Batch integration: partial reading (#460) #445

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Job	Run time
list	53s
build (datasets/processors/subsample, /home/runner/work/openproblems-v2/openproblems-v2/src/datas...	58s
build (datasets/processors/hvg, /home/runner/work/openproblems-v2/openproblems-v2/src/datasets/pr...	2m 44s
build (datasets/processors/svd, /home/runner/work/openproblems-v2/openproblems-v2/src/datasets/pr...	1m 12s
build (datasets/processors/knn, /home/runner/work/openproblems-v2/openproblems-v2/src/datasets/pr...	2m 11s
build (datasets/processors/pca, /home/runner/work/openproblems-v2/openproblems-v2/src/datasets/pr...	1m 2s
build (datasets/loaders/openproblems_v1_multimodal, /home/runner/work/openproblems-v2/openproblem...	13m 19s
build (datasets/loaders/openproblems_v1, /home/runner/work/openproblems-v2/openproblems-v2/src/da...	13m 11s
build (datasets/loaders/cellxgene_census, /home/runner/work/openproblems-v2/openproblems-v2/src/d...	2m 27s
build (datasets/loaders/cellxgene_census_from_source_h5ad, /home/runner/work/openproblems-v2/open...	3m 54s
build (datasets/loaders/openproblems_neurips2021_bmmc, /home/runner/work/openproblems-v2/openprob...	2m 20s
build (datasets/loaders/openproblems_neurips2022_pbmc, /home/runner/work/openproblems-v2/openprob...	1m 8s
build (datasets/normalization/prot_clr, /home/runner/work/openproblems-v2/openproblems-v2/src/dat...	1m 10s
build (datasets/normalization/log_cp, /home/runner/work/openproblems-v2/openproblems-v2/src/datas...	1m 4s
build (datasets/normalization/sqrt_cp, /home/runner/work/openproblems-v2/openproblems-v2/src/data...	1m 4s
build (datasets/normalization/l1_sqrt, /home/runner/work/openproblems-v2/openproblems-v2/src/data...	1m 31s
build (datasets/normalization/atac_tfidf, /home/runner/work/openproblems-v2/openproblems-v2/src/d...	2m 27s
build (datasets/normalization/log_scran_pooling, /home/runner/work/openproblems-v2/openproblems-v...	3m 16s
build (migration/check_migration_status, /home/runner/work/openproblems-v2/openproblems-v2/src/mi...	2m 5s
build (migration/list_git_shas, /home/runner/work/openproblems-v2/openproblems-v2/src/migration/l...	1m 12s
build (migration/update_bibtex, /home/runner/work/openproblems-v2/openproblems-v2/src/migration/u...	2m 44s
build (common/decompress_gzip, /home/runner/work/openproblems-v2/openproblems-v2/src/common/decom...	1m 14s
build (common/create_component, /home/runner/work/openproblems-v2/openproblems-v2/src/common/crea...	54s
build (common/check_yaml_schema, /home/runner/work/openproblems-v2/openproblems-v2/src/common/che...	1m 12s
build (common/extract_metadata, /home/runner/work/openproblems-v2/openproblems-v2/src/common/extr...	2m 6s
build (common/process_task_results/get_metric_info, /home/runner/work/openproblems-v2/openproblem...	1m 24s
build (common/process_task_results/get_method_info, /home/runner/work/openproblems-v2/openproblem...	2m 35s
build (common/process_task_results/generate_qc, /home/runner/work/openproblems-v2/openproblems-v2...	2m 5s
build (common/process_task_results/yaml_to_json, /home/runner/work/openproblems-v2/openproblems-v...	1m 6s
build (common/process_task_results/get_results, /home/runner/work/openproblems-v2/openproblems-v2...	1m 27s
build (common/process_task_results/get_task_info, /home/runner/work/openproblems-v2/openproblems-...	2m 30s
build (common/process_task_results/get_dataset_info, /home/runner/work/openproblems-v2/openproble...	2m 43s
build (common/sync_test_resources, /home/runner/work/openproblems-v2/openproblems-v2/src/common/s...	2m 1s
build (common/check_dataset_schema, /home/runner/work/openproblems-v2/openproblems-v2/src/common/...	1m 1s
build (common/create_task_readme, /home/runner/work/openproblems-v2/openproblems-v2/src/common/cr...	1m 56s
build (denoising/methods/alra, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/denois...	1m 51s
build (denoising/methods/magic, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/denoi...	1m 50s
build (denoising/methods/dca, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/denoisi...	4m 52s
build (denoising/methods/knn_smoothing, /home/runner/work/openproblems-v2/openproblems-v2/src/tas...	1m 46s
build (denoising/process_dataset, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/den...	2m 34s
