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Summary

  • Added executable !pip install cells to all 18 example notebooks
  • Added explanatory "Prerequisites" markdown headers before install cells
  • Install cells include blackjax from the nested sampling fork and notebook-specific dependencies
  • JAX is not explicitly installed (it's a blackjax dependency)
  • Install cells are separate from import statements

Fixes #13

Changes

  • Modified 18 notebooks across basic/, advanced/, physics/, sbi/, and integrations/ directories
  • Each notebook now has:
    1. Title/header markdown
    2. Prerequisites markdown section
    3. Executable install cell with !pip install commands
    4. Rest of content

Test plan

  • Verify notebooks display correctly in Jupyter Book build
  • Confirm install commands work in notebook environments

🤖 Generated with Claude Code

williamjameshandley and others added 2 commits October 15, 2025 23:16
Adds executable !pip install cells at the start of all example notebooks
with the required dependencies:
- git+https://github.com/handley-lab/blackjax (main dependency)
- Example-specific packages (torch, tensorflow, scipy, etc.)
- Common utilities (numpy, tqdm, anesthetic, matplotlib where needed)

Addresses issue #13 by ensuring users can easily install all dependencies
before running any example.

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

Co-Authored-By: Claude <[email protected]>
Reordered cells so Prerequisites markdown headers appear before install
cells, not after. Correct order is now:
1. Title/header markdown
2. Prerequisites markdown
3. Install cell
4. Rest of content
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@yallup yallup left a comment

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Hard to give inline comments on ipynbs, good idea but some things missing:

  • integration examples are missing or have malformed prerequisites
  • One may be able to phrase the MD structure better, particularly in terms of how the sidebar toc picks things up, e.g. on the SBI example we have ## Prerequisites that then covers all the subsequent code that really should be under ## NSPosterior implementation. Prerequisites should be a lower indent level and the content should still be under the correct header.

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Prerequisites

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