Yet again a new getting_started.ipynb using simulated data and simpler preprocessing pipeline

ConnectivityMetricsTutorials-main/.github/copilot-instructions.md

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+# Copilot Instructions — Hyperscanning Workshop
+
+## Language
+All code, comments, docstrings, and documentation must be written in English.
+
+## File Management
+Never create, delete, or edit any file without explicit user consent.
+
+## Project Structure
+- Notebooks: `01_foundations/` and `02_connectivity_metrics/`, by category (A, B, C...)
+- Reusable functions: `src/` directory
+- Naming: `A01_`, `A02_`, `B01_`, etc.
+- Quick notebooks: `*_quick.ipynb` (import from src/ instead of inline definitions)
+
+## Git Workflow
+- One branch per notebook: `feature/<notebook_id>`
+- Clear commit messages
+- Merge to main after review
+
+## Dependencies
+Managed with Poetry. Core: numpy, scipy, matplotlib, mne, hypyp.
+
+## Typed Python
+- Complete type hints on all functions (params + return)
+- Use `numpy.typing.NDArray` for arrays
+- Use `typing` module (Optional, Union, Tuple, Callable)
+- mypy strict compatible
+
+## Coding Standards
+- PEP 8 compliant
+- NumPy-style docstrings
+- Functions over 20 lines go to `src/`
+- No hardcoded values
+
+## Notebook Structure
+- **Full notebooks**: See `docs/NOTEBOOK_TEMPLATE.md`
+- **Quick notebooks**: See `docs/NOTEBOOK_QUICK_TEMPLATE.md`
+- Structure: Introduction → Intuition → Implementation → Visualization → HyPyP comparison → Application → Summary → Discussion
+
+## Notebook Cell Order (CRITICAL)
+For ALL notebooks (full and quick):
+1. Cell 1 = Header (`# [ID]: Title` + Duration + Prerequisites + Learning Objectives)
+2. Cell 2 = Table of Contents (`## Table of Contents` with `#section-X-...` anchors)
+3. Cell 3 = Imports (Code cell with `# =====` style headers)
+4. Cells 4+ = Sections
+5. Last 3 cells = Summary, External Resources, Discussion Questions
+
+## Colors (CRITICAL)
+- Always import: `from colors import COLORS`
+- Use ONLY these keys: `signal_1`, `signal_2`, `signal_3`, `signal_4`, `signal_5`, `signal_6`
+- For EEG bands: `delta`, `theta`, `alpha`, `beta`, `gamma`
+- NEVER use: `primary`, `secondary`, `accent1`, `accent2` (these keys DO NOT EXIST)
+
+## NotebookLM Resources (CRITICAL)
+In External Resources section, use this EXACT format:
+```markdown
+### 🎧 NotebookLM Resources
+
+- [📺 Video Overview](URL) - Video overview of [topic] concepts
+- [📝 Quiz](URL) - Test your understanding
+- [🗂️ Flashcards](URL) - Review key concepts
+```
+- ALWAYS say "Video" — NEVER say "Audio"
+- The 📺 emoji is for VIDEO, not audio
+- Description must start with "Video overview of..."
+
+## Exercises Format (CRITICAL)
+Use this EXACT format for exercises:
+```markdown
+---
+
+<a id="section-N-exercises"></a>
+## N. Exercises
+
+### 🎯 Exercise 1: Title
+
+**Task:** Description of what to do.
+
+- Bullet point instructions
+- More instructions
+
+\`\`\`python
+# Your code here
+\`\`\`
+
+<details>
+<summary>💡 Click to reveal solution</summary>
+
+\`\`\`python
+# Solution code
+\`\`\`
+
+</details>
+```
+- Always include 🎯 emoji before exercise title
+- Always use `<details>` for solutions
+- Always include `<a id="..."></a>` anchor before section title
+
+## Visualization
+Follow STYLE_GUIDE.md for colors, dimensions, fonts.

ConnectivityMetricsTutorials-main/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+.mypy_cache/
+.ruff_cache/
+
+# Jupyter
+.ipynb_checkpoints/
+*.ipynb_checkpoints
+
+# Environment
+.venv/
+.env
+*.egg-info/
+
+# IDE
+.vscode/
+.idea/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Data (large files)
+data/raw/
+data/processed/
+*.fif
+*.edf
+*.bdf
+
+# Outputs
+outputs/
+figures/
+*.png
+*.pdf
+
+# Documentation (internal)
+docs/
+
+# Poetry
+poetry.lock

ConnectivityMetricsTutorials-main/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - numpy
+          - types-setuptools
+        args: [--ignore-missing-imports]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: [--maxkb=1000]

ConnectivityMetricsTutorials-main/LICENSE

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+Creative Commons Attribution 4.0 International License
+
+Copyright (c) 2025 Social Neuro AI Lab
+
+You are free to:
+- Share: copy and redistribute the material in any medium or format
+- Adapt: remix, transform, and build upon the material for any purpose, even commercially
+
+Under the following terms:
+- Attribution: You must give appropriate credit, provide a link to the license, and indicate if changes were made.
+
+Full license text: https://creativecommons.org/licenses/by/4.0/legalcode

ConnectivityMetricsTutorials-main/README.md

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+