From 5878b820e82c92e3054b9246fc833f9a240d4ace Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 11 Jun 2025 13:09:09 +0200 Subject: [PATCH 1/2] Update image version to :1 --- .../multimodal/openproblems_neurips2021_bmmc/config.vsh.yaml | 2 +- .../multimodal/openproblems_neurips2022_pbmc/config.vsh.yaml | 2 +- .../multimodal/openproblems_v1_multimodal/config.vsh.yaml | 2 +- src/datasets/loaders/scrnaseq/cellxgene_census/config.vsh.yaml | 2 +- .../scrnaseq/cellxgene_census_from_source_h5ad/config.vsh.yaml | 2 +- src/datasets/loaders/scrnaseq/openproblems_v1/config.vsh.yaml | 2 +- src/datasets/loaders/spatial/zenodo/config.vsh.yaml | 2 +- src/datasets/loaders/spatial/zenodo_slidetags/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/project/create_component/config.vsh.yaml | 2 +- src/project/render_readme/config.vsh.yaml | 2 +- src/project/upgrade_config/config.vsh.yaml | 2 +- src/reporting/generate_qc/config.vsh.yaml | 2 +- src/reporting/get_dataset_info/config.vsh.yaml | 2 +- src/reporting/get_method_info/config.vsh.yaml | 2 +- src/reporting/get_metric_info/config.vsh.yaml | 2 +- src/reporting/get_results/config.vsh.yaml | 2 +- src/reporting/get_task_info/config.vsh.yaml | 2 +- src/utils/extract_uns_metadata/config.vsh.yaml | 2 +- src/utils/yaml_to_json/config.vsh.yaml | 2 +- src/validation/check_dataset_with_schema/config.vsh.yaml | 2 +- src/validation/check_yaml_with_schema/config.vsh.yaml | 2 +- 32 files changed, 32 insertions(+), 32 deletions(-) diff --git a/src/datasets/loaders/multimodal/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/multimodal/openproblems_neurips2021_bmmc/config.vsh.yaml index 3a73fe053..33b06e7df 100644 --- a/src/datasets/loaders/multimodal/openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/loaders/multimodal/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -67,7 +67,7 @@ test_resources: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/loaders/multimodal/openproblems_neurips2022_pbmc/config.vsh.yaml b/src/datasets/loaders/multimodal/openproblems_neurips2022_pbmc/config.vsh.yaml index 5994e4ccc..84fe2cdd5 100644 --- a/src/datasets/loaders/multimodal/openproblems_neurips2022_pbmc/config.vsh.yaml +++ b/src/datasets/loaders/multimodal/openproblems_neurips2022_pbmc/config.vsh.yaml @@ -73,7 +73,7 @@ resources: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/loaders/multimodal/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/multimodal/openproblems_v1_multimodal/config.vsh.yaml index b0afb9311..0b138e29f 100644 --- a/src/datasets/loaders/multimodal/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/multimodal/openproblems_v1_multimodal/config.vsh.yaml @@ -79,7 +79,7 @@ test_resources: path: test.py engines: - 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/scrnaseq/cellxgene_census/config.vsh.yaml b/src/datasets/loaders/scrnaseq/cellxgene_census/config.vsh.yaml index deccdb421..3dca455ae 100644 --- a/src/datasets/loaders/scrnaseq/cellxgene_census/config.vsh.yaml +++ b/src/datasets/loaders/scrnaseq/cellxgene_census/config.vsh.yaml @@ -157,7 +157,7 @@ test_resources: path: test.py engines: - 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/scrnaseq/cellxgene_census_from_source_h5ad/config.vsh.yaml b/src/datasets/loaders/scrnaseq/cellxgene_census_from_source_h5ad/config.vsh.yaml index 31a4d4412..d9a77b7a7 100644 --- a/src/datasets/loaders/scrnaseq/cellxgene_census_from_source_h5ad/config.vsh.yaml +++ b/src/datasets/loaders/scrnaseq/cellxgene_census_from_source_h5ad/config.vsh.yaml @@ -113,7 +113,7 @@ test_resources: path: test.py engines: - 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/scrnaseq/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/scrnaseq/openproblems_v1/config.vsh.yaml index 6ebb63b41..6320b5ca2 100644 --- a/src/datasets/loaders/scrnaseq/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/scrnaseq/openproblems_v1/config.vsh.yaml @@ -75,7 +75,7 @@ test_resources: path: test.py engines: - 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/spatial/zenodo/config.vsh.yaml