From 3cd94fe9bb5bd29186c37b5957c31cc19745208e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Sep 2025 07:03:02 +0000 Subject: [PATCH 1/2] Update rdflib requirement from <7.2,>=4.2.2 to >=4.2.2,<7.3 Updates the requirements on [rdflib](https://github.com/RDFLib/rdflib) to permit the latest version. - [Release notes](https://github.com/RDFLib/rdflib/releases) - [Changelog](https://github.com/RDFLib/rdflib/blob/main/CHANGELOG.md) - [Commits](https://github.com/RDFLib/rdflib/compare/4.2.2...7.2.1) --- updated-dependencies: - dependency-name: rdflib dependency-version: 7.2.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 47fafda8f..ebe37e494 100644 --- a/requirements.txt +++ b/requirements.txt @@ -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 diff --git a/setup.py b/setup.py index 80fc69370..a6817bcab 100644 --- a/setup.py +++ b/setup.py @@ -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", From 6f933deb30551075db122bf0c2a34e1befc0b733 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 25 Sep 2025 15:41:31 +0200 Subject: [PATCH 2/2] skip some too-flaky biocontainers tests --- tests/test_dependencies.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/test_dependencies.py b/tests/test_dependencies.py index f5ac0274b..046756f05 100644 --- a/tests/test_dependencies.py +++ b/tests/test_dependencies.py @@ -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") @@ -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())