fix: missing initialization of uint32_t in config struct. Set default value in ConfigSpecification instead.

[taepper]

Summary

The struct did not initialize the field, therefore it contained random bytes, when no value was given. I talked with Chaoran and we think setting it to 0 by default is best for users. (no need for configuration in e.g. Loculus)

PR Checklist

• All necessary documentation has been adapted or there is an issue to do so.
• The implemented feature is covered by an appropriate test.

[github-actions]

This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog.

Note that this might contain changes that are on main, but not yet released.

Changelog:

0.7.0 (2025-06-18)

⚠ BREAKING CHANGES

• rename DatabaseInfo field totalSize to verticalBitmapsSize and nBitmapsSize to horizontalBitmapsSize
• the field sequenceName in the Fasta and FastaAligned is now named sequenceNames and required to be an array
• streaming implementation of Details action. select-k also for Fasta and FastaAligned
• streaming implementation of the Fasta action with the arrow framework

Features

• arrow framework for query engine and specialized implementation for FastaAligned action (b719e15), closes #654
• cache DatabaseInfo, add amino acid sequence columns to size info (bc0d0a2)
• silo: add recommended vscode extensions to .vscode folder for developers using vscode (d2c74db)
• silo: improve the docs and update build_with_conan.py (#779) (f176fd6)
• streaming implementation of the Fasta action with the arrow framework (0392207)
• update onetbb, nlohmann_json, gtest, roaring, yaml-cpp and zstd to most recent versions (3abd2d9)

Bug Fixes

• bug in table_scan, that confused row_id in the database with row_id in the current batch (9b7dce4)
• correctly error when the input data contains illegal insertion characters (4867c32)
• make better use of the arrow::acero API, no longer rely on passing the stream inside an extra operator (dabb186)
• missing initialization of uint32_t in config struct. Set default value in ConfigSpecification instead. (97edeb3)
• properly catch exceptions during arrow execution to avoid program termination (6caee0e)
• remove erroneous warning printed on every preprocessing run (82b65c8)

Code Refactoring

• make sequenceName in Fasta and FastaAligned actions an array (6c345fb)
• streaming implementation of Details action. select-k also for Fasta and FastaAligned (bfbb3ee)