From c4e19284a89e0783cafac80335083d2f3f503325 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 11 Jun 2025 13:10:39 +0200 Subject: [PATCH] Update image version to :1 --- src/common/check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_yaml_schema/config.vsh.yaml | 2 +- src/common/create_task_readme/config.vsh.yaml | 2 +- src/common/extract_metadata/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/common/ontology/check_obsolete_terms/config.vsh.yaml | 2 +- src/common/process_task_results/generate_qc/config.vsh.yaml | 2 +- src/common/process_task_results/get_api_info/config.vsh.yaml | 2 +- .../process_task_results/get_dataset_info/config.vsh.yaml | 2 +- src/common/process_task_results/get_method_info/config.vsh.yaml | 2 +- src/common/process_task_results/get_metric_info/config.vsh.yaml | 2 +- src/common/process_task_results/get_results/config.vsh.yaml | 2 +- src/common/process_task_results/get_task_info/config.vsh.yaml | 2 +- src/common/process_task_results/yaml_to_json/config.vsh.yaml | 2 +- src/datasets/loaders/cellxgene_census/config.vsh.yaml | 2 +- .../loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml | 2 +- .../loaders/openproblems_neurips2021_bmmc/config.vsh.yaml | 2 +- .../loaders/openproblems_neurips2022_pbmc/config.vsh.yaml | 2 +- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 2 +- src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml | 2 +- src/datasets/normalization/atac_tfidf/config.vsh.yaml | 2 +- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 2 +- src/datasets/normalization/log_cp/config.vsh.yaml | 2 +- src/datasets/normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/prot_clr/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cp/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- src/datasets/processors/subsample/config.vsh.yaml | 2 +- src/datasets/processors/svd/config.vsh.yaml | 2 +- src/migration/check_migration_status/config.vsh.yaml | 2 +- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- .../control_methods/no_integration/batch_embed/config.vsh.yaml | 2 +- .../control_methods/no_integration/global_embed/config.vsh.yaml | 2 +- .../no_integration/global_feature/config.vsh.yaml | 2 +- .../control_methods/no_integration/global_graph/config.vsh.yaml | 2 +- .../perfect_integration/celltype_embed/config.vsh.yaml | 2 +- .../perfect_integration/celltype_jitter_embed/config.vsh.yaml | 2 +- .../random_integration/batch_embed/config.vsh.yaml | 2 +- .../random_integration/batch_feature/config.vsh.yaml | 2 +- .../random_integration/batch_graph/config.vsh.yaml | 2 +- .../random_integration/celltype_embed/config.vsh.yaml | 2 +- .../random_integration/celltype_feature/config.vsh.yaml | 2 +- .../random_integration/celltype_graph/config.vsh.yaml | 2 +- .../random_integration/global_embed/config.vsh.yaml | 2 +- .../random_integration/global_feature/config.vsh.yaml | 2 +- .../random_integration/global_graph/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/bbknn/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 2 +- .../batch_integration/methods/fastmnn_embedding/config.vsh.yaml | 2 +- .../batch_integration/methods/fastmnn_feature/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/liger/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/pyliger/config.vsh.yaml | 2 +- .../batch_integration/methods/scalex_embed/config.vsh.yaml | 2 +- .../batch_integration/methods/scalex_feature/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_feature/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scanvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml | 2 +- .../metrics/cell_cycle_conservation/config.vsh.yaml | 2 +- .../metrics/clustering_overlap/config.vsh.yaml | 2 +- .../metrics/graph_connectivity/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml | 2 +- .../metrics/isolated_label_asw/config.vsh.yaml | 2 +- .../batch_integration/metrics/isolated_label_f1/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/kbet/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/lisi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/pcr/config.vsh.yaml | 2 +- src/tasks/batch_integration/process_dataset/config.vsh.yaml | 2 +- .../transformers/embed_to_graph/config.vsh.yaml | 2 +- .../transformers/feature_to_embed/config.vsh.yaml | 2 +- .../denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- .../denoising/control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/tasks/denoising/methods/alra/config.vsh.yaml | 2 +- src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/tasks/denoising/methods/magic/config.vsh.yaml | 2 +- src/tasks/denoising/methods/saver/config.vsh.yaml | 2 +- src/tasks/denoising/metrics/mse/config.vsh.yaml | 2 +- src/tasks/denoising/metrics/poisson/config.vsh.yaml | 2 +- src/tasks/denoising/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/spectral_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/densmap/config.vsh.yaml | 2 +- .../methods/diffusion_map/config.vsh.yaml | 2 +- src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml | 2 +- src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/neuralee/config.vsh.yaml | 2 +- src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/pymde/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/simlr/config.vsh.yaml | 2 +- src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- .../metrics/clustering_performance/config.vsh.yaml | 2 +- .../dimensionality_reduction/metrics/coranking/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 2 +- .../metrics/distance_correlation/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../dimensionality_reduction/process_dataset/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/knn/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/mlp/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/scanvi/config.vsh.yaml | 2 +- .../label_projection/methods/scanvi_scarches/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/xgboost/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/f1/config.vsh.yaml | 2 +- src/tasks/label_projection/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml | 2 +- .../match_modalities/methods/harmonic_alignment/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/procrustes/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/scot/config.vsh.yaml | 2 +- src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml | 2 +- src/tasks/match_modalities/metrics/mse/config.vsh.yaml | 2 +- src/tasks/match_modalities/process_dataset/config.vsh.yaml | 2 +- .../control_methods/meanpergene/config.vsh.yaml | 2 +- .../control_methods/random_predict/config.vsh.yaml | 2 +- .../predict_modality/control_methods/solution/config.vsh.yaml | 2 +- .../predict_modality/control_methods/zeros/config.vsh.yaml | 2 +- .../predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/lm/config.vsh.yaml | 2 +- .../predict_modality/methods/lmds_irlba_rf/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml | 2 +- .../predict_modality/methods/novel/predict/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/novel/train/config.vsh.yaml | 2 +- .../predict_modality/methods/random_forest/config.vsh.yaml | 2 +- .../predict_modality/methods/simple_mlp/predict/config.vsh.yaml | 2 +- .../predict_modality/methods/simple_mlp/train/config.vsh.yaml | 2 +- src/tasks/predict_modality/metrics/correlation/config.vsh.yaml | 2 +- src/tasks/predict_modality/metrics/mse/config.vsh.yaml | 2 +- src/tasks/predict_modality/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_proportions/config.vsh.yaml | 2 +- .../control_methods/true_proportions/config.vsh.yaml | 2 +- .../spatial_decomposition/dataset_simulator/config.vsh.yaml | 2 +- .../spatial_decomposition/methods/cell2location/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml | 2 +- .../spatial_decomposition/methods/stereoscope/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml | 2 +- .../spatial_decomposition/methods/vanillanmf/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml | 2 +- src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml | 2 +- 160 files changed, 160 insertions(+), 160 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 08449c3e7d..bdba77fa45 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: python packages: viashpy diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml index b87bec5429..22d3384783 100644 --- a/src/common/check_yaml_schema/config.vsh.yaml +++ b/src/common/check_yaml_schema/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index d268974ce8..3d93002b1a 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: dest: openproblems-v2/_viash.yaml platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, processx] diff --git a/src/common/extract_metadata/config.vsh.yaml b/src/common/extract_metadata/config.vsh.yaml index 76e73cb975..eeeef991d8 100644 --- a/src/common/extract_metadata/config.vsh.yaml +++ b/src/common/extract_metadata/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: python packages: viashpy diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 72270b7a95..aeac948f53 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/ontology/check_obsolete_terms/config.vsh.yaml b/src/common/ontology/check_obsolete_terms/config.vsh.yaml index fc006f6cf9..5bac2b8acc 100644 --- a/src/common/ontology/check_obsolete_terms/config.vsh.yaml +++ b/src/common/ontology/check_obsolete_terms/config.vsh.yaml @@ -70,7 +70,7 @@ functionality: - path: /resources_test/common/cellxgene_census platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r packages: [ dplyr, tidyr, tibble, ontologyIndex, processx ] \ No newline at end of file diff --git a/src/common/process_task_results/generate_qc/config.vsh.yaml b/src/common/process_task_results/generate_qc/config.vsh.yaml index 68a5d19682..7ad363ad62 100644 --- a/src/common/process_task_results/generate_qc/config.vsh.yaml +++ b/src/common/process_task_results/generate_qc/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_api_info/config.vsh.yaml b/src/common/process_task_results/get_api_info/config.vsh.yaml index 0e7eb1696e..2c225b2da1 100644 --- a/src/common/process_task_results/get_api_info/config.vsh.yaml +++ b/src/common/process_task_results/get_api_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_dataset_info/config.vsh.yaml b/src/common/process_task_results/get_dataset_info/config.vsh.yaml index 10247a22ba..ba280462e3 100644 --- a/src/common/process_task_results/get_dataset_info/config.vsh.yaml +++ b/src/common/process_task_results/get_dataset_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_method_info/config.vsh.yaml b/src/common/process_task_results/get_method_info/config.vsh.yaml index 053bbac53c..cd3c93ffae 100644 --- a/src/common/process_task_results/get_method_info/config.vsh.yaml +++ b/src/common/process_task_results/get_method_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_metric_info/config.vsh.yaml b/src/common/process_task_results/get_metric_info/config.vsh.yaml index ee5833b5b9..b8e3c12c5e 100644 --- a/src/common/process_task_results/get_metric_info/config.vsh.yaml +++ b/src/common/process_task_results/get_metric_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index cd639fad4d..2d5261906c 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ purrr, yaml, rlang, dplyr, tidyr, readr, lubridate, dynutils, processx ] diff --git a/src/common/process_task_results/get_task_info/config.vsh.yaml b/src/common/process_task_results/get_task_info/config.vsh.yaml index 2e8fbd2b66..db79f96a10 100644 --- a/src/common/process_task_results/get_task_info/config.vsh.yaml +++ b/src/common/process_task_results/get_task_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/yaml_to_json/config.vsh.yaml b/src/common/process_task_results/yaml_to_json/config.vsh.yaml index 7231cdcdbf..8ea76caf7d 100644 --- a/src/common/process_task_results/yaml_to_json/config.vsh.yaml +++ b/src/common/process_task_results/yaml_to_json/config.vsh.yaml @@ -11,6 +11,6 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow - type: native diff --git a/src/datasets/loaders/cellxgene_census/config.vsh.yaml b/src/datasets/loaders/cellxgene_census/config.vsh.yaml index 667e1c6a6b..e501da3a5e 100644 --- a/src/datasets/loaders/cellxgene_census/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census/config.vsh.yaml @@ -151,7 +151,7 @@ functionality: path: test.py platforms: - type: docker - #image: openproblems/base_python:1.0.0 + #image: openproblems/base_python:1 image: python:3.11 setup: - type: python diff --git a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml index 7ee4166d9d..effd7dc92f 100644 --- a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml @@ -114,7 +114,7 @@ functionality: path: test.py platforms: - type: docker - #image: openproblems/base_python:1.0.0 + #image: openproblems/base_python:1 image: python:3.11 setup: - type: python diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml index 96dad30e76..bf926fe49a 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [highmem, midcpu, midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml index b2141482f1..6a783deef6 100644 --- a/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml @@ -74,7 +74,7 @@ functionality: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ highmem, midcpu, midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index a07a60d0ac..5d709677c8 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -72,7 +72,7 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: apt packages: git diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 812e52be62..d3ec2d5bd7 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -80,7 +80,7 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: apt packages: git diff --git a/src/datasets/normalization/atac_tfidf/config.vsh.yaml b/src/datasets/normalization/atac_tfidf/config.vsh.yaml index 5a8f56306a..ca57f451ee 100644 --- a/src/datasets/normalization/atac_tfidf/config.vsh.yaml +++ b/src/datasets/normalization/atac_tfidf/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 212eadc968..1a557df875 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index 89b2a283f9..3c35dd5f08 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell. When set to -1, will use None." platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 4cbf81ff5a..0d22e85c69 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ Matrix, rlang, scran, BiocParallel ] diff --git a/src/datasets/normalization/prot_clr/config.vsh.yaml b/src/datasets/normalization/prot_clr/config.vsh.yaml index 8f6bbe269f..80f02759f2 100644 --- a/src/datasets/normalization/prot_clr/config.vsh.yaml +++ b/src/datasets/normalization/prot_clr/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index 4d95636f4c..52d25d933a 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index aed18c6d38..0f0517c3f1 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 9908fe9086..889d2c7e06 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 7f0213b922..07ec578bee 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 4e52e93db5..2a03db8c70 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: python packages: diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index bbad17f58c..448937e555 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: [scikit-learn] diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index bd8107381c..7d2b43acc0 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,6 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow - type: native diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index c70366612a..068157ebea 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 147e0b6c22..662425be7b 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml index c2484fbaa2..0e2387330d 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml index 95212518c5..1c123a63bd 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml index b20701c8f1..66b6944c1a 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml index 86886ce263..59436b8f86 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml index 6c853a7719..c09b177228 100644 --- a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml index e945e3bc58..795aef68d4 100644 --- a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml index d8bcee01d4..8e9e2ffa4f 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml index 5f98284bb9..f446293e13 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml index 72a12c5031..4e65cd9edf 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml index b4457498c9..9b023bfc73 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml index 7c483739c2..9db3c4194e 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml index 6015185616..6b01f2e0a0 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml index 0343c37817..6095691b02 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml index f49ee146a1..f987815aea 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml index 1b92cbc70a..5e002ad259 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 8eff37339f..eb477c01ab 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index f94333627d..3f64d02605 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, lowcpu] diff --git a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index cd885da3cd..8c3a8758a8 100644 --- a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: ../fastmnn_feature/script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r bioc: diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index e28406eb54..3e10186b78 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r bioc: batchelor diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index 4c638d467b..ba06f1ecc9 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: apt packages: cmake diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 1c999fa540..1b3b8104b1 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r bioc: diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index cf16b2e684..ef431ff7cd 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index 3437df19c9..d64905ca00 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index 1874bc190e..475afae407 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index b5dcd8f54a..57a64be3f2 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 3f735ddffd..efe199c8ba 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 5615fd72cd..3d430fa400 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 45eb09d5cf..474d7eab2d 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index be6567271c..a58a331df5 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -40,7 +40,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 068381b9e3..0de87aed5b 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 3852029a60..9a9dedad7f 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 8d92033e40..8b3b67f3a9 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -51,7 +51,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml index 6384feca62..2f4c582c34 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml index a8025783d6..41447f4f0f 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml index 65e1970c4f..19e0d99f17 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -30,7 +30,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml index 6b8f0703bf..1d5c88cb15 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml index aca556a8fc..5b2307a186 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r github: theislab/kBET diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml index 750574f84a..3218637fc3 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index d3391fb528..f5508841fc 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 