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## Better Code, Better Science
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An open-source book on building better code for science using AI.
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Author: [Russ Poldrack](http://poldrack.github.io)
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Contributors: @giorgioarcara, @yarikoptic
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Content will be posted on [Substack](https://russpoldrack.substack.com/p/better-code-better-science) and added here as it is released.
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A rendered version of the complete book is available at [https://poldrack.github.io/BetterCodeBetterScience/](https://poldrack.github.io/BetterCodeBetterScience/).
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### Table of contents (see [here](https://russpoldrack.substack.com/p/upcoming-content-for-better-code) for a more detailed roadmap)
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- Introduction
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- [Part 1](https://russpoldrack.substack.com/p/better-code-better-science)
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- [Part 2](https://russpoldrack.substack.com/p/why-better-code-can-lead-to-better)
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- Essential Tools and Techniques
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- [Part 1: Version control](https://russpoldrack.substack.com/p/essential-tools-for-writing-better?r=1n86gc)
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- [Part 2: Large Language Models](https://russpoldrack.substack.com/p/essential-tools-for-writing-better-f69?r=1n86gc)
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- [Part 3: Managing environments](https://russpoldrack.substack.com/p/essential-tools-for-writing-better-f11?r=1n86gc)
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- Principles of Software Engineering
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- [Part 1: Intro](https://open.substack.com/pub/russpoldrack/p/principles-of-software-engineering)
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- [Part 2: Clean Coding](https://russpoldrack.substack.com/p/clean-coding)
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- [Part 3: Modularity and the "God object"](https://russpoldrack.substack.com/p/modularity-and-the-god-object)
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- [Part 4: Global variables](https://russpoldrack.substack.com/p/global-variables)
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- [Part 5: Defensive coding](https://open.substack.com/pub/russpoldrack/p/defensive-coding)
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- [Part 6: Coding portably](https://russpoldrack.substack.com/p/coding-portably?r=1n86gc)
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- [Part 7: Code formatting tools](https://russpoldrack.substack.com/p/code-formatting-tools?r=1n86gc)
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- [Part 8: Managing technical debt](https://russpoldrack.substack.com/p/managing-technical-debt?r=1n86gc)
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- Software Testing
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- [Part 1: Introduction](https://russpoldrack.substack.com/p/software-testing?r=1n86gc)
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- [Part 2: The structure of a good software test](https://russpoldrack.substack.com/p/the-structure-of-a-good-software?r=1n86gc)
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- [Part 3: The challenges of AI-generated tests](https://russpoldrack.substack.com/p/the-challenges-of-ai-generated-tests?r=1n86gc)
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- [Part 4: Test-driven development and AI-assisted coding](https://russpoldrack.substack.com/p/test-driven-development-and-ai-assisted?r=1n86gc)
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- [Part 5: Text fixtures and mocking](https://russpoldrack.substack.com/p/test-fixtures-and-mocking?r=1n86gc)
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- [Part 6: Parameterized testing](https://russpoldrack.substack.com/p/parameterized-testing?r=1n86gc)
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- [Part 7: Property-based testing](https://russpoldrack.substack.com/p/property-based-testing?r=1n86gc)
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- [Part 8: Automated testing with GitHub Actions](https://russpoldrack.substack.com/p/automated-testing-with-github-actions?r=1n86gc)
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- Part 9: Optimizing the testing workflow
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- Coding with AI
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- Using AI coding assistants
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- AI-assisted coding approaches
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- Project Structure and Management
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- Validating Scientific Analyses
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- Optimizing Performance
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- Data Organization and Management
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- Workflow Management
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- High-Performance Computing
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- Sharing Research Objects
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## Setup to run code
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### Database examples
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The examples in Chapter 7 require several database systems to be installed.
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#### Mongodb
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Install: https://www.mongodb.com/docs/v7.0/administration/install-community/
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#### Neo4j
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Install: https://neo4j.com/docs/operations-manual/current/installation/
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This repo has been broken into several individual repos that can be found under the [BetterCodeBetterScience Github organization](https://github.com/bettercodebetterscience). The latest version of the rendered book is now available [here](https://bettercodebetterscience.github.io/book/).

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