Hide advanced sorting configuration options #11
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Simplifies the user interface by hiding detailed sorting config options. Users only see --no-sort as the main control, but advanced options remain functional if you know about them. Hidden from help (but still work): - --skip-sgd, --skip-groom, --skip-topo - --sgd-iter-max, --sgd-eta-max - --sgd-theta, --sgd-eps, --sgd-cooling-start Visible: - --no-sort (simple on/off for all sorting) This keeps the interface clean for most users while preserving advanced configuration for developers and power users.
- Updated sparsification format from 'tree:K,K2,F,SIZE' to 'tree:neighbor,stranger,random,k-mer' for clearer parameter names (neighbor=k-nearest, stranger=k-farthest) - Removed legacy sparsification parsing code that was causing confusing error messages when using tree sampling - Removed unused sparsity_threshold field from SeqRush struct - sparsification now handled entirely at the aligner level through SparsificationStrategy enum - Updated all test code to match new SeqRush::new() signature This eliminates the "Invalid sparsification value" warning that appeared when using tree sampling, making the output cleaner.
Allow shorter forms of tree sampling for convenience: - tree:3 → TreeSampling(3, 0, 0.0, 16) - tree:3,2 → TreeSampling(3, 2, 0.0, 16) - tree:3,2,0.1 → TreeSampling(3, 2, 0.1, 16) - tree:3,2,0.1,21 → TreeSampling(3, 2, 0.1, 21) Defaults: - stranger count: 0 - random fraction: 0.0 - k-mer size: 16 This makes the most common case (just specifying k-nearest neighbors) much simpler to type.
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Summary
Hides advanced sorting configuration options from
--helpoutput to simplify the CLI interface while keeping them functional for power users.Changes
Added
hide = trueto 8 sorting-related flags:--skip-sgd,--skip-groom,--skip-topo- Skip individual pipeline stages--sgd-iter-max,--sgd-eta-max- SGD iteration parameters--sgd-theta,--sgd-eps,--sgd-cooling-start- SGD tuning parametersThe main user-facing control
--no-sortremains visible.Rationale
Most users don't need to tune SGD parameters or selectively skip pipeline stages. Hiding these options:
Hidden flags remain fully functional if specified on the command line.
Testing
cargo test)--helpshows simplified output--skip-sgd)