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Agent-Logs-Url: https://github.com/sequana/trf/sessions/55f99df6-8b27-4e97-b85c-43654b0ade42 Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
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April 3, 2026 22:38
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Sequana-wrappers missing from dependrncies. Poetry lock should be removed
Agent-Logs-Url: https://github.com/sequana/trf/sessions/0d5aeb2a-bfab-44ca-b34f-712ecf4de178 Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
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Done in 199b70e: added |
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fix: use bash to execute trf.sh in test_full
fix: use bash to execute trf.sh, add sequana-wrappers dependency, and remove poetry.lock
Apr 4, 2026
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Apptainers are failing. Change sh call to bash
Agent-Logs-Url: https://github.com/sequana/trf/sessions/a052469f-6f6e-4c78-a3b9-8be90d91bf74 Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
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Fixed in d9b2393: changed |
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test_fullwas failing becausetrf.shis generated withset -o pipefail, a bash-specific option, but the test invoked it viash(dash on Ubuntu), which rejects that option and exits early — leavingsummary.htmlnever produced. The same issue affected the Apptainer CI workflow.Changes
test/test_main.py: replacesh trf.shwithbash trf.shto match the#!/bin/bashshebang and bash-specific options in the generated script..github/workflows/apptainer.yml: replacesh trf.shwithbash trf.shfor the same reason.pyproject.toml: addsequana-wrappersas a package dependency so it is installed alongside the pipeline.poetry.lock: removed — lock files for libraries/pipelines should not be tracked in version control.