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workflow RDF #478

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aa7cdc6
draft workflow RDF
FynnBe Oct 26, 2022
7924b2f
update passthrough module generation
FynnBe Oct 26, 2022
825cad3
Tensor -> Arg; ArgType
FynnBe Oct 26, 2022
891093f
test examples
FynnBe Oct 26, 2022
8f06f9e
add schema validation
FynnBe Oct 26, 2022
6889bf8
add test_workflow_rdf.py
FynnBe Oct 26, 2022
9f0eed2
fix missing workflow import
FynnBe Oct 26, 2022
8639d8d
update generate_rdf_docs.py and generate_json_specs.py
FynnBe Oct 26, 2022
1476670
fix typing import
FynnBe Oct 26, 2022
fe9243e
test_steps and better workflow kwargs
FynnBe Oct 27, 2022
7afc2c6
Merge branch 'main' into workflow_rdf
FynnBe Oct 27, 2022
5645d4c
Update example_specs/workflows/hpa/single_cell_classification.yaml
FynnBe Oct 28, 2022
218b67a
wip discussion with constantin
FynnBe Oct 28, 2022
94d1292
wip2
FynnBe Oct 28, 2022
5831b04
Merge branch 'main' into workflow_rdf
FynnBe Oct 31, 2022
428d605
axes and options
FynnBe Oct 31, 2022
491e7b4
Merge branch 'main' into workflow_rdf
FynnBe Nov 3, 2022
6dacb68
update workflow RDF schema and raw_nodes
FynnBe Nov 3, 2022
9768848
finish first draft of workflow RDF spec
FynnBe Nov 3, 2022
e3d963e
inputs/options/outputs -> *_spec
FynnBe Nov 4, 2022
cd4bd4c
enforce unique step ids
FynnBe Nov 4, 2022
d894da9
detect type workflow
FynnBe Nov 4, 2022
7ace197
don't accept emtpy strings
FynnBe Nov 4, 2022
f5af22f
also log binarized
FynnBe Nov 4, 2022
96376e5
Merge branch 'main' into workflow_rdf
FynnBe Nov 8, 2022
9fe4ca2
wip remove wf steps
FynnBe Nov 24, 2022
31ecba9
rename importable sources
FynnBe Nov 24, 2022
ea1b826
black
FynnBe Nov 24, 2022
283da9a
update changelog
FynnBe Nov 24, 2022
73b31b9
remove steps from workflow spec
FynnBe Nov 24, 2022
9c4a81d
split up CallableSource field
FynnBe Nov 24, 2022
91e6783
set format_version as default
FynnBe Nov 24, 2022
8bdb9c9
prohibit serializing a list from a string
FynnBe Nov 24, 2022
a89bf07
remove specialized axes classes
FynnBe Nov 24, 2022
5670cbc
remove redundant brackets
FynnBe Nov 24, 2022
9b82e90
update workflow tests
FynnBe Nov 25, 2022
0243665
rename DEFAULT_TYPE_NAME_MAP
FynnBe Nov 28, 2022
91d141f
rename ArbitraryAxes to UnknownAxes
FynnBe Nov 28, 2022
a3d97c8
make nested_errors optional
FynnBe Nov 30, 2022
b7b51a9
assert for mypy
FynnBe Dec 6, 2022
eb4e3f8
some aliases for backward compatibility
FynnBe Dec 6, 2022
1102f6a
add AXIS_LETTER_TO_NAME and AXIS_NAME_TO_LETTER
FynnBe Dec 8, 2022
6780a70
Merge branch 'main' into workflow_rdf
FynnBe Feb 1, 2023
924d667
Merge branch 'main' into workflow_rdf
FynnBe Feb 9, 2023
b66798a
update hello workflow example
FynnBe Feb 9, 2023
c90cdd4
Merge branch 'main' into workflow_rdf
FynnBe Mar 3, 2023
ff5cc6e
Merge branch 'main' into workflow_rdf
FynnBe Mar 15, 2023
052c553
remove +\n from CLI help
FynnBe Mar 15, 2023
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add test_workflow_rdf.py
FynnBe committed Oct 26, 2022

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commit 6889bf81996019a1d6f068dfd2d189f44f245b78
24 changes: 24 additions & 0 deletions tests/test_workflow_rdf.py
Original file line number Diff line number Diff line change
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from bioimageio.spec.shared import yaml
from bioimageio.spec.workflow import raw_nodes


def test_workflow_rdf_stardist_example(stardist_workflow_rdf):
from bioimageio.spec.workflow.schema import Workflow

data = yaml.load(stardist_workflow_rdf)
# data["root_path"] = stardist_workflow_rdf.parent

workflow = Workflow().load(data)
assert isinstance(workflow, raw_nodes.Workflow)
assert workflow.steps[0].op == "zero_mean_unit_variance"


def test_workflow_rdf_hpa_example(hpa_workflow_rdf):
from bioimageio.spec.workflow.schema import Workflow

data = yaml.load(hpa_workflow_rdf)
# data["root_path"] = hpa_workflow_rdf.parent

workflow = Workflow().load(data)
assert isinstance(workflow, raw_nodes.Workflow)
assert workflow.outputs[0].name == "cells"