Repo updates

CHANGELOG.md

@@ -0,0 +1,81 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+<!-- insertion marker -->
+## Unreleased
+
+<small>[Compare with latest](https://github.com/WMD-group/ElementEmbeddings/compare/v0.1...HEAD)</small>
+
+### Added
+
+- added doc and pypi badges to README ([8ea476c](https://github.com/WMD-group/ElementEmbeddings/commit/8ea476cf1422ca0d94d795fcd7b58ebd0ea858fe) by Anthony Onwuli).
+- Added citation file ([8d0baa1](https://github.com/WMD-group/ElementEmbeddings/commit/8d0baa1cd17b787e465300452d3c2d16a56c009b) by Anthony Onwuli).
+
+<!-- insertion marker -->
+## [v0.1](https://github.com/WMD-group/ElementEmbeddings/releases/tag/v0.1) - 2023-06-30
+
+<small>[Compare with first commit](https://github.com/WMD-group/ElementEmbeddings/compare/262c7e99a438a3527fb73866093ae8cb1ee85ee6...v0.1)</small>
+
+### Added
+
+- added documentation ([a9264f4](https://github.com/WMD-group/ElementEmbeddings/commit/a9264f41035e8b6bdeeb2255ef0f9743a7d1be19) by Anthony Onwuli).
+- Added scaled magpie embedding ([eb33ab4](https://github.com/WMD-group/ElementEmbeddings/commit/eb33ab4921343889f7583abe11eccdc2f34d8ffd) by Anthony Onwuli).
+- Added tests for the plotting module ([6e1098d](https://github.com/WMD-group/ElementEmbeddings/commit/6e1098db830e8168ab3f65a5e4b50ed0bf8221b2) by Anthony Onwuli).
+- added pytest-cov to dev reqs ([6db996f](https://github.com/WMD-group/ElementEmbeddings/commit/6db996f9981fa991ffb1435dec4d0a6ef3ec6544) by Anthony Onwuli).
+- added adjustText to requirements ([6ebd9ad](https://github.com/WMD-group/ElementEmbeddings/commit/6ebd9ad45b6e178904ae8c3e9fa4e260fb0012f1) by Anthony Onwuli).
+- added scaling to dimension reduction calcs ([3f177d8](https://github.com/WMD-group/ElementEmbeddings/commit/3f177d89f1aca2406372ff62f750d13ac3ec1c26) by Anthony Onwuli).
+- added function for plotting reduced Dims ([4085b94](https://github.com/WMD-group/ElementEmbeddings/commit/4085b948f46e2cd490d7dec9d309513f2ad7c69e) by Anthony).
+- added DR functions ([f755dc8](https://github.com/WMD-group/ElementEmbeddings/commit/f755dc870d9e494fd2dcac9d748d7a46e8844db0) by Anthony).
+- Added similarity plots in notebook ([0118932](https://github.com/WMD-group/ElementEmbeddings/commit/011893228b6aba848df060796a30696de7db4a7a) by Anthony Onwuli).
+- Added new random embedding for all 118 elements ([c6e9d8b](https://github.com/WMD-group/ElementEmbeddings/commit/c6e9d8bfecfa68fad37f47146fbeb43e06489c1c) by Anthony).
+- added axis sorting argument to plotter function ([d1a11b0](https://github.com/WMD-group/ElementEmbeddings/commit/d1a11b04cf8a32cc8164b727b71aaac27af8883a) by Anthony).
+- added sorting options to distance methods ([1947bb5](https://github.com/WMD-group/ElementEmbeddings/commit/1947bb58c00ba78842bfe237a1bff822476cb7e0) by Anthony).
+- added deprecation warnings ([fcc53a2](https://github.com/WMD-group/ElementEmbeddings/commit/fcc53a23772ce1e2bfd9d450e5530e2e3030f123) by Anthony).
+- added files for periodic table information ([ea2e40a](https://github.com/WMD-group/ElementEmbeddings/commit/ea2e40ac045ce620d025de2fc756bab6a22fcb19) by Anthony).
+- Added composition featuriser to the example ([a16b780](https://github.com/WMD-group/ElementEmbeddings/commit/a16b7802a9ab243b3766de54e2bfafd6f1ee0aca) by Anthony).
+- Added a multi plotter function ([e26f31c](https://github.com/WMD-group/ElementEmbeddings/commit/e26f31cac0366f259e92b0c4abbe49eeddcc2524) by Anthony).
+- added tests for utils module ([eefa232](https://github.com/WMD-group/ElementEmbeddings/commit/eefa232b8bad56e2f662f7898732de94fbcffa06) by Anthony).
+- added cosine measures to core.py ([e75af55](https://github.com/WMD-group/ElementEmbeddings/commit/e75af558b930c66204b05882e333a81fc34e8bbd) by Anthony).
+- added hook to remove nb outputs in pre-commit ([6d9c32d](https://github.com/WMD-group/ElementEmbeddings/commit/6d9c32dc6d5c19e4e0259f1c2e978573369e2485) by Anthony).
+- Added docstrings to utils/io.py ([962f79a](https://github.com/WMD-group/ElementEmbeddings/commit/962f79a4c4936f322a3fe5fed23a4789f261283d) by Anthony).
+- Added docstrings to test_core.py ([eddc26e](https://github.com/WMD-group/ElementEmbeddings/commit/eddc26e31468e89c324873352736c1e7f8f61eb1) by Anthony).
+- Added flake8 ([eebbc8a](https://github.com/WMD-group/ElementEmbeddings/commit/eebbc8a5450f6239df76a01b364fb0583ace5e60) by Anthony).
