2; extra == "dev"
+Requires-Dist: pytest-subtests==0.10.0; extra == "dev"
+Requires-Dist: nbqa==1.7.1; extra == "dev"
+Requires-Dist: flake8==7.0.0; extra == "dev"
+Requires-Dist: pyupgrade==3.13.0; extra == "dev"
+Requires-Dist: autopep8==2.0.2; extra == "dev"
+Requires-Dist: pytest-cov==5.0.0; extra == "dev"
+Requires-Dist: pytest-mpl==0.16.1; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs==1.6.0; extra == "docs"
+Requires-Dist: mkdocs-material==9.5.16; extra == "docs"
+Requires-Dist: mkdocstrings==0.25.1; extra == "docs"
+Requires-Dist: mkdocstrings-python==1.9.0; extra == "docs"
+Requires-Dist: mike==2.0.0; extra == "docs"
+
 # ElementEmbeddings
 
 [![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
@@ -166,6 +213,20 @@ Please use the [issue tracker](https://github.com/WMD-group/ElementEmbeddings/is
 
 We welcome new contributions to this project. See [the contributing guide](contributing.md) for detailed instructions on how to contribute to our project.
 
+### Add an embedding scheme
+
+The steps required to add a new representation scheme are:
+1. Add data file to [data/element_representations](src/elementembeddings/data/element_representations).
+2. Edit docstring table in [core.py](src/elementembeddings/core.py).
+3. Edit [utils/config.py](src/elementembeddings/utils/config.py) to include the representation in `DEFAULT_ELEMENT_EMBEDDINGS` and `CITATIONS`.
+4. Add the represention to the documentation in the [reference.md](docs/reference.md) file.
+
 ### Developer
 
 * [Anthony Onwuli](https://github.com/AntObi) (Department of Materials, Imperial College London)
+
+
+## References
+[H. Park et al, "Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
+
+[A. Onwuli et al, "Element similarity in high-dimensional materials representations" *Digital Discovery* **2**, 1558 (2023)](https://pubs.rsc.org/en/content/articlelanding/2023/dd/d3dd00121k)

{ElementEmbeddings-0.4 → elementembeddings-0.5}/src/ElementEmbeddings.egg-info/SOURCES.txt

@@ -7,6 +7,7 @@ src/ElementEmbeddings.egg-info/dependency_links.txt
 src/ElementEmbeddings.egg-info/requires.txt
 src/ElementEmbeddings.egg-info/top_level.txt
 src/elementembeddings/__init__.py
+src/elementembeddings/_base.py
 src/elementembeddings/composition.py
 src/elementembeddings/core.py
 src/elementembeddings/plotter.py
@@ -16,6 +17,8 @@ src/elementembeddings/data/element_data/ordered_periodic.txt
 src/elementembeddings/data/element_data/periodic-table-lookup-symbols.json
 src/elementembeddings/data/element_data/periodic-table-lookup.json
 src/elementembeddings/data/element_representations/atomic.json
+src/elementembeddings/data/element_representations/cgnf.json
+src/elementembeddings/data/element_representations/crystallm_v24c.dim512_atom_vectors.csv
 src/elementembeddings/data/element_representations/magpie.csv
 src/elementembeddings/data/element_representations/magpie_sc.json
 src/elementembeddings/data/element_representations/mat2vec.csv
@@ -28,11 +31,14 @@ src/elementembeddings/data/element_representations/oliynyk_sc.json
 src/elementembeddings/data/element_representations/random_200.csv
 src/elementembeddings/data/element_representations/random_200_new.csv
 src/elementembeddings/data/element_representations/skipatom_20201009_induced.csv
+src/elementembeddings/data/element_representations/xenonpy_element_features.csv
 src/elementembeddings/tests/__init__.py
 src/elementembeddings/tests/test_composition.py
 src/elementembeddings/tests/test_core.py
 src/elementembeddings/tests/test_plotter.py
 src/elementembeddings/tests/test_utils.py
 src/elementembeddings/utils/__init__.py
+src/elementembeddings/utils/config.py
 src/elementembeddings/utils/io.py
-src/elementembeddings/utils/math.py
+src/elementembeddings/utils/math.py
+src/elementembeddings/utils/species.py

elementembeddings-0.5/src/ElementEmbeddings.egg-info/requires.txt

@@ -0,0 +1,30 @@
+numpy<2,>=1.23.3
+scipy>=1.10.1
+pymatgen>2022.9.21
+seaborn>=0.13.0
+matplotlib>=3.7.1
+scikit-learn>=1.3.0
+umap-learn>=0.5.3
+adjustText>=0.8
+openTSNE>=1.0.0
+typing-extensions
+
+[dev]
+pre-commit==3.6.0
+black==24.3.0
+isort==5.13.2
+pytest==8.0.2
+pytest-subtests==0.10.0
+nbqa==1.7.1
+flake8==7.0.0
+pyupgrade==3.13.0
+autopep8==2.0.2
+pytest-cov==5.0.0
+pytest-mpl==0.16.1
+
+[docs]
+mkdocs==1.6.0
+mkdocs-material==9.5.16
+mkdocstrings==0.25.1
+mkdocstrings-python==1.9.0
+mike==2.0.0