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Patch: Update image version for openproblems/base_* images #928

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Merged
rcannood merged 2 commits into from
Jun 23, 2025
Merged

Patch: Update image version for openproblems/base_* images #928

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5878b82
Update image version to :1
github-actions[bot] Jun 11, 2025
e0b70ae
trigger ci
rcannood Jun 20, 2025
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2 changes: 1 addition & 1 deletion src/datasets/loaders/multimodal/openproblems_neurips2021_bmmc/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/multimodal/openproblems_neurips2022_pbmc/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/multimodal/openproblems_v1_multimodal/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/scrnaseq/cellxgene_census/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/scrnaseq/cellxgene_census_from_source_h5ad/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/scrnaseq/openproblems_v1/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/spatial/zenodo/config.vsh.yaml
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/datasets/loaders/spatial/zenodo_slidetags/config.vsh.yaml
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/datasets/normalization/atac_tfidf/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/normalization/l1_sqrt/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/normalization/log_cp/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/normalization/log_scran_pooling/config.vsh.yaml
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Expand Up @@ -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]
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2 changes: 1 addition & 1 deletion src/datasets/normalization/prot_clr/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/normalization/sqrt_cp/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/processors/hvg/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/processors/knn/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/processors/pca/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/processors/subsample/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/processors/svd/config.vsh.yaml
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Expand Up @@ -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]
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2 changes: 1 addition & 1 deletion src/project/create_component/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/project/render_readme/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/project/upgrade_config/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/reporting/generate_qc/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/reporting/get_dataset_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/reporting/get_method_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/reporting/get_metric_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/reporting/get_results/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/reporting/get_task_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/utils/extract_uns_metadata/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/utils/yaml_to_json/config.vsh.yaml
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/validation/check_dataset_with_schema/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/validation/check_yaml_with_schema/config.vsh.yaml
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Expand Up @@ -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:
Expand Down