+- added progress bars to composition_featuriser ([bf9c608](https://github.com/WMD-group/ElementEmbeddings/commit/bf9c60894ca57f8552940a7c17cce3bc6c63ae19) by Anthony).
+- added composition featurizer ([e116efa](https://github.com/WMD-group/ElementEmbeddings/commit/e116efa3ba4b09087a70cebebee377f66fec4f2a) by Anthony).
+- added codecov badge to the main README ([2eb93a9](https://github.com/WMD-group/ElementEmbeddings/commit/2eb93a9af7c58688e49a98b121562f1ef3732e6f) by Anthony).
+- added stats functions to composition.py ([e11bec3](https://github.com/WMD-group/ElementEmbeddings/commit/e11bec301a0a504b693be1d5c69b88e6ec0a1b16) by Anthony).
+- add dependabot bot to repo ([3139fba](https://github.com/WMD-group/ElementEmbeddings/commit/3139fba592bc7acc810714a5bf082265b3e46244) by Anthony).
+- added .svg files to gitignore ([1129e71](https://github.com/WMD-group/ElementEmbeddings/commit/1129e71296c20d227f739b82d7b5383fdaa34c75) by Anthony).
+- added jupyter qa to pre-commit ([17796f5](https://github.com/WMD-group/ElementEmbeddings/commit/17796f5d34ed3fc6f5dd439982ad745b008934f3) by Anthony).
+- added new IO options to Embedding class ([af219f0](https://github.com/WMD-group/ElementEmbeddings/commit/af219f0252caaf13ac1fad2e1e76091114c19e9c) by Anthony).
+- added a Refactoring document ([e885382](https://github.com/WMD-group/ElementEmbeddings/commit/e885382e70679862f7bbaba9ace1855c34f7dcb6) by Anthony).
+- Added qa to Github actions ([42f478c](https://github.com/WMD-group/ElementEmbeddings/commit/42f478cc5ef5b8c5e497366de37e99554ea25674) by Anthony).
+- added test modules ([1864e1d](https://github.com/WMD-group/ElementEmbeddings/commit/1864e1d55ad56d9aaed9fa176c7904124779ef72) by Anthony).
+- added scaled versions of magpie and oliynyk ([9418c7c](https://github.com/WMD-group/ElementEmbeddings/commit/9418c7c0afb644e4f7e3424f4bb06bd8ca605517) by Anthony).
+- added a README in the data folder ([5568057](https://github.com/WMD-group/ElementEmbeddings/commit/55680575e46bc4c361fcf7714c8f375e22d5c084) by Anthony).
+- added new element representations ([bb7c19e](https://github.com/WMD-group/ElementEmbeddings/commit/bb7c19ef6cb5218a84414981b92bfee309b4a880) by Anthony).
+- added matscholar embeddings in data dir ([e49c8a4](https://github.com/WMD-group/ElementEmbeddings/commit/e49c8a4b2bcbc084d3753e734b416dfc12beceac) by Anthony).
+- added README.md to the repo ([262c7e9](https://github.com/WMD-group/ElementEmbeddings/commit/262c7e99a438a3527fb73866093ae8cb1ee85ee6) by Anthony).
+
+### Fixed
+
+- Fix error with using spearman ([7afb186](https://github.com/WMD-group/ElementEmbeddings/commit/7afb1865069648e8554e0ebd385696358c694833) by Anthony Onwuli).
+- fixed dimension plotter and added adjusttext ([ccca970](https://github.com/WMD-group/ElementEmbeddings/commit/ccca970d435d96499f62f69d74560cb523a39033) by Anthony Onwuli).
+- Fixed code block in file ([ef524e7](https://github.com/WMD-group/ElementEmbeddings/commit/ef524e7b91f90ca9db15313fc41e2c6d9b2a781b) by Anthony).
+- Fixed formatting on setup.py ([8be3961](https://github.com/WMD-group/ElementEmbeddings/commit/8be396121e47e4bd8bca605aff98eaf095bd4608) by Anthony).
+- fixed typing errors ([5b005f6](https://github.com/WMD-group/ElementEmbeddings/commit/5b005f64d8513e941122b8b594739e1d84b270bb) by Anthony).
+- fixed indentation error in Atomic_Embeddings class ([b7e39ab](https://github.com/WMD-group/ElementEmbeddings/commit/b7e39ab88ebc4807ef276c50be36e7c27ac47d5f) by Anthony).
+
+### Removed
+
+- remove unused method ([46d20af](https://github.com/WMD-group/ElementEmbeddings/commit/46d20af77797e452152a2af139e72b4d9f6145c4) by Anthony Onwuli).
+- removed heatmap image ([868fe92](https://github.com/WMD-group/ElementEmbeddings/commit/868fe92c3d41b60fc6b988273e2a1ac1e5065f13) by Anthony).
+- removed backup pyproject and setup files ([33f2cce](https://github.com/WMD-group/ElementEmbeddings/commit/33f2cce0e341f6837641c98cba29c22de2942252) by Anthony).
+- removed numba from requirements.txt ([1eb833e](https://github.com/WMD-group/ElementEmbeddings/commit/1eb833ec1769ead345de23e2c09c92cee72cc545) by Anthony).
+- removed the old AtomicEmbeddings.py file ([9b1b2e8](https://github.com/WMD-group/ElementEmbeddings/commit/9b1b2e82e0426136020f5112d12c18051d9b7c30) by Anthony).
+- removed itertools from reqssetup.py ([c9c21ca](https://github.com/WMD-group/ElementEmbeddings/commit/c9c21ca8a8e242fc99f19d1fee204da7a1bbdc62) by Anthony).
+

