From a97c5bee66610370c4864b715282b281340b4691 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 10 May 2023 07:58:10 +0000 Subject: [PATCH 1/3] Update ruamel-yaml requirement Updates the requirements on [ruamel-yaml](https://sourceforge.net/p/ruamel-yaml/code/ci/default/tree) to permit the latest version. --- updated-dependencies: - dependency-name: ruamel-yaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- mypy-requirements.txt | 2 +- pyproject.toml | 2 +- requirements.txt | 4 ++-- setup.py | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/mypy-requirements.txt b/mypy-requirements.txt index 2820ce859..51972f3fd 100644 --- a/mypy-requirements.txt +++ b/mypy-requirements.txt @@ -1,5 +1,5 @@ mypy==1.2.0 # also update pyproject.toml -ruamel.yaml>=0.16.0,<0.17.22 +ruamel.yaml>=0.16.0,<0.17.27 schema-salad>=8.4,<9 cwl-utils >=0.22 types-requests diff --git a/pyproject.toml b/pyproject.toml index 7535f5926..12f4a145a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ requires = [ "types-pkg_resources", "types-requests", "types-psutil", - "ruamel.yaml>=0.16.0,<0.17.22", + "ruamel.yaml>=0.16.0,<0.17.27", "schema-salad>=8.2.20211104054942,<9", "cwl-utils >=0.19", 'toml', diff --git a/requirements.txt b/requirements.txt index 1758dab6e..c9afa7688 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ requests>=2.6.1 -ruamel.yaml>=0.16.0,<0.17.22;python_version>='3.10' -ruamel.yaml>=0.15,<0.17.22 +ruamel.yaml>=0.16.0,<0.17.27;python_version>='3.10' +ruamel.yaml>=0.15,<0.17.27 rdflib>=4.2.2,<6.4 rdflib>= 4.2.2, < 6.0.0;python_version<='3.6' shellescape>=3.4.1,<3.9 diff --git a/setup.py b/setup.py index 6f1449e40..d9062ceff 100644 --- a/setup.py +++ b/setup.py @@ -107,7 +107,7 @@ "setuptools", "requests >= 2.6.1", # >= 2.6.1 to workaround # https://github.com/ionrock/cachecontrol/issues/137 - "ruamel.yaml >= 0.15, < 0.17.22", + "ruamel.yaml >= 0.15, < 0.17.27", "rdflib >= 4.2.2, < 6.4.0", "rdflib >= 4.2.2, < 6.0.0;python_version<='3.6'", "shellescape >= 3.4.1, < 3.9", From 5f3d61a0a166972c964fa7ce8bac405fbdd3126b Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 11 May 2023 11:59:07 +0200 Subject: [PATCH 2/3] set upper pin on flake8-bugbear to avoid surprises --- lint-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lint-requirements.txt b/lint-requirements.txt index a4d2f0a3c..0b8dc8bff 100644 --- a/lint-requirements.txt +++ b/lint-requirements.txt @@ -1,3 +1,3 @@ -flake8-bugbear +flake8-bugbear < 23.6 black ~= 23.3 codespell From 8ee00d29ac4ce2cd703520f1a1502701d4c20462 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 11 May 2023 11:59:24 +0200 Subject: [PATCH 3/3] tests: address B908 by only checking one statement for the expected exception --- tests/test_examples.py | 3 +-- tests/test_mpi.py | 8 ++++---- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/tests/test_examples.py b/tests/test_examples.py index e39a079a3..3e07f9c69 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -816,8 +816,7 @@ def test_lifting() -> None: # fails if the step 'out' doesn't match. factory = cwltool.factory.Factory() with pytest.raises(ValidationException): - echo = factory.make(get_data("tests/test_bad_outputs_wf.cwl")) - assert echo(inp="foo") == {"out": "foo\n"} + factory.make(get_data("tests/test_bad_outputs_wf.cwl")) def test_malformed_outputs() -> None: diff --git a/tests/test_mpi.py b/tests/test_mpi.py index 7322f9e30..3eb011972 100644 --- a/tests/test_mpi.py +++ b/tests/test_mpi.py @@ -347,15 +347,15 @@ def test_docker_required(schema_ext11: Names) -> None: def test_docker_mpi_both_required(schema_ext11: Names) -> None: # Both required - error + lc, rc, tool = mk_tool(schema_ext11, [], reqs=[mpiReq, containerReq]) + clt = CommandLineTool(tool, lc) with pytest.raises(cwltool.errors.UnsupportedRequirement): - lc, rc, tool = mk_tool(schema_ext11, [], reqs=[mpiReq, containerReq]) - clt = CommandLineTool(tool, lc) clt.make_job_runner(rc) def test_docker_mpi_both_hinted(schema_ext11: Names) -> None: # Both hinted - error + lc, rc, tool = mk_tool(schema_ext11, [], hints=[mpiReq, containerReq]) + clt = CommandLineTool(tool, lc) with pytest.raises(cwltool.errors.UnsupportedRequirement): - lc, rc, tool = mk_tool(schema_ext11, [], hints=[mpiReq, containerReq]) - clt = CommandLineTool(tool, lc) clt.make_job_runner(rc)