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@LeonHafner
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Setting up this PR draft to add tacco to the pipeline

not finished yet

@LeonHafner
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The module currently only supports native engine, docker needs to be added.

@Kraftfahrzeughaftpflichtversicherung
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The test is failing because there are no installed packages, for example openproblems

you can solve it with adding in config the docker engines

for example:
engines:

  • type: docker
    image: openproblems/base_python:1.0.0
    merge:
    • /src/base/setup_txsim_partial.yaml
      setup:
    • type: python
      pypi: [planktonspace]

you can find it here: https://github.com/openproblems-bio/task_ist_preprocessing/blob/main/src/methods_cell_type_annotation/ssam/config.vsh.yaml#L24C1-L31C30

and the other examples in other methods like here: https://github.com/openproblems-bio/task_ist_preprocessing/blob/main/src/methods_segmentation/cellpose/config.vsh.yaml

important thing here is
setup:
- type: python
pypi: spatialdata

the packages that you need to install: https://viash.io/versioned/0_7_5/reference/config/platforms/docker/setup/pythonRequirements.html

I know that you cannot build the component with docker in VM, but this can help you to pass the tests

@LouisK92 LouisK92 merged commit 3bac6a5 into openproblems-bio:dev Mar 10, 2025
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3 participants