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@github-actions github-actions released this 20 Nov 15:05
· 77 commits to main since this release
v1.4.0
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Learn about vigilant mode.

Changes

  • Minor documentation changes because of drevalpy command-line command
  • #270
  • #285
  • #304 Removed safety action: was unneccessary and always failing.
  • #307
    • Run tests: fail-fast: true to save some GitHub action resources
    • Restructured loader.py to reduce duplicated code
    • Gene lists are now in the meta directory of Zenodo to avoid duplication. Had to adapt the loaders to always download the meta/ directory and adapt load_and_select_gene_features to load the gene lists from meta/.
  • #315
    • Included data/meta in .gitignore because of new Zenodo structure
    • Updated README.md to now include expected demo runtimes and all commands to reproduce the manuscript results
    • Updated colab demo to contain expected results

Bug fixes

  • #263 Added missing dependabot label
  • #248 Added ignoring flake8 S615 in pre-commit yaml: it thought load_dataset loads from huggingface
  • #281 Fixed various bugs related to curve curator (e.g., the units of concentrations were inconsistent, now consistently uM)
  • #278 critical difference diagram p-values are now adjuted with Benjamini-Hochberg
  • #304 Fixed raytune, added tests
  • #307 Added pydantic dependency until new ray version because of ray-project/ray#58354: ray.tune automatically imports ray.train which requires pydantic

New features

  • #283, #293 New DrugGNN Model that uses drug-molecule graphs as inputs (and gene expression for the cell lines)
  • #284 New ChemBERTaNeuralNetwork that uses ChemBERTa pre-trained embeddings for the drugs
  • #304 drevalpy can now be installed with an optional ray dependency: pip install drevalpy[multiprocessing]
  • #281, #307 PDX_Bruna and BeatAML2 dataset added
  • #305 featurizer scripts for automatically creating drug features for new drugs in drevalpy/datasets/featurizer: ChemBERTa embeddings, drug graphs, and MolGNet embeddings + tests (are right now skipped because transformers and rdkit are not automatically installed)

Maintenance

  • updated actions and package versions
  • updated poetry version
  • #287 new memes
  • #304 Updated Python version for coverage action to 3.13.
  • #309
    • Updated summary png to include ChemBERTaNeuralNetwork, DrugGNN, BeatAML2, and PDX_Bruna.
    • Updated documentation to include DrugGNN API. Updated SimpleNeuralNetwork-related files where ChemBERTaNeuralNetwork wasn't yet mentioned.
    • Added documentation information to usage.rst.
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