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2 changes: 1 addition & 1 deletion requirements.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
requests>=2.6.1
ruamel.yaml>=0.16.0,<0.19
rdflib>=4.2.2,<7.2
rdflib>=4.2.2,<7.3
schema-salad>=8.9,<9
prov==1.5.1
mypy-extensions
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2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,7 @@ def _find_package_data(base: str, globs: list[str], root: str = "cwltool") -> li
"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, < 7.2.0",
"rdflib >= 4.2.2, < 7.3.0",
"schema-salad >= 8.9, < 9",
"prov == 1.5.1",
"mypy-extensions",
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2 changes: 2 additions & 0 deletions tests/test_dependencies.py
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@

@needs_docker
@pytest.mark.skipif(not deps, reason="galaxy-tool-util is not installed")
@pytest.mark.skip(reason="too flaky")
@pytest.mark.flaky(retries=3)
def test_biocontainers(tmp_path: Path) -> None:
wflow = get_data("tests/seqtk_seq.cwl")
Expand All @@ -46,6 +47,7 @@ def test_biocontainers(tmp_path: Path) -> None:

@needs_docker
@pytest.mark.skipif(not deps, reason="galaxy-tool-util is not installed")
@pytest.mark.skip(reason="too flaky")
def test_biocontainers_resolution(tmp_path: Path) -> None:
"""Confirm expected container name for --beta-use-biocontainers."""
tool = load_tool(get_data("tests/seqtk_seq.cwl"), LoadingContext())
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