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Update repository links to reflect new ownership and ensure consistency across documentation
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‎AGENTS.md‎

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# AGENTS.md
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This repository contains the online guide. The runnable exercise is at https://github.com/ilarsf/practical-genai-agentic-coding-example.
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This repository contains the online guide. The runnable exercise is at https://github.com/FritscheLab/practical-genai-agentic-coding-example.
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Read README.md and the relevant lesson before editing. Keep the two language paths, relative links, lab theme, and Part 1 navigation intact. Use synthetic examples and copyable fenced prompts. Check provider claims against their official sources and preserve source review dates.
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‎CITATION.cff‎

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given-names: "Lars G."
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affiliation: "University of Michigan"
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website: "https://fritschelab.org/"
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repository-code: "https://github.com/ilarsf/practical-genai-agentic-coding-guide"
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url: "https://ilarsf.github.io/practical-genai-agentic-coding-guide/"
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repository-code: "https://github.com/FritscheLab/practical-genai-agentic-coding-guide"
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url: "https://fritschelab.org/practical-genai-agentic-coding-guide/"
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license: "GPL-3.0-only"
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keywords:
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- "agentic coding"

‎README.md‎

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# Practical GenAI Agentic Coding Guide
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**[Read the online guide](https://ilarsf.github.io/practical-genai-agentic-coding-guide/).** Choose [Python](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/paths/python/) or [R](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/paths/r/), then follow six lessons through one reporting change, verification, review, and a short handoff.
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**[Read the online guide](https://fritschelab.org/practical-genai-agentic-coding-guide/).** Choose [Python](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/paths/python/) or [R](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/paths/r/), then follow six lessons through one reporting change, verification, review, and a short handoff.
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This is Part 2 of the [Practical GenAI series](https://fritschelab.org/practical-genai-coding-guide/), from [Lars G. Fritsche](https://medschool.umich.edu/profile/4980/lars-fritsche) and the [Fritsche Lab](https://fritschelab.org/) at the University of Michigan.
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## Get the exercise
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The runnable Python/R pipeline, synthetic data, tests, and agent instructions are in the **[example repository](https://github.com/ilarsf/practical-genai-agentic-coding-example)**. Download only that repository and follow along online. It also includes the language walkthroughs for offline use.
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The runnable Python/R pipeline, synthetic data, tests, and agent instructions are in the **[example repository](https://github.com/FritscheLab/practical-genai-agentic-coding-example)**. Download only that repository and follow along online. It also includes the language walkthroughs for offline use.
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```bash
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git clone https://github.com/ilarsf/practical-genai-agentic-coding-example.git
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git clone https://github.com/FritscheLab/practical-genai-agentic-coding-example.git
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cd practical-genai-agentic-coding-example
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```
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Start with its README and your chosen language's setup. You should be comfortable running a Python or R script and using a terminal; the lessons explain the Git steps. The baseline uses synthetic data and needs no model API or credentials. Use an institution-approved coding assistant for the agent exercise.
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## Explore the guide
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- [Agent setup](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/platforms/): configure your coding client and check its access.
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- [Repository practices](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/practices/): context, testing, logs, and handoffs.
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- [Teaching materials](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/lab_meeting/): a 45-minute workshop and slides.
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- [Lab data guidance](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/reference/lab-data-policy.html): institutional requirements before adapting the workflow to study data.
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- [Agent setup](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/platforms/): configure your coding client and check its access.
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- [Repository practices](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/practices/): context, testing, logs, and handoffs.
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- [Teaching materials](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/lab_meeting/): a 45-minute workshop and slides.
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- [Lab data guidance](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/reference/lab-data-policy.html): institutional requirements before adapting the workflow to study data.
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## Preview the website
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## Attribution and citation
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The site uses the Fritsche Lab theme and Just the Docs. Synthetic data and reusable templates build on Part 1; see [synthetic data provenance](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/reference/synthetic-data.html).
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The site uses the Fritsche Lab theme and Just the Docs. Synthetic data and reusable templates build on Part 1; see [synthetic data provenance](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/reference/synthetic-data.html).
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Use [CITATION.cff](CITATION.cff) to cite this guide. [GNU General Public License v3.0](LICENSE).

