Copilot/vscode1760774048067 (#6)

* update project files

* Checkpoint from VS Code for coding agent session

* [WIP] Update dependencies and requirements with enhancements and refactoring (#5)

* Checkpoint from VS Code for coding agent session

* Apply suggestion from @Copilot

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Apply suggestion from @Copilot

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Apply suggestion from @Copilot

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: qrcode1337 <69130457+QRcode1337@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Bump requests from 2.32.3 to 2.32.4 in the pip group across 1 directory (#4)

Bumps the pip group with 1 update in the / directory: [requests](https://github.com/psf/requests).


Updates `requests` from 2.32.3 to 2.32.4
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.32.3...v2.32.4)

---
updated-dependencies:
- dependency-name: requests
  dependency-version: 2.32.4
  dependency-type: direct:production
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump certifi in the pip group across 1 directory (#3)

Bumps the pip group with 1 update in the / directory: [certifi](https://github.com/certifi/python-certifi).


Updates `certifi` from 2024.6.2 to 2024.7.4
- [Commits](certifi/python-certifi@2024.06.02...2024.07.04)

---
updated-dependencies:
- dependency-name: certifi
  dependency-version: 2024.7.4
  dependency-type: indirect
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump h11 from 0.14.0 to 0.16.0 in the pip group across 1 directory (#2)

Bumps the pip group with 1 update in the / directory: [h11](https://github.com/python-hyper/h11).


Updates `h11` from 0.14.0 to 0.16.0
- [Commits](python-hyper/h11@v0.14.0...v0.16.0)

---
updated-dependencies:
- dependency-name: h11
  dependency-version: 0.16.0
  dependency-type: indirect
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump urllib3 from 2.2.2 to 2.5.0 in the pip group across 1 directory (#1)

Bumps the pip group with 1 update in the / directory: [urllib3](https://github.com/urllib3/urllib3).


Updates `urllib3` from 2.2.2 to 2.5.0
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](urllib3/urllib3@2.2.2...2.5.0)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-version: 2.5.0
  dependency-type: indirect
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Improve performance, robustness, and documentation

- Optimize network graph physics with collision detection improvements
  • Add physics settling detection to skip unnecessary calculations
  • Implement Newton's third law for bidirectional forces
  • Reduce redundant pair-wise checks by processing node pairs once

- Enhance signal handling robustness in Worker threads
  • Add null checks to prevent signal emission after object cleanup
  • Maintain strong signal reference to prevent garbage collection
  • Improve error handling with safe signal checks

- Optimize conversation message filtering
  • Replace O(n²) duplicate detection with O(1) set-based approach
  • Add content tracking to prevent duplicate messages efficiently

- Expand project documentation in AGENTS.md
  • Add comprehensive architecture overview
  • Document module structure and threading model
  • Include conversation data model and branching system details

- Clean up conversation_full.html (removed 2000+ lines)
- Update dependencies in pyproject.toml

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Add macOS system files to gitignore

- Add .DS_Store, .AppleDouble, .LSOverride to prevent tracking
- Prevents macOS-specific files from cluttering repository

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Merge main into copilot/vscode1760774048067

Resolved conflicts:
- AGENTS.md: Kept comprehensive project documentation from copilot branch
- Removed VS Code MCP settings file (should not be in repository)

Changes from main:
- .gitignore: Added macOS system files (.DS_Store, .AppleDouble, .LSOverride)
- poetry.lock: Updated dependencies
- pyproject.toml: Dependency updates

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Preserve accumulated node velocities during collision handling

* Add untracked files

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Claude <noreply@anthropic.com>

Author: 5 people

gui.py

@@ -227,7 +227,11 @@ def apply_collision_dynamics(self):
             if node_id not in self.node_positions:
                 continue
 
-            vx, vy = self.node_velocities.get(node_id, (0, 0))
+            # Start with any velocity already accumulated for this node
+            vx, vy = new_velocities.get(
+                node_id,
+                self.node_velocities.get(node_id, (0, 0))
+            )
             x1, y1 = self.node_positions[node_id]
 
             # Apply repulsion between nodes - only check nodes after current (avoid duplicate pairs)