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Added loop support #5

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merged 9 commits into from
Oct 7, 2024
Merged

Added loop support #5

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5a85d83
Added loop support
GlassOfWhiskey Dec 24, 2022
891cb8b
Make `LoopInput` extend `OutputSink`
GlassOfWhiskey Jan 3, 2023
45c4cab
spelling fixes
mr-c Jan 3, 2023
d80c7da
(multiple -> multiple_input) in test labels
GlassOfWhiskey Jan 4, 2023
78c8fdd
AbstractWorkflowStep needs to be marked as 'abstract: true'
tetron Jul 16, 2024
f9f327b
conformance tests: report the names of the failures
mr-c Jul 17, 2024
caa03de
loops: remove invalid-no-when and invalid-loop-scatter tests
mr-c Sep 17, 2024
72d2835
loops: test with recent cwltool, not github download
mr-c Sep 17, 2024
e43a673
Rename `outputMethod` values
GlassOfWhiskey Sep 18, 2024
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6 changes: 6 additions & 0 deletions .github/config/wordlist.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
abstractworkflowstep
acyclic
amstutz
arrayschema
Expand Down Expand Up @@ -160,6 +161,9 @@ loadlistingrequirement
localhost
lookahead
loopback
loopinput
loopoutputmethod
loopworkflowstep
maccallum
macos
mappredicate
Expand Down Expand Up @@ -194,6 +198,7 @@ outputbinding
outputenumschema
outputeval
outputformat
outputmethod
outputschema
outputsink
outputsource
Expand Down Expand Up @@ -231,6 +236,7 @@ saladversion
sbgenomics
scatterfeaturerequirement
scattermethod
scatterworkflowstep
schemadefrequirement
schemaorg
schemas
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4 changes: 2 additions & 2 deletions .github/workflows/cwltool.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
python-version: '3.9.x'

- name: Setup prerequirements
run: pip install "cwltest>=2.3" pytest-xdist "git+https://github.com/common-workflow-language/cwltool.git@main#egg=cwltool"
run: pip install "cwltest>=2.3" pytest-xdist "cwltool>=3.1.20240909164951"
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Suggested change
run: pip install "cwltest>=2.3" pytest-xdist "cwltool>=3.1.20240909164951"
run: pip install "cwltest>=2.3" pytest-xdist "cwltool>=3.1.20241007082533"


- name: Copy in cwltool-specific configuration for the cwltest pytest plugin
run: cp "$(python -c 'from cwltool.tests.util import get_data; print(get_data("tests/cwl-conformance/cwltool-conftest.py"))')" conftest.py
Expand All @@ -33,4 +33,4 @@ jobs:
run: cp conformance_tests.yaml conformance_tests.cwltest.yaml

- name: Run tests against the reference runner
run: python -m pytest conformance_tests.cwltest.yaml -n auto -rs
run: python -m pytest conformance_tests.cwltest.yaml -n auto -rsfE
4 changes: 2 additions & 2 deletions CONFORMANCE_TESTS.md
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Expand Up @@ -144,7 +144,7 @@ We will use this single entry to explain the format
Must include one or more of the following tags: `command_line_tool`, `expression_tool` or `workflow`.
If the test does not test any optional features, the tag `required` is required.

Because `conformance_tests.yaml` is a `schema-salad` processed document, [`$import`](https://www.commonwl.org/v1.2/SchemaSalad.html#Import)
Because `conformance_tests.yaml` is a `schema-salad` processed document, [`$import`](https://www.commonwl.org/v1.3/SchemaSalad.html#Import)
can be used to organize the tests into separate files.

Currently, the main file is too big (over 3400 lines); we are slowly re-organizing it.
Expand All @@ -166,7 +166,7 @@ At any level, if there is an extra field, then that will be considered an error.
An exception to this is `class: File` and `class: Directory` objects, the `cwl-runner` under test can add additional fields here without causing a test to fail.
Likewise, if you don't want to test some aspect of a `class: File` or `class: Directory` object (like `nameext`) you can just omit it.

[According to the CWL standards](https://www.commonwl.org/v1.2/CommandLineTool.html#File), the format of the `location` field in
[According to the CWL standards](https://www.commonwl.org/v1.3/CommandLineTool.html#File), the format of the `location` field in
`class: File` and `class: Directory` is implementation specific and we should not be testing them.
Please remember to use `location: Any` for them.

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