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Dev bilayers#29

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TorecLuik wants to merge 48 commits into
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dev-bilayers
Open

Dev bilayers#29
TorecLuik wants to merge 48 commits into
mainfrom
dev-bilayers

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@TorecLuik
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This pull request introduces support for new workflow schema formats, expands test coverage with example descriptors, and adds configuration and resource files for new workflows. The changes enhance the system's ability to handle multiple workflow descriptor standards, enable testing of schema parsing, and provide templates for new job types.

Support for Multiple Workflow Schema Formats:

  • Added the schema_formats class to biomero/constants.py to enumerate supported workflow descriptor schema formats, including BIAFLOWS, CYTOMINE, BIOMERO_SCHEMA, BILAYERS, CWL, and OpenAPI.

Dependency and Configuration Updates:

  • Updated pyproject.toml to include pyyaml and the biomero-schema package for parsing new schema formats.
  • Added configuration for a new workflow (mito_segmentation) in resources/slurm-config.ini, specifying its container, repository, and job script.

New Job and Descriptor Examples:

  • Added a SLURM job template script for bilayers workflows as resources/job_template_bilayers.sh.
  • Added example workflow descriptors for testing:
    • tests/W_NucleiSegmentation-ImageJ.descriptor.json for BIAFLOWS/Cytomine format.
    • tests/example_workflow.json for biomero-schema format.
    • tests/bilayers_example.yaml for bilayers format.

Testing Infrastructure:

  • Added shared pytest fixtures in tests/conftest.py to load and provide access to the example descriptors for tests.

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