build (denoising/control_methods/perfect_denoising, /home/runner/work/openproblems-v2/openproblem...	1m 4s
build (denoising/control_methods/no_denoising, /home/runner/work/openproblems-v2/openproblems-v2/...	1m 7s
build (denoising/metrics/poisson, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/den...	1m 17s
build (denoising/metrics/mse, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/denoisi...	1m 41s
build (spatial_decomposition/methods/stereoscope, /home/runner/work/openproblems-v2/openproblems-...	11m 52s
build (spatial_decomposition/methods/vanillanmf, /home/runner/work/openproblems-v2/openproblems-v...	2m 29s
build (spatial_decomposition/methods/rctd, /home/runner/work/openproblems-v2/openproblems-v2/src/...	25m 36s
build (spatial_decomposition/methods/nnls, /home/runner/work/openproblems-v2/openproblems-v2/src/...	1m 19s
build (spatial_decomposition/methods/tangram, /home/runner/work/openproblems-v2/openproblems-v2/s...	8m 49s
build (spatial_decomposition/methods/seurat, /home/runner/work/openproblems-v2/openproblems-v2/sr...	1m 35s
build (spatial_decomposition/methods/nmfreg, /home/runner/work/openproblems-v2/openproblems-v2/sr...	2m 31s
build (spatial_decomposition/methods/cell2location, /home/runner/work/openproblems-v2/openproblem...	10m 49s
build (spatial_decomposition/methods/destvi, /home/runner/work/openproblems-v2/openproblems-v2/sr...	10m 38s
build (spatial_decomposition/process_dataset, /home/runner/work/openproblems-v2/openproblems-v2/s...	1m 9s
build (spatial_decomposition/dataset_simulator, /home/runner/work/openproblems-v2/openproblems-v2...	2m 33s
build (spatial_decomposition/control_methods/random_proportions, /home/runner/work/openproblems-v...	1m 11s
build (spatial_decomposition/control_methods/true_proportions, /home/runner/work/openproblems-v2/...	1m 5s
build (spatial_decomposition/metrics/r2, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	2m 30s
build (predict_modality/methods/knnr_r, /home/runner/work/openproblems-v2/openproblems-v2/src/tas...	2m 35s
build (predict_modality/methods/lm, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/p...	2m 43s
build (predict_modality/methods/lmds_irlba_rf, /home/runner/work/openproblems-v2/openproblems-v2/...	3m 38s
build (predict_modality/methods/guanlab_dengkw_pm, /home/runner/work/openproblems-v2/openproblems...	3m 10s
build (predict_modality/methods/knnr_py, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	2m 3s
build (predict_modality/methods/simplemlp_predict, /home/runner/work/openproblems-v2/openproblems...	6m 16s
build (predict_modality/methods/simplemlp_train, /home/runner/work/openproblems-v2/openproblems-v...	6m 20s
build (predict_modality/methods/novel_predict, /home/runner/work/openproblems-v2/openproblems-v2/...	5m 51s
build (predict_modality/methods/novel_train, /home/runner/work/openproblems-v2/openproblems-v2/sr...	6m 6s
build (predict_modality/process_dataset, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	1m 12s
build (predict_modality/control_methods/solution, /home/runner/work/openproblems-v2/openproblems-...	1m 58s
build (predict_modality/control_methods/zeros, /home/runner/work/openproblems-v2/openproblems-v2/...	1m 13s
build (predict_modality/control_methods/random_predict, /home/runner/work/openproblems-v2/openpro...	1m 32s
build (predict_modality/control_methods/mean_per_gene, /home/runner/work/openproblems-v2/openprob...	1m 16s
build (predict_modality/metrics/correlation, /home/runner/work/openproblems-v2/openproblems-v2/sr...	1m 16s
build (predict_modality/metrics/mse, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/...	1m 10s
build (label_projection/methods/scanvi_scarches, /home/runner/work/openproblems-v2/openproblems-v...	9m 54s
build (label_projection/methods/logistic_regression, /home/runner/work/openproblems-v2/openproble...	1m 17s
build (label_projection/methods/scanvi, /home/runner/work/openproblems-v2/openproblems-v2/src/tas...	10m 50s
build (label_projection/methods/naive_bayes, /home/runner/work/openproblems-v2/openproblems-v2/sr...	1m 35s
build (label_projection/methods/xgboost, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	3m 38s
build (label_projection/methods/knn, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/...	1m 13s
