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workflow RDF#478

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FynnBe wants to merge 48 commits intomainbioimage-io/spec-bioimage-io:mainfrom workflow_rdfbioimage-io/spec-bioimage-io:workflow_rdfCopy head branch name to clipboard

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Commits on Oct 26, 2022

• draft workflow RDF

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• update passthrough module generation

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• Tensor -> Arg; ArgType

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• test examples

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• add schema validation

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• add test_workflow_rdf.py

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• fix missing workflow import

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• update generate_rdf_docs.py and generate_json_specs.py

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• fix typing import

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Commits on Oct 27, 2022

• test_steps and better workflow kwargs

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• Merge branch 'main' into workflow_rdf

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Commits on Oct 28, 2022

• Update example_specs/workflows/hpa/single_cell_classification.yaml

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• wip discussion with constantin

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• wip2

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Commits on Oct 31, 2022

• Merge branch 'main' into workflow_rdf

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• axes and options

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Commits on Nov 3, 2022

• Merge branch 'main' into workflow_rdf

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• update workflow RDF schema and raw_nodes

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• finish first draft of workflow RDF spec

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Commits on Nov 4, 2022

• inputs/options/outputs -> *_spec

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• enforce unique step ids

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• detect type workflow

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• don't accept emtpy strings

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• also log binarized

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Commits on Nov 8, 2022

• Merge branch 'main' into workflow_rdf

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Commits on Nov 24, 2022

• wip remove wf steps

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• rename importable sources

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• black

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• update changelog

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• remove steps from workflow spec

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• split up CallableSource field

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• set format_version as default

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• prohibit serializing a list from a string

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• remove specialized axes classes

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• remove redundant brackets

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Commits on Nov 25, 2022

• update workflow tests

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Commits on Nov 28, 2022

• rename DEFAULT_TYPE_NAME_MAP

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• rename ArbitraryAxes to UnknownAxes

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Commits on Nov 30, 2022

• make nested_errors optional

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Commits on Dec 6, 2022

• assert for mypy

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• some aliases for backward compatibility

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Commits on Dec 8, 2022

• add AXIS_LETTER_TO_NAME and AXIS_NAME_TO_LETTER

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Commits on Feb 1, 2023

• Merge branch 'main' into workflow_rdf

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Commits on Feb 9, 2023

• Merge branch 'main' into workflow_rdf

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• update hello workflow example

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Commits on Mar 3, 2023

• Merge branch 'main' into workflow_rdf

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Commits on Mar 15, 2023

• Merge branch 'main' into workflow_rdf

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• remove +\n from CLI help

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