fix: Resolve critical bugs in pattern detection, zarr portability, an…#2
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fix: Resolve critical bugs in pattern detection, zarr portability, an…#2
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…d GUI help system Fixed multiple critical issues that were causing silent failures and portability problems: Changes by functional area: * Storage Backend: Fix zarr filename mapping to use only filenames instead of full paths, making zarr files portable across different machines and directory structures * Core Pipeline: Convert pattern detection warnings to errors for fail-loud behavior, fix critical KeyError bug when wells have no patterns, add detailed error diagnostics * Pattern Detection: Convert pattern generation warning to ValueError with actionable guidance when no patterns can be generated from files * GUI System: Fix parameter order bug in help window constructors that caused AttributeError when HelpIndicator objects were passed as color_scheme parameter All changes enforce fail-loud behavior instead of silent failures, improving debugging and preventing data loss from undetected processing failures.
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Oct 4, 2025
Comprehensive documentation of all fixes: - Bug #1: OMERO data directory path (CRITICAL) - Bug #2: Docker Compose version warning - Bug #3: Execution server default path - Bug #4: Demo script path Includes: - Problem descriptions - Solutions implemented - Code changes - Technical details of dual-mode architecture - Migration guide - Testing status
popjell
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Oct 15, 2025
Comprehensive documentation of all fixes: - Bug OpenHCSDev#1: OMERO data directory path (CRITICAL) - Bug OpenHCSDev#2: Docker Compose version warning - Bug OpenHCSDev#3: Execution server default path - Bug OpenHCSDev#4: Demo script path Includes: - Problem descriptions - Solutions implemented - Code changes - Technical details of dual-mode architecture - Migration guide - Testing status
popjell
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Oct 15, 2025
Comprehensive documentation of all fixes: - Bug OpenHCSDev#1: OMERO data directory path (CRITICAL) - Bug OpenHCSDev#2: Docker Compose version warning - Bug OpenHCSDev#3: Execution server default path - Bug OpenHCSDev#4: Demo script path Includes: - Problem descriptions - Solutions implemented - Code changes - Technical details of dual-mode architecture - Migration guide - Testing status
trissim
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Nov 5, 2025
Fixed bug where sequential processing filtering was comparing group_by component values against sequential_components values, which only worked when both were the same component (e.g., both CHANNEL). Changes: - Added _filter_patterns_by_component() helper function that filters patterns by extracting metadata from pattern strings - Moved sequential filtering to BEFORE prepare_patterns_and_functions() so it filters raw patterns before they're grouped by group_by component - Removed old broken filtering code that compared grouped_patterns keys (from group_by) with sequential component values This ensures sequential processing works correctly when sequential_components != group_by, for example: - sequential_components=[Z_INDEX] with group_by=CHANNEL - sequential_components=[TIMEPOINT] with group_by=Z_INDEX Implements fix strategy from plans/sequential-processing-fixes.md (Bug #2) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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…d GUI help system
Fixed multiple critical issues that were causing silent failures and portability problems:
Changes by functional area:
All changes enforce fail-loud behavior instead of silent failures, improving debugging and preventing data loss from undetected processing failures.