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Update to Viash 0.9 #71

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Jul 15, 2024
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2 changes: 1 addition & 1 deletion src/control_methods/ground_truth/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
cran: [ arrow, dplyr ]
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2 changes: 1 addition & 1 deletion src/control_methods/mean_across_celltypes/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ resources:
- path: ../../utils/anndata_to_dataframe.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ fastparquet ]
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2 changes: 1 addition & 1 deletion src/control_methods/mean_across_compounds/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ resources:
- path: ../../utils/anndata_to_dataframe.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ fastparquet ]
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2 changes: 1 addition & 1 deletion src/control_methods/mean_outcome/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ resources:
- path: ../../utils/anndata_to_dataframe.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ fastparquet ]
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2 changes: 1 addition & 1 deletion src/control_methods/sample/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
cran: [ arrow, dplyr ]
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2 changes: 1 addition & 1 deletion src/control_methods/zeros/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ resources:
path: script.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ fastparquet ]
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2 changes: 1 addition & 1 deletion src/methods/jn_ap_op2/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ resources:
- path: helper.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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2 changes: 1 addition & 1 deletion src/methods/lgc_ensemble_direct/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ resources:

engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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2 changes: 1 addition & 1 deletion src/methods/lgc_ensemble_predict/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ resources:

engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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2 changes: 1 addition & 1 deletion src/methods/lgc_ensemble_prepare/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ resources:

engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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2 changes: 1 addition & 1 deletion src/methods/lgc_ensemble_train/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ resources:

engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ resources:

engines:
- type: docker
image: nvcr.io/nvidia/tensorflow:24.03-tf2-py3
image: ghcr.io/openproblems-bio/base_images/tensorflow_nvidia:1.1.0
setup:
- type: apt
packages:
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remove packages from line 45 - 54

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thanks!

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2 changes: 1 addition & 1 deletion src/methods/pyboost/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ resources:
- path: ../../utils/anndata_to_dataframe.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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2 changes: 1 addition & 1 deletion src/methods/scape/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ resources:
path: script.py
engines:
- type: docker
image: nvcr.io/nvidia/tensorflow:24.03-tf2-py3
image: ghcr.io/openproblems-bio/base_images/tensorflow_nvidia:1.1.0
setup:
- type: apt
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packages:
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2 changes: 1 addition & 1 deletion src/methods/transformer_ensemble/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ resources:
- path: train.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4
image: ghcr.io/openproblems-bio/base_images/pytorch_nvidia:1.1.0
setup:
- type: python
packages:
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2 changes: 1 addition & 1 deletion src/metrics/mean_rowwise_correlation/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
packages: proxyC
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2 changes: 1 addition & 1 deletion src/metrics/mean_rowwise_error/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
packages: proxyC
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2 changes: 1 addition & 1 deletion src/process_dataset/add_uns_metadata/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ resources:
path: script.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
runners:
- type: executable
- type: nextflow
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2 changes: 1 addition & 1 deletion src/process_dataset/bootstrap/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ resources:
path: script.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
runners:
- type: executable
- type: nextflow
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2 changes: 1 addition & 1 deletion src/process_dataset/compute_pseudobulk/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ resources:
path: script.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ pyarrow ]
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ resources:
- path: ../../utils/anndata_to_dataframe.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ fastparquet, anndata, pandas ]
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Original file line number Diff line number Diff line change
Expand Up @@ -77,10 +77,10 @@ resources:
path: script.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
setup:
- type: python
packages: [ fastparquet, anndata, pandas ]
packages: [ fastparquet, pandas ]
runners:
- type: executable
- type: nextflow
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2 changes: 1 addition & 1 deletion src/process_dataset/filter_obs/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
cran: [ dplyr, tidyr, purrr, tibble ]
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2 changes: 1 addition & 1 deletion src/process_dataset/filter_vars/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
cran: [ edgeR, limma, dplyr, tidyr, purrr, tibble ]
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5 changes: 1 addition & 4 deletions src/process_dataset/generate_id_map/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,7 @@ resources:
path: script.py
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
setup:
- type: python
packages: [ anndata ]
image: ghcr.io/openproblems-bio/base_images/python:1.1.0
runners:
- type: executable
- type: nextflow
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2 changes: 1 addition & 1 deletion src/process_dataset/run_limma/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ resources:
path: script.R
engines:
- type: docker
image: ghcr.io/openproblems-bio/base_r:1.0.4
image: ghcr.io/openproblems-bio/base_images/r:1.1.0
setup:
- type: r
bioc: [ edgeR, limma, dplyr, tidyr, purrr, tibble, furrr, future ]
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