feat: implement auto strategy for #59#82
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Add comprehensive test suite for CLI strategy routing feature: - Tests for --strategy flag with choices [fast, balanced, sensitive] - Verification that balanced is the default strategy - Routing tests to confirm correct built-in workflow selection - Error handling when --strategy used with torch-embedded workflows - Help text validation for strategy options and restrictions - Integration tests with multi-scheme torch support - Path resolution and workflow discovery interaction tests All tests currently fail as expected (RED phase of TDD). Feature implementation will make these tests pass. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Implement CLI strategy routing with --strategy flag for torchbase run command. Key features: - Added --strategy flag with choices [fast, balanced, sensitive] - Default strategy is 'balanced' - CLI routes to appropriate built-in workflow based on strategy selection - Error handling: raises error if --strategy used with torch-embedded workflows - Integrated with multi-scheme support from #53 - Help text explains strategy options and restrictions Built-in workflows: - fast_typing.wdl: MinHash-only pipeline (fastest) - balanced_typing.wdl: MinHash + alignment fallback (default) - sensitive_typing.wdl: Full alignment-based calling (most accurate) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Add comprehensive test suite for auto strategy decision logic: - Tests for --strategy auto flag with CLI integration - Pre-analysis sequence inspection tests (length, N50, format) - Decision routing tests for contigs (fast), reads (balanced), edge cases - Decision rationale validation in workflow output notes - Helper function tests for _analyze_sequences (mean length, N50, type detection) - Integration tests for end-to-end auto strategy workflow - Error handling tests for embedded workflows and analysis failures All tests currently fail as expected (RED phase of TDD). Feature implementation will make these tests pass. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Implements automatic strategy detection and selection based on input sequence characteristics: - Added _analyze_sequences() function that inspects input files and extracts statistics (mean length, N50) - Decision logic: contigs (mean >1000bp) route to fast, reads (mean <500bp) route to balanced, edge cases default to balanced - Added 'auto' as a valid --strategy choice alongside 'fast', 'balanced', 'sensitive' - Updated help text to document auto strategy behavior - Decision rationale included in workflow inputs as 'auto_decision' parameter - Handles both FASTA and FASTQ formats - Gracefully defaults to balanced strategy on analysis errors or empty files - Updated WDL files to accept optional auto_decision input parameter Tests: 28/29 passing. One test fails due to excessive Path mocking that prevents file reading in a unit test scenario, but integration tests and all core functionality tests pass. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Removed overly broad Path mock that was causing workflow path to be a MagicMock instead of actual path string. This prevented the test from checking if fast_typing was correctly selected.
- Add FileReaderWithPath wrapper class to store original file paths - Use wrapper in ReadsFile converter for all compressed formats - Simplify auto strategy path extraction to use _original_path attribute - Replace dummy workflow files with real implementations from main - All 29 auto strategy tests pass Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
# Conflicts: # torchbase/cli.py
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Summary
Implements
--strategy autofeature for automatic input type detection and strategy selection:Implementation Details
_analyze_sequences()function that reads FASTA/FASTQ files and calculates length statisticsTest Status
Acceptance Criteria Met
--strategy autooption works in CLI