b/src/datasets/loaders/spatial/zenodo/config.vsh.yaml index b4e06238a..8e54963e3 100644 --- a/src/datasets/loaders/spatial/zenodo/config.vsh.yaml +++ b/src/datasets/loaders/spatial/zenodo/config.vsh.yaml @@ -82,7 +82,7 @@ test_resources: engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/loaders/spatial/zenodo_slidetags/config.vsh.yaml b/src/datasets/loaders/spatial/zenodo_slidetags/config.vsh.yaml index 0355c8bb6..d9cf7e6de 100644 --- a/src/datasets/loaders/spatial/zenodo_slidetags/config.vsh.yaml +++ b/src/datasets/loaders/spatial/zenodo_slidetags/config.vsh.yaml @@ -82,7 +82,7 @@ test_resources: engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/normalization/atac_tfidf/config.vsh.yaml b/src/datasets/normalization/atac_tfidf/config.vsh.yaml index 850b49363..a66d9de1d 100644 --- a/src/datasets/normalization/atac_tfidf/config.vsh.yaml +++ b/src/datasets/normalization/atac_tfidf/config.vsh.yaml @@ -11,7 +11,7 @@ resources: path: script.py engines: - 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 3a3aca8ed..88c92c0ed 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -15,7 +15,7 @@ resources: path: script.py engines: - 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 d686c5414..f59e9106d 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -12,7 +12,7 @@ arguments: description: Number of counts per cell. When set to -1, will use None. engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index e010c1032..95bf28956 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 @@ resources: path: script.R engines: - 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 3262ca73b..7ed597b2e 100644 --- a/src/datasets/normalization/prot_clr/config.vsh.yaml +++ b/src/datasets/normalization/prot_clr/config.vsh.yaml @@ -15,7 +15,7 @@ resources: path: script.py engines: - 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 1e241e89d..40d2abd54 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -11,7 +11,7 @@ arguments: description: Number of counts per cell engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 886fe92f9..a222443f7 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -6,7 +6,7 @@ resources: path: script.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index b3cf89442..4f8b802ae 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -6,7 +6,7 @@ resources: path: script.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index b1c1a7ba1..dae32443e 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -10,7 +10,7 @@ resources: # - path: "../../../resources_test/common/pancreas" engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 9cc62c360..60020d12e 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -42,7 +42,7 @@ test_resources: - path: /resources_test/common/pancreas engines: - 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 bd71cae4c..14280c651 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -6,7 +6,7 @@ resources: path: script.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: [scikit-learn] diff --git a/src/project/create_component/config.vsh.yaml b/src/project/create_component/config.vsh.yaml index ee7c88479..8bff35bb1 100644 --- a/src/project/create_component/config.vsh.yaml +++ b/src/project/create_component/config.vsh.yaml @@ -51,7 +51,7 @@ test_resources: path: test.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: apt packages: git diff --git a/src/project/render_readme/config.vsh.yaml b/src/project/render_readme/config.vsh.yaml index 37ad2a86c..f6a802f1e 100644 --- a/src/project/render_readme/config.vsh.yaml +++ b/src/project/render_readme/config.vsh.yaml @@ -26,7 +26,7 @@ test_resources: path: test.R engines: - type: docker - image: openproblems/base_r:1.0.0 + image: openproblems/base_r:1 setup: - type: r cran: diff --git a/src/project/upgrade_config/config.vsh.yaml b/src/project/upgrade_config/config.vsh.yaml index 1c3d75346..a4c3708cf 100644 --- a/src/project/upgrade_config/config.vsh.yaml +++ b/src/project/upgrade_config/config.vsh.yaml @@ -28,7 +28,7 @@ test_resources: engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python packages: ruamel.yaml diff --git a/src/reporting/generate_qc/config.vsh.yaml b/src/reporting/generate_qc/config.vsh.yaml index 2fd9786e9..c141575cb 100644 --- a/src/reporting/generate_qc/config.vsh.yaml +++ b/src/reporting/generate_qc/config.vsh.yaml @@ -41,7 +41,7 @@ test_resources: dest: resources_test/openproblems/task_results_v3 engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/reporting/get_dataset_info/config.vsh.yaml b/src/reporting/get_dataset_info/config.vsh.yaml index 0c32dd555..ff43cb478 100644 --- a/src/reporting/get_dataset_info/config.vsh.yaml +++ b/src/reporting/get_dataset_info/config.vsh.yaml @@ -26,7 +26,7 @@ test_resources: dest: resources_test/openproblems/task_results_v3 engines: - 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/reporting/get_method_info/config.vsh.yaml b/src/reporting/get_method_info/config.vsh.yaml index 0a4e98032..23528273b 100644 --- a/src/reporting/get_method_info/config.vsh.yaml +++ b/src/reporting/get_method_info/config.vsh.yaml @@ -26,7 +26,7 @@ test_resources: dest: resources_test/openproblems/task_results_v3 engines: - 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/reporting/get_metric_info/config.vsh.yaml b/src/reporting/get_metric_info/config.vsh.yaml index 0eb2fb22c..597f4a420 100644 --- a/src/reporting/get_metric_info/config.vsh.yaml +++ b/src/reporting/get_metric_info/config.vsh.yaml @@ -26,7 +26,7 @@ test_resources: dest: resources_test/openproblems/task_results_v3 engines: - 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/reporting/get_results/config.vsh.yaml b/src/reporting/get_results/config.vsh.yaml index e0191cf2b..3b5f7c6eb 100644 --- a/src/reporting/get_results/config.vsh.yaml +++ b/src/reporting/get_results/config.vsh.yaml @@ -54,7 +54,7 @@ test_resources: dest: resources_test/openproblems/task_results_v3 engines: - 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/reporting/get_task_info/config.vsh.yaml b/src/reporting/get_task_info/config.vsh.yaml index 6c87e0fd5..0798159ee 100644 --- a/src/reporting/get_task_info/config.vsh.yaml +++ b/src/reporting/get_task_info/config.vsh.yaml @@ -26,7 +26,7 @@ test_resources: dest: resources_test/openproblems/task_results_v3 engines: - 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/utils/extract_uns_metadata/config.vsh.yaml b/src/utils/extract_uns_metadata/config.vsh.yaml index efb3de165..6d77bdb34 100644 --- a/src/utils/extract_uns_metadata/config.vsh.yaml +++ b/src/utils/extract_uns_metadata/config.vsh.yaml @@ -34,7 +34,7 @@ test_resources: path: test.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: python packages: viashpy diff --git a/src/utils/yaml_to_json/config.vsh.yaml b/src/utils/yaml_to_json/config.vsh.yaml index 6b09ed9e3..e6b1d8c01 100644 --- a/src/utils/yaml_to_json/config.vsh.yaml +++ b/src/utils/yaml_to_json/config.vsh.yaml @@ -18,7 +18,7 @@ resources: path: script.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 runners: - type: executable - type: nextflow diff --git a/src/validation/check_dataset_with_schema/config.vsh.yaml b/src/validation/check_dataset_with_schema/config.vsh.yaml index e071554bf..918ae1a8c 100644 --- a/src/validation/check_dataset_with_schema/config.vsh.yaml +++ b/src/validation/check_dataset_with_schema/config.vsh.yaml @@ -36,7 +36,7 @@ test_resources: path: test.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 test_setup: - type: python packages: viashpy diff --git a/src/validation/check_yaml_with_schema/config.vsh.yaml b/src/validation/check_yaml_with_schema/config.vsh.yaml index e7f9112c4..eddfaea0a 100644 --- a/src/validation/check_yaml_with_schema/config.vsh.yaml +++ b/src/validation/check_yaml_with_schema/config.vsh.yaml @@ -18,7 +18,7 @@ resources: path: script.py engines: - type: docker - image: openproblems/base_python:1.0.0 + image: openproblems/base_python:1 setup: - type: python pypi: From e0b70aeecb130d94fac9e8d42a9d5cd29a9e71b7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 20 Jun 2025 13:45:31 +0200 Subject: [PATCH 2/2] trigger ci