feat: implement full TMT analysis pipeline, result visualizations, and Windows compatibility.#392
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…orkflow - Add visualization scripts for abundance, database search, heatmap, etc. - Add `get_abundance_data` helper in `results_helpers.py` to load data. - Update `src/Workflow.py` to support TMT analysis pipeline and group assignment UI. - Register new result visualization pages and clean up legacy menus in `app.py`.
- Update `StreamlitUI` to handle `flag_parameters` and render them as selectboxes. - Persist flag parameter metadata into session state and JSON configurations. - Update `CommandExecutor` to conditionally append flags without appending values. - Add readable command logging/printing before execution.
- Use Windows `taskkill` command via subprocess to forcefully terminate process trees on Windows. - Fallback to `os.kill` with `SIGTERM` on Linux/macOS environments. - Improve exception handling and stale PID file cleanup logic during process stop.
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Changes
TMT Analysis Workflow & Interactive Dashboard (
feat)src/Workflow.pyto transition from generic widgets to a comprehensive TMT workflow includingIsobaricAnalyzer,CometAdapter,PerocolatorAdapter,IDFilter,ProteinInterference, andProteinQuantifierapp.pylinked to modular visualization scripts (content/results_*.py) for interactive data exploration (Abundance, Volcano plots, PCA, Heatmaps, Pathway Analysis, etc.).2. Core Engine: Support for No-Value CLI Flags (
feat)StreamlitUIandCommandExecutorto cleanly handle boolean parameters that act as value-less CLI flags (e.g., passing-forceinstead of-force true).3. Cross-Platform Compatibility (
fix)WorkflowManager.py.subprocesswith Windows nativetaskkill /F /T /PIDfor robust tree-termination on Windows, while gracefully falling back to standardos.kill(pid, signal.SIGTERM)on Unix-like environments.Related Issues
Testing Checklist