build (label_projection/methods/mlp, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/...	3m 6s
build (label_projection/process_dataset, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	1m 11s
build (label_projection/control_methods/true_labels, /home/runner/work/openproblems-v2/openproble...	1m 12s
build (label_projection/control_methods/majority_vote, /home/runner/work/openproblems-v2/openprob...	1m 11s
build (label_projection/control_methods/random_labels, /home/runner/work/openproblems-v2/openprob...	2m 33s
build (label_projection/metrics/accuracy, /home/runner/work/openproblems-v2/openproblems-v2/src/t...	1m 8s
build (label_projection/metrics/f1, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/l...	2m 33s
build (dimensionality_reduction/methods/densmap, /home/runner/work/openproblems-v2/openproblems-v...	2m 10s
build (dimensionality_reduction/methods/simlr, /home/runner/work/openproblems-v2/openproblems-v2/...	1m 53s
build (dimensionality_reduction/methods/ivis, /home/runner/work/openproblems-v2/openproblems-v2/s...	4m 44s
build (dimensionality_reduction/methods/umap, /home/runner/work/openproblems-v2/openproblems-v2/s...	1m 49s
build (dimensionality_reduction/methods/lmds, /home/runner/work/openproblems-v2/openproblems-v2/s...	1m 19s
build (dimensionality_reduction/methods/pymde, /home/runner/work/openproblems-v2/openproblems-v2/...	10m 2s
build (dimensionality_reduction/methods/neuralee, /home/runner/work/openproblems-v2/openproblems-...	10m 51s
build (dimensionality_reduction/methods/phate, /home/runner/work/openproblems-v2/openproblems-v2/...	2m 40s
build (dimensionality_reduction/methods/pca, /home/runner/work/openproblems-v2/openproblems-v2/sr...	2m 24s
build (dimensionality_reduction/methods/diffusion_map, /home/runner/work/openproblems-v2/openprob...	1m 24s
build (dimensionality_reduction/methods/tsne, /home/runner/work/openproblems-v2/openproblems-v2/s...	3m 15s
build (dimensionality_reduction/process_dataset, /home/runner/work/openproblems-v2/openproblems-v...	2m 44s
build (dimensionality_reduction/control_methods/random_features, /home/runner/work/openproblems-v...	2m 14s
build (dimensionality_reduction/control_methods/spectral_features, /home/runner/work/openproblems...	1m 25s
build (dimensionality_reduction/control_methods/true_features, /home/runner/work/openproblems-v2/...	1m 11s
build (dimensionality_reduction/metrics/trustworthiness, /home/runner/work/openproblems-v2/openpr...	1m 20s
build (dimensionality_reduction/metrics/density_preservation, /home/runner/work/openproblems-v2/o...	1m 33s
build (dimensionality_reduction/metrics/coranking, /home/runner/work/openproblems-v2/openproblems...	2m 45s
build (dimensionality_reduction/metrics/clustering_performance, /home/runner/work/openproblems-v2...	2m 26s
build (dimensionality_reduction/metrics/distance_correlation, /home/runner/work/openproblems-v2/o...	2m 5s
build (batch_integration/methods/scvi, /home/runner/work/openproblems-v2/openproblems-v2/src/task...	11m 7s
build (batch_integration/methods/fastmnn_embedding, /home/runner/work/openproblems-v2/openproblem...	2m 46s
build (batch_integration/methods/fastmnn_feature, /home/runner/work/openproblems-v2/openproblems-...	2m 22s
build (batch_integration/methods/scanorama_embed, /home/runner/work/openproblems-v2/openproblems-...	2m 21s
build (batch_integration/methods/pyliger, /home/runner/work/openproblems-v2/openproblems-v2/src/t...	3m 50s
build (batch_integration/methods/scanvi, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	9m 39s
build (batch_integration/methods/combat, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	2m 36s
build (batch_integration/methods/mnn_correct, /home/runner/work/openproblems-v2/openproblems-v2/s...	3m 2s
build (batch_integration/methods/scalex_embed, /home/runner/work/openproblems-v2/openproblems-v2/...	9m 5s
build (batch_integration/methods/scalex_feature, /home/runner/work/openproblems-v2/openproblems-v...	7m 44s
build (batch_integration/methods/liger, /home/runner/work/openproblems-v2/openproblems-v2/src/tas...	2m 53s
build (batch_integration/methods/bbknn, /home/runner/work/openproblems-v2/openproblems-v2/src/tas...	2m 9s
build (batch_integration/methods/mnnpy, /home/runner/work/openproblems-v2/openproblems-v2/src/tas...	2m 12s
