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Document ProteomicsLFQ automatic median normalization behavior

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## Description ProteomicsLFQ applies median normalization automatically to consensus features when multiple runs are provided, but this was undocumented, causing confusion about when normalization occurs and how to disable it....

Add __repr__ to pyOpenMS core classes for readable object inspection

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pyOpenMS objects currently display as memory addresses in Jupyter notebooks (``), making interactive exploration difficult. ## Changes Added `__repr__` and `__str__` methods via Cython addon files for: - **PeptideEvidence**: Shows...

Remove dependency on Enzymes.xml for EnzymesDB

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## Description Fixes #7698. Makes `Enzymes.xml` optional by embedding built-in enzyme definitions directly in C++, following the pattern established in PR #5092 for `ResidueDB`. **Changes:** - `DigestionEnzymeDB.h`: Added `readEnzymesFromFileIfPresent_()` that...

Fix ProtXMLFile to merge probability=0 proteins into leader's indistinguishable group

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## Description Fixes #5769 ProteinProphet assigns `probability=0` to "unneeded" proteins that are fully explained by other proteins in the same ``. Previously, these were parsed as separate indistinguishable groups, causing...

Merge compatible variable modifications in CometAdapter for improved performance

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Comet runs 3x+ slower when modifications with the same mass are specified as separate entries (e.g., `Carbamyl (K)`, `Carbamyl (R)`) instead of merged (`KR`). This also unnecessarily consumes the 9-entry...

Fix NASE to use average mass for precursor when use_avg_mass is selected

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## Description Fixes #8191: NASE always writes monoisotopic mass to MZtab output, ignoring the `use_avg_mass` flag. **Root cause:** `IdentificationDataConverter::exportMzTab` unconditionally called `getMonoWeight()` when calculating precursor mass, never checking the `mass_type`...

Fix MapAlignerPoseClustering crash on mzML files with insufficient data

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## Description MapAlignerPoseClustering crashes with "FATAL: uncaught exception!" when aligning mzML files that lack sufficient data points (e.g., blank files), as `TransformationModelLinear` throws exceptions that were not being caught. ##...

Improve parseRange_ error messages with parameter names and better guidance

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- [x] Understand the issue: parseRange_ error messages are unclear when user provides wrong delimiter - [x] Modify parseRange_ methods in TOPPBase.cpp to accept parameter name and provide better error...

Improve access method for DefaultParamHandler parameters

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- [x] Understand current DefaultParamHandler implementation and usage patterns - [x] Make updateMembers_() pure virtual (= 0) to enforce implementation in all derived classes - [x] Add empty updateMembers_() override...

Replace host and port parameters with unified endpoint parameter for HTTP and MQTT connections

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This PR replaces separate `host` and `port` parameters with a single `endpoint` parameter for HTTP and MQTT connections, unifying the configuration approach with the Kafka connection feature introduced in issue...