Feature/tool catalog implementation#3

Merged

ypriverol merged 15 commits intomainfrom

feature/tool-catalog-implementation

Mar 25, 2026

Commits on Mar 24, 2026

Add tool catalog design spec with 145 CLI tools for proteomics/metabolomics

ypriverol
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claude
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Commits on Mar 25, 2026

Add 134 new pyopenms CLI tools across 13 categories

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Reorganize tools by topic and remove 20 non-pyopenms scripts

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Rewrite README with purpose, AI disclaimer, tool structure docs

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Rename scripts/ to tools/ and update all references

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Migrate all 123 CLI tools from argparse to click

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Fix metabolite_class_predictor: use correct pyopenms API and widen amino acid H:C range

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Fix 22 failing tests: pyopenms API fixes, logic bugs, click test migration

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Fix idxml_to_tsv_exporter: add required document_id param to IdXMLFile.store

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Fix idxml_to_tsv_exporter for pyopenms 3.5.0 compatibility

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minor changes
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update markdown
timosachsenberg
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Address Copilot PR #3 review: fix paths, API safety, docs, and CLI UX

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Update tools/proteomics/peptide_analysis/charge_state_predictor/tests/test_charge_state_predictor.py

ypriverol
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Copilot
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Update tools/proteomics/peptide_analysis/modification_mass_calculator/tests/test_modification_mass_calculator.py

ypriverol
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Copilot
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