Fix _Namespace dict-style assignment in main.py; refresh README#39
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Fix _Namespace dict-style assignment in main.py; refresh README#39
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…o lora style Agent-Logs-Url: https://github.com/sequana/multitax/sessions/eda15c30-5633-42c5-87f2-e4a92b1f8005 Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
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cokelaer
April 5, 2026 18:58
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okay for the readme. the main should not be changed. look at the test/test*py instead to make sure it follows same dict-style access as int he main.py and multitax.rules files
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April 5, 2026 19:09
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manager.config.configreturns a_Namespaceobject that supports attribute access but not item assignment, causingTypeError: '_Namespace' object does not support item assignmentwhen the CLI invokes the pipeline.Changes
main.py— replace allcfg["section"]["key"] = valuewithcfg.section.key = valuein the fourfill_*helpers, consistent with how other sequana pipelines (e.g. lora) write config values:README.rst— restructured to match lora repo conventions: proper title with====underline,---section headings, Quick Start step flow, dedicated sections for multi-DB usage, Apptainer, SLURM, and BLAST on unclassified reads.