CITATION.cff

@@ -0,0 +1,40 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: ElementEmbeddings
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Anthony
+    family-names: Onwuli
+    email: anthony.onwuli16@imperial.ac.uk
+    affiliation: Imperial College London
+    orcid: 'https://orcid.org/0000-0003-2107-153X'
+  - given-names: Aron
+    family-names: Walsh
+    email: a.walsh@imperial.ac.uk
+    affiliation: Imperial College London
+    orcid: 'https://orcid.org/0000-0001-5460-7033'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.8101633
+repository-code: 'https://github.com/WMD-group/ElementEmbeddings'
+url: 'https://wmd-group.github.io/ElementEmbeddings/'
+abstract: >-
+  The Element Embeddings package provides high-level tools
+  for analysing elemental embedding data. This primarily
+  involves visualising the correlation between embedding
+  schemes using different statistical measures.
+keywords:
+  - materials science
+  - computational chemistry
+  - materials informatics
+  - statistics
+  - element representation
+license: MIT
+commit: d3f30602abf825ba3dcd5f247694a174a358ef49
+version: '0.1'
+date-released: '2023-06-30'

README.md

@@ -8,6 +8,8 @@ ElementEmbeddings
 [![CI Status](https://github.com/WMD-group/ElementEmbeddings/actions/workflows/ci.yml/badge.svg)](https://github.com/WMD-group/ElementEmbeddings/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/WMD-group/ElementEmbeddings/branch/main/graph/badge.svg?token=OCMIM5SHL0)](https://codecov.io/gh/WMD-group/ElementEmbeddings)
 [![DOI](https://zenodo.org/badge/493285385.svg)](https://zenodo.org/badge/latestdoi/493285385)
+![PyPI](https://img.shields.io/pypi/v/ElementEmbeddings)
+[![documentation](https://img.shields.io/badge/docs-mkdocs%20material-blue.svg?style=flat)](https://wmd-group.github.io/ElementEmbeddings/)
 
 The **Element Embeddings** package provides high-level tools for analysing elemental
 embeddings data. This primarily involves visualising the correlation between
@@ -33,7 +35,10 @@ importing the class.
 
 Installation
 --------
-
+The latest stable release can be installed via pip using:
+```bash
+pip install ElementEmbeddings
+```
 The latest version can be installed using:
 
 ```bash
@@ -46,7 +51,7 @@ To clone the repository and make a local installation, run the following command
 ```bash
 git clone https://github.com/WMD-group/ElementEmbeddings.git
 cd ElementEmbeddings
-pip install --user -e .
+pip install  -e .
 ```
 
 With -e pip will create links to the source folder so that changes to the code will be immediately reflected on the PATH.

setup.py

@@ -39,9 +39,14 @@
     ],
     classifiers=[
         "Programming Language :: Python",
-        "Development Status :: 3 - Alpha",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Development Status :: 4 - Beta",
         "Intended Audience :: Science/Research",
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Chemistry",
+        "License :: OSI Approved :: MIT License",
     ],
 )