73ea5815c3..aa141c2182 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index e841081a91..35b1d9e204 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index e08013c63b..1429b05437 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, midmem, lowcpu] diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index 64a35f9986..e8b0ce01d0 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index b16862360b..a6d0e14283 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 374d317fce..12fd2de5d0 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ Matrix, rsvd ] diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index b0c55ae0d8..85a07635ff 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 380666a1b5..bbd72c3e73 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/tasks/denoising/methods/saver/config.vsh.yaml b/src/tasks/denoising/methods/saver/config.vsh.yaml index 3c997fc36f..f7119bbdee 100644 --- a/src/tasks/denoising/methods/saver/config.vsh.yaml +++ b/src/tasks/denoising/methods/saver/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r github: mohuangx/SAVER diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 8330a8de31..8622ea23b9 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index e523a9306e..f21fba9d4b 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pip: scprep diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index c9b5b06c1a..f37e1cb641 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: helper.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 6c0d36ad44..280b8e0da9 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, highcpu] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml index b3ae5aa95b..65c9f9be61 100644 --- a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index a83d393072..b1662d4a4e 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index ff5764a561..c5f8eb0960 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index ced082c708..dbcf58de67 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: default: 3 platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r bioc: destiny diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index aa3c5ca0b4..6f25faf7ec 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml index 2b651271a9..cdbfe8e888 100644 --- a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ Matrix, lmds ] diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 0d3d0234c4..82e000fbc4 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -44,7 +44,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 11d3841fb6..ac59850c1d 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index ff63659780..7f13c807dd 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml index 2f733bb714..dd84efcf42 100644 --- a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: pymde diff --git a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml index ba4b7b3b84..896b6552cc 100644 --- a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml @@ -45,7 +45,7 @@ functionality: platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r packages: [ grDevices ] diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index cedaba0484..329704cfb7 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: apt packages: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index a073e9dbe3..57362aeda6 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -39,7 +39,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml index 67f1078f13..4a4909b88d 100644 --- a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml @@ -51,7 +51,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: [ scikit-learn, scanpy, leidenalg ] diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 6787e88f7e..f512eaf8fe 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -157,7 +157,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ coRanking ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 4b1e9f3a32..c26f34c0e9 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -30,7 +30,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index b08c93db2c..eceec0adae 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 5f75fa8e26..f4e866c42a 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index d6f62e0c7e..8c70709143 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, highcpu] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index 8f0915a1dd..c1fc963771 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index 728157a644..78111b9d6d 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scanpy diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index ec536fcc7d..b1f2da695b 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index 499fa69e81..81216d8cee 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: [scikit-learn, jsonschema] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 88f4c2d5af..894ec307dd 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index 9c7e92fc68..e52d99f27a 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml index 90f6e72a52..2da2bbcef4 100644 --- a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml +++ b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 6c36ead072..7e211ff8ef 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python packages: diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index ccf2f449b4..d3d72cafc8 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python pypi: scvi-tools>=1.1.0 diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index d51b532917..091a1dd0fb 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ Matrix>=1.5.3, Seurat, rlang ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index 516308fbdd..bc5264f848 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: xgboost diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index 8fc7021ffa..8bb44b34e6 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index f5abc0caa6..aa69ab459d 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index aa010876cb..f6a4e1bec4 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [highmem, midcpu , midtime] diff --git a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml index 8c021c3bdf..106c62a141 100644 --- a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml index bc897dd821..46aa901b00 100644 --- a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml index 4e143ec67b..da4e6a60c8 100644 --- a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r bioc: batchelor diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml index 3146db56e0..3a977b479b 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python