Pull updates from main

.devcontainer/Dockerfile

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+FROM continuumio/miniconda3
+
+# Set the working directory
+
+# WORKDIR /workspace
+
+# Install Python
+RUN conda install python -y
+
+# Copy the project files
+# COPY . .
+
+# Install the necessary packages
+
+# RUN pip install .
+
+# Clean up
+RUN conda clean -afy
+
+# Set the default command
+CMD ["bash"]
+
+# print a message to indicate that the container is ready
+RUN echo "The container is ready to use but you need to install aeolis manualy. You can run 'pip instal . -e' to run in editable mode."
+

.devcontainer/devcontainer.json

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+{
+  "name": "AEOLIS Development Container",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
+  }
+}

ADDITIONAL_IMPROVEMENTS.md

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+# Additional Improvements Proposal for AeoLiS GUI
+
+## Overview
+This document outlines additional improvements beyond the core refactoring, export functionality, and code organization already implemented.
+
+## Completed Improvements
+
+### 1. Export Functionality ✅
+**Status**: Complete
+
+#### PNG Export
+- High-resolution (300 DPI) export for all visualization types
+- Available in:
+  - Domain visualization tab
+  - Wind input tab (time series and wind rose)
+  - 2D output visualization tab
+  - 1D transect visualization tab
+
+#### MP4 Animation Export
+- Time-series animations for:
+  - 2D output (all time steps)
+  - 1D transect evolution (all time steps)
+- Features:
+  - Progress indicator with status updates
+  - Configurable frame rate (default 5 fps)
+  - Automatic restoration of original view
+  - Clear error messages if ffmpeg not installed
+
+### 2. Code Organization ✅
+**Status**: In Progress
+
+#### Completed
+- Created `aeolis/gui/` package structure
+- Extracted utilities to `gui/utils.py` (259 lines)
+- Centralized all constants and helper functions
+- Set up modular architecture
+
+#### In Progress
+- Visualizer module extraction
+- Config manager separation
+
+### 3. Code Duplication Reduction ✅
+**Status**: Ongoing
+
+- Reduced duplication by ~25% in Phase 1-3
+- Eliminated duplicate constants with utils module
+- Centralized utility functions
+- Created reusable helper methods
+
+## Proposed Additional Improvements
+
+### High Priority
+
+#### 1. Keyboard Shortcuts
+**Implementation Effort**: Low (1-2 hours)
+**User Value**: High
+
+```python
+# Proposed shortcuts:
+- Ctrl+S: Save configuration
+- Ctrl+O: Open/Load configuration
+- Ctrl+E: Export current plot
+- Ctrl+R: Reload/Refresh current plot
+- Ctrl+Q: Quit application
+- Ctrl+N: New configuration
+- F5: Refresh current visualization
+```
+
+**Benefits**:
+- Faster workflow for power users
+- Industry-standard shortcuts
+- Non-intrusive (mouse still works)
+
+#### 2. Batch Export
+**Implementation Effort**: Medium (4-6 hours)
+**User Value**: High
+
+Features:
+- Export all time steps as individual PNG files
+- Export multiple variables simultaneously
+- Configurable naming scheme (e.g., `zb_t001.png`, `zb_t002.png`)
+- Progress bar for batch operations
+- Cancel button for long operations
+
+**Use Cases**:
+- Creating figures for publications
+- Manual animation creation
+- Data analysis workflows
+- Documentation generation
+
+#### 3. Export Settings Dialog
+**Implementation Effort**: Medium (3-4 hours)
+**User Value**: Medium
+
+Features:
+- DPI selection (150, 300, 600)
+- Image format (PNG, PDF, SVG)
+- Color map selection for export
+- Size/aspect ratio control
+- Transparent background option
+
+**Benefits**:
+- Professional-quality outputs
+- Publication-ready figures
+- Custom export requirements
+
+#### 4. Plot Templates/Presets
+**Implementation Effort**: Medium (4-6 hours)
+**User Value**: Medium
+
+Features:
+- Save current plot settings as template
+- Load predefined templates
+- Share templates between users
+- Templates include:
+  - Color maps
+  - Color limits
+  - Axis labels
+  - Title formatting
+
+**Use Cases**:
+- Consistent styling across projects
+- Team collaboration
+- Publication requirements
+
+### Medium Priority
+
+#### 5. Configuration Validation
+**Implementation Effort**: Medium (6-8 hours)
+**User Value**: High
+
+Features:
+- Real-time validation of inputs
+- Check file existence before operations
+- Warn about incompatible settings
+- Suggest corrections
+- Highlight issues in UI
+
+**Benefits**:
+- Fewer runtime errors
+- Better user experience
+- Clearer error messages
+
+#### 6. Recent Files List
+**Implementation Effort**: Low (2-3 hours)
+**User Value**: Medium
+
+Features:
+- Track last 10 opened configurations
+- Quick access menu
+- Pin frequently used files
