Dev bilayers#29
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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:
schema_formatsclass tobiomero/constants.pyto enumerate supported workflow descriptor schema formats, including BIAFLOWS, CYTOMINE, BIOMERO_SCHEMA, BILAYERS, CWL, and OpenAPI.Dependency and Configuration Updates:
pyproject.tomlto includepyyamland thebiomero-schemapackage for parsing new schema formats.mito_segmentation) inresources/slurm-config.ini, specifying its container, repository, and job script.New Job and Descriptor Examples:
resources/job_template_bilayers.sh.tests/W_NucleiSegmentation-ImageJ.descriptor.jsonfor BIAFLOWS/Cytomine format.tests/example_workflow.jsonfor biomero-schema format.tests/bilayers_example.yamlfor bilayers format.Testing Infrastructure:
tests/conftest.pyto load and provide access to the example descriptors for tests.