build (batch_integration/methods/scanorama_feature, /home/runner/work/openproblems-v2/openproblem...	2m 19s
build (batch_integration/process_dataset, /home/runner/work/openproblems-v2/openproblems-v2/src/t...	1m 14s
build (batch_integration/control_methods/perfect_integration/celltype_embed, /home/runner/work/op...	1m 10s
build (batch_integration/control_methods/perfect_integration/celltype_jitter_embed, /home/runner/...	2m 43s
build (batch_integration/control_methods/random_integration/global_graph, /home/runner/work/openp...	1m 54s
build (batch_integration/control_methods/random_integration/global_feature, /home/runner/work/ope...	2m 40s
build (batch_integration/control_methods/random_integration/celltype_embed, /home/runner/work/ope...	1m 22s
build (batch_integration/control_methods/random_integration/celltype_feature, /home/runner/work/o...	2m 20s
build (batch_integration/control_methods/random_integration/batch_graph, /home/runner/work/openpr...	1m 49s
build (batch_integration/control_methods/random_integration/celltype_graph, /home/runner/work/ope...	1m 19s
build (batch_integration/control_methods/random_integration/batch_embed, /home/runner/work/openpr...	1m 17s
build (batch_integration/control_methods/random_integration/global_embed, /home/runner/work/openp...	2m 42s
build (batch_integration/control_methods/random_integration/batch_feature, /home/runner/work/open...	1m 13s
build (batch_integration/control_methods/no_integration/global_graph, /home/runner/work/openprobl...	2m 5s
build (batch_integration/control_methods/no_integration/global_feature, /home/runner/work/openpro...	2m 13s
build (batch_integration/control_methods/no_integration/batch_embed, /home/runner/work/openproble...	1m 9s
build (batch_integration/control_methods/no_integration/global_embed, /home/runner/work/openprobl...	1m 9s
build (batch_integration/transformers/embed_to_graph, /home/runner/work/openproblems-v2/openprobl...	1m 7s
build (batch_integration/transformers/feature_to_embed, /home/runner/work/openproblems-v2/openpro...	1m 11s
build (batch_integration/metrics/clustering_overlap, /home/runner/work/openproblems-v2/openproble...	2m 26s
build (batch_integration/metrics/isolated_label_asw, /home/runner/work/openproblems-v2/openproble...	2m 1s
build (batch_integration/metrics/isolated_label_f1, /home/runner/work/openproblems-v2/openproblem...	1m 20s
build (batch_integration/metrics/cell_cycle_conservation, /home/runner/work/openproblems-v2/openp...	1m 18s
build (batch_integration/metrics/asw_batch, /home/runner/work/openproblems-v2/openproblems-v2/src...	2m 34s
build (batch_integration/metrics/pcr, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks...	2m 28s
build (batch_integration/metrics/graph_connectivity, /home/runner/work/openproblems-v2/openproble...	1m 11s
build (batch_integration/metrics/hvg_overlap, /home/runner/work/openproblems-v2/openproblems-v2/s...	2m 30s
build (batch_integration/metrics/asw_label, /home/runner/work/openproblems-v2/openproblems-v2/src...	1m 25s
build (batch_integration/metrics/kbet, /home/runner/work/openproblems-v2/openproblems-v2/src/task...	1m 18s
build (match_modalities/methods/procrustes, /home/runner/work/openproblems-v2/openproblems-v2/src...	1m 24s
build (match_modalities/methods/harmonic_alignment, /home/runner/work/openproblems-v2/openproblem...	1m 13s
build (match_modalities/methods/fastmnn, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	1m 58s
build (match_modalities/methods/scot, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks...	13m 31s
build (match_modalities/process_dataset, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	1m 7s
build (match_modalities/control_methods/random_features, /home/runner/work/openproblems-v2/openpr...	1m 54s
build (match_modalities/control_methods/true_features, /home/runner/work/openproblems-v2/openprob...	1m 59s
build (match_modalities/metrics/knn_auc, /home/runner/work/openproblems-v2/openproblems-v2/src/ta...	1m 16s
build (match_modalities/metrics/mse, /home/runner/work/openproblems-v2/openproblems-v2/src/tasks/...	3m 25s
	7h 59m 8s

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Batch integration: partial reading (#460) #445

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Batch integration: partial reading (#460) #445

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