github: diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml index db7b49383b..def58ab8f2 100644 --- a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index e86fe4438a..fe3c9bc0dd 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: apt packages: git diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index e7067a20b5..2125b7f343 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index b1dfc15746..67d4067759 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/match_modalities/process_dataset/config.vsh.yaml b/src/tasks/match_modalities/process_dataset/config.vsh.yaml index 35dc757809..d08bf4b369 100644 --- a/src/tasks/match_modalities/process_dataset/config.vsh.yaml +++ b/src/tasks/match_modalities/process_dataset/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [highmem, midcpu , midtime] diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml index 9521b90508..6ab24de2c8 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml index 3324c53a91..d9b00f89aa 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml index 350b0e79ea..1585fa198c 100644 --- a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml index 344df9c338..4d9e248e7a 100644 --- a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml index 8663123ad9..5de87e60b7 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 543ee71fa1..640c2fe7d0 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [hightime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index 448b3ca0b8..65e717783d 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ lmds, FNN, proxyC] diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 3fdbc0f243..d007559411 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ lmds, RcppArmadillo, pbapply] diff --git a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml index ba86f0631e..6397db329f 100644 --- a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [lmds, ranger, pbapply, irlba] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index 385f1234bb..c0a2da974c 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ lmds, FNN, proxy, proxyC ] diff --git a/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml index 72e3292407..8e10050645 100644 --- a/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: - path: ../helper_functions.py platforms: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python packages: diff --git a/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml index 87ea471301..36da84970a 100644 --- a/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: - path: ../helper_functions.py platforms: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python packages: diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index a1ee69041d..7dcfc32daa 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ lmds, ranger, pbapply] diff --git a/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml b/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml index ef972e416f..f2ba748919 100644 --- a/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: platforms: - type: docker # image: pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 # run_args: ["--gpus all --ipc=host"] setup: - type: python diff --git a/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml b/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml index 8bcf75b97d..cfc950e325 100644 --- a/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: platforms: - type: docker # image: pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 # run_args: ["--gpus all --ipc=host"] setup: - type: python diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml index 9d297a147d..c61759a13f 100644 --- a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -56,7 +56,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ proxyC, testthat, dynutils ] diff --git a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml index 78fbcc8efc..de8318fac2 100644 --- a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index ec52472896..24d0655399 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.R platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 - type: nextflow directives: label: [hightime, highmem, highcpu] diff --git a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml index 4134e7b7d5..f1e38658e7 100644 --- a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: numpy diff --git a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml index 0c58473acc..f7a78c33fa 100644 --- a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: native - type: nextflow directives: diff --git a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml index 5295a9e79d..6456a31d4f 100644 --- a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml @@ -191,7 +191,7 @@ functionality: dest: resources_test/common/cxg_mouse_pancreas_atlas platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: [numpy, scanpy] diff --git a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml index 14ca1fb518..48f45bfdb1 100644 --- a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml @@ -71,7 +71,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml index 3a642e0a23..fcd0e676af 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: platforms: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml index 0d32f2d410..be7169885c 100644 --- a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml index 100458b95a..b04df59f4a 100644 --- a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml index 57ab923a75..61d82b8766 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [ Matrix, pak ] diff --git a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml index 86c15cff30..4c4bcae6ba 100644 --- a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: platforms: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: [Matrix, Seurat] diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml index 4c8ca98bb1..b1c5d11086 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: platforms: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml index 652b276927..141bf72edf 100644 --- a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: tangram-sc diff --git a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml index 7b04a40e93..bcd21e5ff8 100644 --- a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml index 96679c5be4..7ced2c765a 100644 --- a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml index d6f62e0c7e..8c70709143 100644 --- a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 - type: nextflow directives: label: [midtime, highmem, highcpu]