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Nicola Soranzo
4e650b4e9a
(which started failing since ubuntu-latest was moved to 24.04) by upgrading apptainer to >=1.3.3 to include https://github.com/apptainer/apptainer/pull/2262 . Fix: ``` > assert "samtools:1.0--1" in results["passed"], results E AssertionError: E {'failed': [{'commands': ['python -c "import pyBigWig; assert(pyBigWig.numpy ' E '== 1); assert(pyBigWig.remote == 1)"'], E 'container': 'pybigwig:0.3.22--py36h54a71a5_0', E 'errors': [{'command': 'python -c "import pyBigWig; ' E 'assert(pyBigWig.numpy == 1); ' E 'assert(pyBigWig.remote == 1)"', E 'output': '\x1b[91mERROR : Could not write info to ' E 'setgroups: Permission denied\n' E '\x1b[0m\x1b[91mERROR : Error while ' E 'waiting event for user namespace mappings: ' E 'no event received\n' E '\x1b[0m'}, E {'import': 'pyBigWig', E 'output': '\x1b[91mERROR : Could not write info to ' E 'setgroups: Permission denied\n' E '\x1b[0m\x1b[91mERROR : Error while ' E 'waiting event for user namespace mappings: ' E 'no event received\n' E '\x1b[0m'}], E 'import_lang': 'python -c', E 'imports': ['pyBigWig']}, E {'commands': ['samtools view --help 2>&1 | grep Notes > /dev/null'], E 'container': 'samtools:1.0--1', E 'errors': [{'command': 'samtools view --help 2>&1 | grep Notes > ' E '/dev/null', E 'output': '\x1b[91mERROR : Could not write info to ' E 'setgroups: Permission denied\n' E '\x1b[0m\x1b[91mERROR : Error while ' E 'waiting event for user namespace mappings: ' E 'no event received\n' E '\x1b[0m'}], E 'import_lang': 'python -c'}], E 'notest': ['yasm:1.3.0--0'], E 'passed': []} E assert 'samtools:1.0--1' in [] ``` Also: - Improve assertion messages to facilitate debugging
49 lines
2.6 KiB
INI
49 lines
2.6 KiB
INI
[pytest]
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addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
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asyncio_mode = auto
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log_level = DEBUG
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# Install pytest-memray and set memray to true here to enable memory profiling of tests
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# memray = true
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pythonpath = lib
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markers =
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data_manager: marks test as a data_manager test
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external_dependency_management: slow tests which resolves dependencies with e.g. conda
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require_new_history: test that needs to be given a new history
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tool: marks test as a tool test
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requires_tool_id: marks API test as requiring specified tool id
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gtn_screenshot: marks test as a screenshot producer for galaxy training network
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local: mark indicates, that it is sufficient to run test locally to get relevant artifacts (e.g. screenshots)
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external: mark indicates, that test has to be run against external production server to get relevant artifacts (e.g. screenshots)
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green: test expected to pass
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red: test expected to fail
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command_line_tool: CWL conformance test tagged command_line_tool
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conditional: CWL conformance test tagged conditional
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docker: CWL conformance test tagged docker
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env_var: CWL conformance test tagged env_var
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expression_tool: CWL conformance test tagged expression_tool
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format_checking: CWL conformance test tagged format_checking
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initial_work_dir: CWL conformance test tagged initial_work_dir
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inline_javascript: CWL conformance test tagged inline_javascript
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inplace_update: CWL conformance test tagged inplace_update
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input_object_requirements: CWL conformance test tagged input_object_requirements
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load_listing: CWL conformance test tagged load_listing
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multiple: CWL conformance test tagged multiple
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multiple_input: CWL conformance test tagged multiple_input
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networkaccess: CWL conformance test tagged networkaccess
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required: required for CWL conformance
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resource: CWL conformance test tagged resource
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scatter: CWL conformance test tagged scatter
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schema_def: CWL conformance test tagged schema_def
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secondary_files: CWL conformance test tagged secondary_files
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shell_command: CWL conformance test tagged shell_command
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step_input: CWL conformance test tagged step_input
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step_input_expression: CWL conformance test tagged step_input_expression
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subworkflow: CWL conformance test tagged subworkflow
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timelimit: CWL conformance test tagged timelimit
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workflow: CWL conformance test tagged workflow
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work_reuse: CWL conformance test tagged work_reuse
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cwl_conformance: all CWL conformance tests
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cwl_conformance_v1_0: CWL v1.0 conformance tests
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cwl_conformance_v1_1: CWL v1.1 conformance tests
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cwl_conformance_v1_2: CWL v1.2 conformance tests
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