Code

Species#100

Code

Merged

AntObi merged 61 commits intomainWMD-group/ElementEmbeddings:mainfrom speciesWMD-group/ElementEmbeddings:speciesCopy head branch name to clipboardApr 9, 2024

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Commits

Commits on Oct 5, 2023

• Add .github/release.yml

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• Fix typo in docstring

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• Initial commit for EmbeddingBase

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• Refactored Embedding class

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• Update test_core.py

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• Update plotting functions due to refactor

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• Add pytest-mpl to dev requirements

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• Remove hidden dimension variables in __init__

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• Simplified plotter code

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• Add image tests

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• Add .idea/ to .gitignore

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• Add baseline images for pytest-mpl

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• Update GitHub actions ci.yml

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Commits on Oct 6, 2023

• Update dimension reduction tests

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• Add py3.11 to CI, show package versions

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• Fix with ruff, ran pre-commit

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• Add hash library path

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• Add hash comparison test to CI

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• Set adjusttext to false for umap plot test

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• Disable pytest-mpl test for umap plot (temp)

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Commits on Nov 3, 2023

• Update .pre-commit-config.yaml

  

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• Add parse_species function

  

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• Update test_utils.py

  

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Commits on Nov 6, 2023

• Fix parse_species to handle X0 cases

  

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• Add correlation & distance functions to Base class

  

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• Add functions to SpeciesEmbedding

  

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• Add config.py

  

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• Validate elements/species for computing correlation

  

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• Update Embedding tests for checking elements

  

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• Change load_data and citation methods to use config variables

  

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Commits on Nov 9, 2023

• Update __init__ in _base.py for the EmbeddingBase class

  

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• Add argument to allow users to select elements/species to include in the plot

  

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• Fix bug in 3D plotting

  

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  5db1b45

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• Remove __init__ constructor from Embedding and SpeciesEmbedding class

  

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• Updated test functions

  

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• Merge branch 'main' into species

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• use openTSNE instead of sklearn.manifold.TSNE

  

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• Add openTSNE to requirements

  

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• Update baseline tsne image

  

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• Remove dataframe methods from Embedding class

  

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• Add dataframe methods to base class

  

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• Update mpl hash library

  

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• Add species_embedding test file

  

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Commits on Nov 10, 2023

• Add SpeciesEmbedding tests

  

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• Add from_json method to SpeciesEmbedding class

  

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• Add tests for plotting SpeciesEmbedding class and update hashes

  

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• Add baseline images for pytest-mpl

  

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• Remove unused lines in composition module

  

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Commits on Jan 30, 2024

• Add crystalllm as a packaged representation

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• Add crystallm and specify palette for element groups

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• Fix palette for element groups

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• Add crystallm to README

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Commits on Mar 8, 2024

• Add function to get oxidation states

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• Fix parse_species function

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Commits on Apr 9, 2024

• Update .gitignore

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  6f43fe5

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• Merge branch 'main' into species

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  2a54d62

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• Add openTSNE to requirements

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  c786590

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• Update mpl tests

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• Update mpl tests

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• Add mpl hash

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• Disable hash comparison

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