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Patch: Update image version for openproblems/base_* images #469

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Patch: Update image version for openproblems/base_* images #469

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2 changes: 1 addition & 1 deletion src/common/check_dataset_schema/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/common/check_yaml_schema/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/common/create_task_readme/config.vsh.yaml
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Expand Up @@ -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]
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2 changes: 1 addition & 1 deletion src/common/extract_metadata/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/common/extract_scores/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/ontology/check_obsolete_terms/config.vsh.yaml
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Expand Up @@ -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 ]
2 changes: 1 addition & 1 deletion src/common/process_task_results/generate_qc/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/common/process_task_results/get_api_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/process_task_results/get_dataset_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/process_task_results/get_method_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/process_task_results/get_metric_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/process_task_results/get_results/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/process_task_results/get_task_info/config.vsh.yaml
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Expand Up @@ -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 ]
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2 changes: 1 addition & 1 deletion src/common/process_task_results/yaml_to_json/config.vsh.yaml
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/datasets/loaders/cellxgene_census/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/datasets/loaders/openproblems_v1/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/datasets/normalization/atac_tfidf/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/normalization/l1_sqrt/config.vsh.yaml
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Expand Up @@ -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:
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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 @@ 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]
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 @@ 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 ]
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2 changes: 1 addition & 1 deletion src/datasets/normalization/prot_clr/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/normalization/sqrt_cp/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/datasets/processors/hvg/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/datasets/processors/knn/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/datasets/processors/pca/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/datasets/processors/subsample/config.vsh.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/datasets/processors/svd/config.vsh.yaml
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Expand Up @@ -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]
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2 changes: 1 addition & 1 deletion src/migration/check_migration_status/config.vsh.yaml
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/migration/list_git_shas/config.vsh.yaml
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion src/migration/update_bibtex/config.vsh.yaml
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml
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Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml
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Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml
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Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion ...asks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion ...tch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml
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Expand Up @@ -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]
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml
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Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml
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Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml
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Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion ...tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml
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Expand Up @@ -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"]
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