From 2077e79e1793e34d2975d1bbbd90de2ee83834c1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 12 Oct 2023 20:25:30 +0200 Subject: [PATCH] bump base images to base_*:1.0.2 (#263) --- src/common/check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_yaml_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 4 ++-- src/common/create_task_readme/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/common/get_api_info/config.vsh.yaml | 2 +- src/common/get_method_info/config.vsh.yaml | 2 +- src/common/get_metric_info/config.vsh.yaml | 2 +- src/common/get_results/config.vsh.yaml | 2 +- src/common/get_task_info/config.vsh.yaml | 2 +- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 2 +- .../loaders/openproblems_v1_multimodal/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/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/config.vsh.yaml | 2 +- .../control_methods/random_embed_cell/config.vsh.yaml | 2 +- .../control_methods/random_embed_cell_jitter/config.vsh.yaml | 2 +- .../control_methods/random_integration/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/bbknn/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/liger/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/pyliger/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../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 +- .../batch_integration/metrics/hvg_overlap/config.vsh.yaml | 2 +- .../metrics/isolated_label_asw/config.vsh.yaml | 2 +- .../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 +- 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 +- .../dimensionality_reduction/methods/ivis/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/neuralee/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/pca/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- .../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 +- .../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 +- .../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/predict_modality/process_dataset/config.vsh.yaml | 2 +- 87 files changed, 88 insertions(+), 88 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index b86c36efa9..d72ca46949 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 7c78fd9d94..44922bdf50 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 76d95679f9..aa2b9ef201 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -141,11 +141,11 @@ def generate_resources(par, script_path) -> str: def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" if par["language"] == "python": - image_str = "ghcr.io/openproblems-bio/base_python:1.0.1" + image_str = "ghcr.io/openproblems-bio/base_python:1.0.2" setup_type = "python" package_example = "scib==1.1.3" elif par["language"] == "r": - image_str = "ghcr.io/openproblems-bio/base_r:1.0.1" + image_str = "ghcr.io/openproblems-bio/base_r:1.0.2" setup_type = "r" package_example = "tidyverse" return strip_margin(f'''\ diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index d7ca9914da..b869dbf5eb 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: dest: openproblems-v2/_viash.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64] diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 057c152583..40cabb5d39 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: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 03a8958d7b..7314795ab8 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 3c901f57cf..fb858e3e85 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 13ab319a02..ffe1f03ea9 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 3bc4f93974..1a6bd543ed 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index 924fceadfc..2822fa9443 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -8,6 +8,6 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow - type: native diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 6e4fa0e20d..0e8e75c428 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 dc2db19f50..65cf2808a2 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: apt packages: git diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 1be6c0a5d0..81e8ac9bdb 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 ea476d9a2b..858677d284 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" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index cd23327af4..6ac7bcc811 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: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ Matrix, rlang, bit64, scran, BiocParallel ] diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index b350031697..be80374d67 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 376009359c..f0f5e87efe 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,5 +7,5 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 8626769323..ecc3bd6a82 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,5 +7,5 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 1d6cd05a51..5af00240cf 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,5 +11,5 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 9a80d32143..c0a7673eeb 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 test_setup: - type: python packages: diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index 550d540e1d..5e97eab73f 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 f41f58a353..56e2c4b1b0 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - 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 4c626ca6cc..1dbbb90ae4 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 8214a5925c..013704966a 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml index b29d9ea2b1..1f18bb0bee 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml index 37e69892a3..bf525fad0f 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml index 7f6060e9ff..d0ab554ec3 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml index 9bd2cd7450..a190913dba 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 7c5a443999..52217665c3 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 c3b39a7c28..bd857f4e4a 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index 60494ca364..f262c931d5 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: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: rliger diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index e1346e1117..8255a85a97 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 5b1d53862d..7bd2d56107 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 8d14bcf41a..2cec87c577 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 8e33c9b30e..7eaf674b26 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 c233d44ff9..89af44209e 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -21,7 +21,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 a28cf98f70..14b47fc7b4 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 341a9e58db..f4d037f296 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 2f3545481a..78bae7b655 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 @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 182a6312b1..a9643660e6 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -49,7 +49,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 62582c327b..cacda59b01 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 33304872b4..a458636f27 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 2ccd2fd4c7..5e81c2e303 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 @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 89d831ca30..ad452e452f 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 @@ -40,7 +40,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 d08b79dfed..4a46752754 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -40,7 +40,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 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 7ab0048384..66531afcbd 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -43,7 +43,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 10715a43e0..53c7307756 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 c463d416a6..5b8b7447a5 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 77a2d076f6..694cd6e2b0 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 @@ -11,7 +11,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: scanpy 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 85e5be5dff..0cf8b5f002 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 @@ -12,7 +12,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: scanpy diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 747733efe3..057663cb29 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 8f7a7aed35..bf2f1d61c4 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - 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 6aaad03d4d..295b30c8f6 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: /src/tasks/dimensionality_reduction/methods/diffusion_map/script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 82244872c0..5b534b356a 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - 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 8890a89795..d168caaada 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 c1a22ef996..35ad00d903 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index c4681c86d5..d369c90298 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 02f7e88b56..c665d23a12 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 3b4dd6d400..ea6565a461 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 6d4b7943ac..8b060e796c 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 75159f80ec..3502f49d01 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 143af87aaa..6b26daae75 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 0f81b422c5..eb23ba8ece 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: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ coRanking, bit64 ] 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 f3e1b6aacc..168531b210 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 a69c14283c..7867071dd1 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 88b707e9a8..79c3f5dde8 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 55fb1e71e3..d320b8eb8f 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - 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 48a2ba8f3c..5cc589db65 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - 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 027781c078..8e75645036 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 13df85ac08..c43152d7c1 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - 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 aa8e25533a..782757f2e8 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 3b908ae7b2..449a0757c9 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 2c490e80c0..580d663cf8 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scikit-learn 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 0dbfce04ad..039f256e47 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 # Add custom dependencies here setup: - type: python 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 928c85a5e4..8c81554e21 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: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ Matrix>=1.5.3, Seurat, rlang, bit64 ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index 11d99ed5d3..4d3271b571 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 11674fde5c..896175c452 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 ec6eece949..9c8c91c86a 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 eb5a564cdb..5f9b8f363b 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,5 +25,5 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow 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 921d746133..440184da0a 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 8a0d1872b7..3c5f47eee8 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file 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 ef34705c68..f45eacd319 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 e21b3febe5..69f3fcda29 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 82ec6690fb..e6dddc9ccb 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 61b0013a01..16a66a4853 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 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 cd3f22bf0d..06fff957c8 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: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index 8ec27a6c46..ece7137647 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ bit64 ]