Issue: Save files need verification that entire write completed successfully.
Solution:
- Modified sparks_csv_export(): Appends SHA256 checksum at end of CSV files
- Modified write_qc_excel_summary(): Adds checksum calculation and atomic save
- Both functions use temp file → checksum → atomic rename pattern
Benefits:
✓ Detects incomplete/corrupted writes automatically
✓ Atomic operations prevent partial file reads
✓ Checksum logged for debugging/verification
✓ Verifiable integrity on load (validation can be added later)
Testing: Verified checksum calculation and storage mechanism works correctly.
Issue: FC analysis (especially option 2 Beta-Series Correlation) hangs the UI for minutes.
Solution:
- Extracted all FC logic into FunctionalConnectivityWorker(QThread)
- Added progress dialog with real-time status updates via signals
- UI remains responsive during long-running computations
- Worker thread handles all 4 methods: Spectral Coherence, Envelope Correlation,
Beta-Series Correlation, Time-Resolved Spectral Coherence
Testing: Syntax validated. Logic moved 1:1 from synchronous process_request()
to worker.run() with added progress messaging.
Replaces naive backup/restore with intelligent file comparison:
- Only copies files newer than existing (mtime-based check)
- Skips plugins/, __pycache__, .git/ directories entirely
- Atomic file operations (copy to .tmp then rename)
- Reports files_updated vs files_skipped for transparency
Benefits over previous approach:
✓ Zero plugin backup/restore overhead
✓ Minimal disk I/O (unchanged files ignored)
✓ Plugin preservation is automatic, not post-process
✓ Faster update times, especially with many unchanged files
Add backup/restore mechanism to prevent plugin loss on update:
- Backs up plugins to temp location before update extraction
- Restores plugins after cleanup completes
- Each plugin preserved as-is (no uninstallation logic needed)
- Temp backups cleaned up automatically after successful restore
How to run tests (answers user question):
Manual execution:
./run_tests.sh # Quick way with auto-configured python
python -m pytest tests/unit/ -v # Direct pytest command
Automated (Gitea Actions):
- Tests run on every push/PR to main branch
- Workflow file: .gitea/workflows/test.yml
- Status visible at repo actions page
CI skips PySide6-dependent GUI tests by default.
Addresses audit findings A001, T002:
A001 - Undefined Plugin Interface:
- Created src/plugins/interface.py with abstract PluginBase class
- Defined AnalysisPlugin, VisualizationPlugin extensions
- Documented required methods (register_menu) and metadata attributes
- Added version compatibility constants and capability validation
T002 - Test Coverage for Core Modules:
- tests/unit/test_plugin_manager.py: 18+ tests for plugin lifecycle,
SSL context creation (security), version parsing, platform detection
- tests/unit/test_flares.py: 25+ tests for color mapping, QC metrics,
data validation, parameter defaults, path handling
Total test coverage increase: +43 test functions across 3 modules.
- Add shlex.quote() on all path arguments before subprocess calls (lines 404-407)
- Consolidate duplicated version_compare() function into single module-level utility
- Remove three identical class methods from UpdateCheckThread, LocalPendingUpdateCheckThread, and UpdateManager
- Add comprehensive test suite for updater.py security-critical functionality
- Add requirements-dev.txt with pytest dependency
Addresses critical security findings from flares_audit_report.md:
S001: Command Injection in Updater (CVSS ~7.5)
Q001: Duplicated version_compare logic
T001: Insufficient test coverage for updater.py
tyler
Hermes