development #198
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development #198
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# Conflicts: # immuneML/encodings/protein_embedding/ProtT5Encoder.py # immuneML/encodings/protein_embedding/ProteinEmbeddingEncoder.py # immuneML/encodings/protein_embedding/TCRBertEncoder.py # immuneML/ml_methods/clustering/AgglomerativeClustering.py # immuneML/ml_methods/clustering/DBSCAN.py # immuneML/ml_methods/generative_models/SimpleVAE.py # immuneML/preprocessing/filters/MetadataFilter.py # immuneML/reports/data_reports/CompAIRRClusteringReport.py # immuneML/reports/data_reports/SequenceLengthDistribution.py # immuneML/reports/encoding_reports/DimensionalityReduction.py # requirements.txt # test/preprocessing/filters/test_metadataFilter.py # test/reports/data_reports/test_sequenceLengthDistribution.py
…ser to omit locus
…ser to omit locus
# Conflicts: # immuneML/config/default_params/ml_methods/sonnia_params.yaml # requirements.txt
…n VJGeneDistribution.py
…rwriting report results when running multiple models
* feat: add skeleton for ProGen model * feat: implement sequence generation for progen and update setup * feat: add default progen params, update files names, clean save_model and remove affixes * feat: update save model function * refactor: cleanup of Progen and updating progen test * chore: add detailed documentation for ProGen class and include license file * test: add dummy progen to the test instead of downloading full model * core: clean dependencies
# Conflicts: # immuneML/IO/dataset_export/AIRRExporter.py # immuneML/environment/Constants.py # immuneML/ml_methods/dim_reduction/DimRedMethod.py # immuneML/preprocessing/filters/ChainRepertoireFilter.py # immuneML/presentation/html/Util.py # immuneML/reports/clustering_method_reports/ClusteringVisualization.py # immuneML/reports/clustering_reports/ClusteringStabilityReport.py # immuneML/reports/data_reports/AminoAcidFrequencyDistribution.py # immuneML/reports/data_reports/LabelDist.py # immuneML/reports/data_reports/RepertoireClonotypeSummary.py # immuneML/reports/data_reports/ShannonDiversityOverview.py # immuneML/reports/data_reports/TrueMotifsSummaryBarplot.py # immuneML/reports/encoding_reports/DimensionalityReduction.py # immuneML/reports/ml_reports/ConfusionMatrix.py # immuneML/workflows/instructions/clustering/ClusteringRunner.py # immuneML/workflows/instructions/train_gen_model/TrainGenModelInstruction.py # pyproject.toml # test/preprocessing/filters/test_chainRepertoireFilter.py
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