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bump prov to 2.0.1 #2005

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bump prov to 2.0.1 #2005

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929d216
bump prov to 2.0.0
jfennick May 22, 2024
64f3e8e
bump prov to 2.0.1
jfennick Jun 10, 2024
30d0c7a
remove association assertion
jfennick Jun 11, 2024
74ea21b
use rdflib<7 upper bound (for compatibility with prov)
jfennick Jun 11, 2024
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2 changes: 1 addition & 1 deletion cwltool.Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ RUN rm /wheels/schema_salad*
RUN pip install "black~=22.0"
# galaxy-util 22.1.x depends on packaging<22, but black 23.x needs packaging>22
RUN SCHEMA_SALAD_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad \
$(grep schema.salad requirements.txt) "black~=22.0" --wheel-dir=/wheels # --verbose
$(grep schema.salad requirements.txt) "black~=22.0" "rdflib<7" --wheel-dir=/wheels # --verbose
RUN pip install --force-reinstall --no-index --no-warn-script-location \
--root=/pythonroot/ /wheels/*.whl
# --force-reinstall to install our new mypyc compiled schema-salad package
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4 changes: 2 additions & 2 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
requests>=2.6.1
ruamel.yaml>=0.16.0,<0.19
rdflib>=4.2.2,<7.1
rdflib>=4.2.2,<7
shellescape>=3.4.1,<3.9
schema-salad>=8.4.20230426093816,<9
prov==1.5.1
prov==2.0.1
mypy-extensions
psutil>=5.6.6
importlib_resources>=1.4;python_version<'3.9'
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4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -125,10 +125,10 @@
"requests >= 2.6.1", # >= 2.6.1 to workaround
# https://github.com/ionrock/cachecontrol/issues/137
"ruamel.yaml >= 0.16, < 0.19",
"rdflib >= 4.2.2, < 7.1.0",
"rdflib >= 4.2.2, < 7",
"shellescape >= 3.4.1, < 3.9",
"schema-salad >= 8.4.20230426093816, < 9",
"prov == 1.5.1",
"prov == 2.0.1",
"mypy-extensions",
"psutil >= 5.6.6",
"importlib_resources>=1.4;python_version<'3.9'",
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5 changes: 0 additions & 5 deletions tests/test_provenance.py
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Expand Up @@ -490,11 +490,6 @@ def check_prov(
assert len(engines) == 1, "Found too many WorkflowEngines: %s" % engines
engine = engines.pop()

assert (
main_run,
PROV.wasAssociatedWith,
engine,
) in g, "Wf run not associated with wf engine"
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Why does this need to be removed? Maybe do a side-by-side diff of running cwltool --provenance some_folder tests/wf/sec-wf-out.cwl with this PR and without it.

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The short answer is that I couldn't get the CI to pass without removing it. Yes, I tried doing side by side diffs and/or other ways of debugging it, but I'm all out of energy. I don't think I'm going to be able to fix this particular assertion.

I suspect the change is due to one of the following two commits from the prov repo, but IDK.
trungdong/prov@a8aba63
trungdong/prov@2e19dcc

assert (
engine,
RDF.type,
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