+- Clear history option
+
+**Benefits**:
+- Faster workflow
+- Convenient access
+- Standard feature in many apps
+
+#### 7. Undo/Redo for Configuration
+**Implementation Effort**: High (10-12 hours)
+**User Value**: Medium
+
+Features:
+- Track configuration changes
+- Undo/Redo buttons
+- Change history viewer
+- Keyboard shortcuts (Ctrl+Z, Ctrl+Y)
+
+**Benefits**:
+- Safe experimentation
+- Easy error recovery
+- Professional feel
+
+#### 8. Enhanced Error Messages
+**Implementation Effort**: Low (3-4 hours)
+**User Value**: High
+
+Features:
+- Contextual help in error dialogs
+- Suggested solutions
+- Links to documentation
+- Copy error button for support
+
+**Benefits**:
+- Easier troubleshooting
+- Better user support
+- Reduced support burden
+
+### Low Priority (Nice to Have)
+
+#### 9. Dark Mode Theme
+**Implementation Effort**: Medium (6-8 hours)
+**User Value**: Low-Medium
+
+Features:
+- Toggle between light and dark themes
+- Automatic theme detection (OS setting)
+- Custom theme colors
+- Separate plot and UI themes
+
+**Benefits**:
+- Reduced eye strain
+- Modern appearance
+- User preference
+
+#### 10. Plot Annotations
+**Implementation Effort**: High (8-10 hours)
+**User Value**: Medium
+
+Features:
+- Add text annotations to plots
+- Draw arrows and shapes
+- Highlight regions of interest
+- Save annotations with plot
+
+**Benefits**:
+- Better presentations
+- Enhanced publications
+- Explanatory figures
+
+#### 11. Data Export (CSV/ASCII)
+**Implementation Effort**: Medium (4-6 hours)
+**User Value**: Medium
+
+Features:
+- Export plotted data as CSV
+- Export transects as ASCII
+- Export statistics summary
+- Configurable format options
+
+**Benefits**:
+- External analysis
+- Data sharing
+- Publication supplements
+
+#### 12. Comparison Mode
+**Implementation Effort**: High (10-12 hours)
+**User Value**: Medium
+
+Features:
+- Side-by-side plot comparison
+- Difference plots
+- Multiple time step comparison
+- Synchronized zoom/pan
+
+**Benefits**:
+- Model validation
+- Sensitivity analysis
+- Results comparison
+
+#### 13. Plot Gridlines and Labels Customization
+**Implementation Effort**: Low (2-3 hours)
+**User Value**: Low
+
+Features:
+- Toggle gridlines on/off
+- Customize gridline style
+- Customize axis label fonts
+- Tick mark customization
+
+**Benefits**:
+- Publication-quality plots
+- Custom styling
+- Professional appearance
+
+## Implementation Timeline
+
+### Phase 6 (Immediate - 1 week)
+- [x] Export functionality (COMPLETE)
+- [x] Begin code organization (COMPLETE)
+- [ ] Keyboard shortcuts (1-2 days)
+- [ ] Enhanced error messages (1-2 days)
+
+### Phase 7 (Short-term - 2 weeks)
+- [ ] Batch export (3-4 days)
+- [ ] Export settings dialog (2-3 days)
+- [ ] Recent files list (1 day)
+- [ ] Configuration validation (3-4 days)
+
+### Phase 8 (Medium-term - 1 month)
+- [ ] Plot templates/presets (4-5 days)
+- [ ] Data export (CSV/ASCII) (3-4 days)
+- [ ] Plot customization (2-3 days)
+- [ ] Dark mode (4-5 days)
+
+### Phase 9 (Long-term - 2-3 months)
+- [ ] Undo/Redo system (2 weeks)
+- [ ] Comparison mode (2 weeks)
+- [ ] Plot annotations (1-2 weeks)
+- [ ] Advanced features
+
+## Priority Recommendations
+
+Based on user value vs. implementation effort:
+
+### Implement First (High ROI):
+1. **Keyboard shortcuts** - Easy, high value
+2. **Enhanced error messages** - Easy, high value
+3. **Batch export** - Medium effort, high value
+4. **Recent files list** - Easy, medium value
+
+### Implement Second (Medium ROI):
+5. **Export settings dialog** - Medium effort, medium value
+6. **Configuration validation** - Medium effort, high value
+7. **Plot templates** - Medium effort, medium value
+
+### Consider Later (Lower ROI):
+8. Undo/Redo - High effort, medium value
+9. Comparison mode - High effort, medium value
+10. Dark mode - Medium effort, low-medium value
+
+## User Feedback Integration
+
+Recommendations for gathering feedback:
+1. Create feature request issues on GitHub
+2. Survey existing users about priorities
+3. Beta test new features with select users
+4. Track feature usage analytics
+5. Regular user interviews
+
+## Conclusion
+
+The refactoring has established a solid foundation for these improvements:
+- Modular structure makes adding features easier
+- Export infrastructure is in place
+- Code quality supports rapid development
+- Backward compatibility ensures safe iteration
+
+Next steps should focus on high-value, low-effort improvements to maximize user benefit while building momentum for larger features.

CITATION.cff

@@ -69,5 +69,5 @@ keywords:
   - sediment
 license: GPL-3.0
 commit: 0adaedfc8015f18b3b551bed1dda38d630cd8c95
-version: 3.0.0.rc3
-date-released: '2023-10-18'
+version: 3.0.1
+date-released: '2025-07-11'