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openproblems-bio / task_batch_integration Public

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Test

Add fine-tuned scGPT (#17) #120

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Add fine-tuned scGPT (#17)

Add fine-tuned scGPT (#17) #120

Summary
Jobs
- List components to test
  
  Test (embed_cell_types_jittered, control_methods, src/control_methods/embed_cell_types_jittered/c...
  
  Test (embed_cell_types, control_methods, src/control_methods/embed_cell_types/config.vsh.yaml, sr...
  
  Test (no_integration, control_methods, src/control_methods/no_integration/config.vsh.yaml, src/co...
  
  Test (shuffle_integration_by_batch, control_methods, src/control_methods/shuffle_integration_by_b...
  
  Test (shuffle_integration, control_methods, src/control_methods/shuffle_integration/config.vsh.ya...
  
  Test (shuffle_integration_by_cell_type, control_methods, src/control_methods/shuffle_integration_...
  
  Test (no_integration_batch, control_methods, src/control_methods/no_integration_batch/config.vsh....
  
  Test (isolated_label_asw, metrics, src/metrics/isolated_label_asw/config.vsh.yaml, src/metrics/is...
  
  Test (isolated_label_f1, metrics, src/metrics/isolated_label_f1/config.vsh.yaml, src/metrics/isol...
  
  Test (clustering_overlap, metrics, src/metrics/clustering_overlap/config.vsh.yaml, src/metrics/cl...
  
  Test (asw_batch, metrics, src/metrics/asw_batch/config.vsh.yaml, src/metrics/asw_batch/, python_s...
  
  Test (graph_connectivity, metrics, src/metrics/graph_connectivity/config.vsh.yaml, src/metrics/gr...
  
  Test (kbet, metrics, src/metrics/kbet/config.vsh.yaml, src/metrics/kbet/, python_script, metrics/...
  
  Test (pcr, metrics, src/metrics/pcr/config.vsh.yaml, src/metrics/pcr/, python_script, metrics/pcr)
  
  Test (cell_cycle_conservation, metrics, src/metrics/cell_cycle_conservation/config.vsh.yaml, src/...
  
  Test (hvg_overlap, metrics, src/metrics/hvg_overlap/config.vsh.yaml, src/metrics/hvg_overlap/, py...
  
  Test (asw_label, metrics, src/metrics/asw_label/config.vsh.yaml, src/metrics/asw_label/, python_s...
  
  Test (lisi, metrics, src/metrics/lisi/config.vsh.yaml, src/metrics/lisi/, python_script, metrics/...
  
  Test (transform, data_processors, src/data_processors/transform/config.vsh.yaml, src/data_process...
  
  Test (precompute_clustering_run, data_processors, src/data_processors/precompute_clustering_run/c...
  
  Test (precompute_clustering_merge, data_processors, src/data_processors/precompute_clustering_mer...
  
  Test (process_dataset, data_processors, src/data_processors/process_dataset/config.vsh.yaml, src/...
  
  Test (scanvi, methods, src/methods/scanvi/config.vsh.yaml, src/methods/scanvi/, python_script, me...
  
  Test (batchelor_fastmnn, methods, src/methods/batchelor_fastmnn/config.vsh.yaml, src/methods/batc...
  
  Test (mnnpy, methods, src/methods/mnnpy/config.vsh.yaml, src/methods/mnnpy/, python_script, metho...
  
  Test (scalex, methods, src/methods/scalex/config.vsh.yaml, src/methods/scalex/, python_script, me...
  
  Test (uce, methods, src/methods/uce/config.vsh.yaml, src/methods/uce/, python_script, methods/uce)
  
  Test (scprint, methods, src/methods/scprint/config.vsh.yaml, src/methods/scprint/, python_script,...
  
  Test (scgpt_finetuned, methods, src/methods/scgpt_finetuned/config.vsh.yaml, src/methods/scgpt_fi...
  
  Test (harmonypy, methods, src/methods/harmonypy/config.vsh.yaml, src/methods/harmonypy/, python_s...
  
  Test (scgpt_zeroshot, methods, src/methods/scgpt_zeroshot/config.vsh.yaml, src/methods/scgpt_zero...
  
  Test (liger, methods, src/methods/liger/config.vsh.yaml, src/methods/liger/, r_script, methods/li...
  
  Test (batchelor_mnn_correct, methods, src/methods/batchelor_mnn_correct/config.vsh.yaml, src/meth...
  
  Test (scimilarity, methods, src/methods/scimilarity/config.vsh.yaml, src/methods/scimilarity/, py...
  
  Test (pyliger, methods, src/methods/pyliger/config.vsh.yaml, src/methods/pyliger/, python_script,...
  
  Test (bbknn, methods, src/methods/bbknn/config.vsh.yaml, src/methods/bbknn/, python_script, metho...
  
  Test (scvi, methods, src/methods/scvi/config.vsh.yaml, src/methods/scvi/, python_script, methods/...
  
  Test (combat, methods, src/methods/combat/config.vsh.yaml, src/methods/combat/, python_script, me...
  
  Test (geneformer, methods, src/methods/geneformer/config.vsh.yaml, src/methods/geneformer/, pytho...
  
  Test (scanorama, methods, src/methods/scanorama/config.vsh.yaml, src/methods/scanorama/, python_s...
  
  Test (harmony, methods, src/methods/harmony/config.vsh.yaml, src/methods/harmony/, r_script, meth...
Run details
- Usage
- Workflow file

Usage Workflow file

Annotations

1 warning

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

test / Test (geneformer, methods, src/methods/geneformer/config.vsh.yaml, src/methods/geneformer/, pytho...

succeeded Jan 17, 2025 in 4m 36s

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