From 4a70299f44cc0dca21bab95ccdf63331f941be0c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 3 Apr 2024 07:50:09 +0000 Subject: [PATCH 1/3] Update galaxy-tool-util requirement Updates the requirements on [galaxy-tool-util](https://github.com/galaxyproject/galaxy) to permit the latest version. - [Release notes](https://github.com/galaxyproject/galaxy/releases) - [Commits](https://github.com/galaxyproject/galaxy/compare/galaxy-tool-util-22.1.3...v24.0) --- updated-dependencies: - dependency-name: galaxy-tool-util dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- mypy-requirements.txt | 2 +- setup.py | 2 +- test-requirements.txt | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/mypy-requirements.txt b/mypy-requirements.txt index d89b7d1b8..579f36c44 100644 --- a/mypy-requirements.txt +++ b/mypy-requirements.txt @@ -5,5 +5,5 @@ types-requests types-setuptools types-psutil types-mock -galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3 +galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1 galaxy-util<23.2 diff --git a/setup.py b/setup.py index 63cb6ede3..280a466a4 100644 --- a/setup.py +++ b/setup.py @@ -141,7 +141,7 @@ ], extras_require={ "deps": [ - "galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3", + "galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1", "galaxy-util <23.2", ], }, diff --git a/test-requirements.txt b/test-requirements.txt index 0085cde01..965d5335f 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -9,5 +9,5 @@ pytest-mock>=1.10.0 pytest-cov arcp>=0.2.0 -rrequirements.txt -galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3 +galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1 galaxy-util<23.2 From 0e06938d8f8acad2434b7ab8ca8f5589e6f108d8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 3 Apr 2024 07:50:43 +0000 Subject: [PATCH 2/3] Update galaxy-util requirement from <23.2 to <24.1 Updates the requirements on [galaxy-util](https://github.com/galaxyproject/galaxy) to permit the latest version. - [Release notes](https://github.com/galaxyproject/galaxy/releases) - [Commits](https://github.com/galaxyproject/galaxy/compare/galaxy-util-19.9.0...v24.0) --- updated-dependencies: - dependency-name: galaxy-util dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- mypy-requirements.txt | 2 +- setup.py | 2 +- test-requirements.txt | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/mypy-requirements.txt b/mypy-requirements.txt index 579f36c44..c2db73673 100644 --- a/mypy-requirements.txt +++ b/mypy-requirements.txt @@ -6,4 +6,4 @@ types-setuptools types-psutil types-mock galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1 -galaxy-util<23.2 +galaxy-util<24.1 diff --git a/setup.py b/setup.py index 280a466a4..ddd5ed454 100644 --- a/setup.py +++ b/setup.py @@ -142,7 +142,7 @@ extras_require={ "deps": [ "galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1", - "galaxy-util <23.2", + "galaxy-util <24.1", ], }, python_requires=">=3.8, <4", diff --git a/test-requirements.txt b/test-requirements.txt index 965d5335f..d7901c3a5 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -10,4 +10,4 @@ pytest-cov arcp>=0.2.0 -rrequirements.txt galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1 -galaxy-util<23.2 +galaxy-util<24.1 From 7c801fe23c8bbbaa371e7f316898e59a2b5dcec4 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 3 Apr 2024 18:13:38 +0200 Subject: [PATCH 3/3] dependencies: make resolution test more flexible --- tests/test_dependencies.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/tests/test_dependencies.py b/tests/test_dependencies.py index 2acbf9f48..ae18a41ae 100644 --- a/tests/test_dependencies.py +++ b/tests/test_dependencies.py @@ -49,12 +49,10 @@ def test_biocontainers(tmp_path: Path) -> None: 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()) - assert ( - get_container_from_software_requirements( - True, tool, container_image_cache_path=str(tmp_path) - ) - == "quay.io/biocontainers/seqtk:1.4--he4a0461_1" + container = get_container_from_software_requirements( + True, tool, container_image_cache_path=str(tmp_path) ) + assert container is not None and container.startswith("quay.io/biocontainers/seqtk:1.4--") @pytest.fixture(scope="session")