‎_config.yml‎

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lang: en-US
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timezone: America/Detroit
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url: "https://ilarsf.github.io"
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url: "https://fritschelab.org"
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baseurl: "/practical-genai-agentic-coding-guide"
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repository: ilarsf/practical-genai-agentic-coding-guide
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repository: FritscheLab/practical-genai-agentic-coding-guide
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author:
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name: Lars G. Fritsche
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Part 2 of the Practical GenAI series. Maintained by
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<a href="https://medschool.umich.edu/profile/4980/lars-fritsche">Lars G. Fritsche</a>
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and the <a href="https://fritschelab.org/">Fritsche Lab</a> at the University of Michigan.
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Read the <a href="https://github.com/ilarsf/practical-genai-agentic-coding-guide">guide source</a>
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and download the <a href="https://github.com/ilarsf/practical-genai-agentic-coding-example">runnable exercise</a>
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under the <a href="https://github.com/ilarsf/practical-genai-agentic-coding-guide/blob/main/LICENSE">GNU GPL v3.0</a>.
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Read the <a href="https://github.com/FritscheLab/practical-genai-agentic-coding-guide">guide source</a>
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and download the <a href="https://github.com/FritscheLab/practical-genai-agentic-coding-example">runnable exercise</a>
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under the <a href="https://github.com/FritscheLab/practical-genai-agentic-coding-guide/blob/main/LICENSE">GNU GPL v3.0</a>.
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gh_edit_link: false
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gh_edit_link_text: Edit this page on GitHub
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gh_edit_repository: https://github.com/ilarsf/practical-genai-agentic-coding-guide
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gh_edit_repository: https://github.com/FritscheLab/practical-genai-agentic-coding-guide
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gh_edit_branch: main
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gh_edit_view_mode: edit
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‎_includes/header_custom.html‎

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</ul>
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</details>
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<a href="https://fritschelab.org/practical-genai-coding-guide/" aria-label="Part 1: Practical GenAI Coding Guide">Part 1 <span aria-hidden="true">↗</span></a>
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<a href="https://github.com/ilarsf/practical-genai-agentic-coding-example">Exercise on GitHub <span aria-hidden="true">↗</span></a>
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<a href="https://github.com/FritscheLab/practical-genai-agentic-coding-example">Exercise on GitHub <span aria-hidden="true">↗</span></a>
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</nav>

‎docs/lab_meeting/45min_runbook.md‎

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## Prepare
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Have participants keep the guide open online and download the [example repository](https://github.com/ilarsf/practical-genai-agentic-coding-example). Choose the [Python path](../paths/python/index.md) or [R path](../paths/r/index.md). Run its setup, tests, and six-row example before the presentation. Prepare an approved [coding client](../platforms/index.md). Use synthetic files throughout.
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Have participants keep the guide open online and download the [example repository](https://github.com/FritscheLab/practical-genai-agentic-coding-example). Choose the [Python path](../paths/python/index.md) or [R path](../paths/r/index.md). Run its setup, tests, and six-row example before the presentation. Prepare an approved [coding client](../platforms/index.md). Use synthetic files throughout.
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Open the [six-row example and expected report](../lessons/02-specify.md). Find measurements d, e, and f in the input and `outputs/flagged_rows.tsv` so you can help participants check their counts.
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‎docs/lab_meeting/index.md‎

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- [Demo prompts](demo_prompts.md): concise requests for orientation, implementation, and review.
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- [Six-row example](../lessons/02-specify.md): inputs, expected report, and checks for either language.
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To present the [Quarto slides](https://github.com/ilarsf/practical-genai-agentic-coding-guide/blob/main/docs/lab_meeting/slide_deck.qmd), run `quarto render docs/lab_meeting/slide_deck.qmd` from a local copy of the [guide repository](https://github.com/ilarsf/practical-genai-agentic-coding-guide) and open the resulting HTML file. Participants only need the example repository; the guide source is for presenting or editing the slides.
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To present the [Quarto slides](https://github.com/FritscheLab/practical-genai-agentic-coding-guide/blob/main/docs/lab_meeting/slide_deck.qmd), run `quarto render docs/lab_meeting/slide_deck.qmd` from a local copy of the [guide repository](https://github.com/FritscheLab/practical-genai-agentic-coding-guide) and open the resulting HTML file. Participants only need the example repository; the guide source is for presenting or editing the slides.
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Participants should leave with a reporting change they understand, test results, and a short handoff they can use to continue at home.

‎docs/lab_meeting/slide_deck.qmd‎

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## Choose your path once
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[Python path](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/paths/python/) · [R path](https://ilarsf.github.io/practical-genai-agentic-coding-guide/docs/paths/r/)
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[Python path](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/paths/python/) · [R path](https://fritschelab.org/practical-genai-agentic-coding-guide/docs/paths/r/)
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Download the [example repository](https://github.com/ilarsf/practical-genai-agentic-coding-example) and keep the guide open online.
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Download the [example repository](https://github.com/FritscheLab/practical-genai-agentic-coding-example) and keep the guide open online.
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[Fritsche Lab](https://fritschelab.org/) · [Part 1](https://fritschelab.org/practical-genai-coding-guide/) · [Part 2](https://ilarsf.github.io/practical-genai-agentic-coding-guide/)
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[Fritsche Lab](https://fritschelab.org/) · [Part 1](https://fritschelab.org/practical-genai-coding-guide/) · [Part 2](https://fritschelab.org/practical-genai-agentic-coding-guide/)

‎docs/paths/python/index.md‎

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You need Git and a terminal. If you already have the exercise repository, open a terminal in its root. Otherwise, clone it first:
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```bash
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git clone https://github.com/ilarsf/practical-genai-agentic-coding-example.git
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git clone https://github.com/FritscheLab/practical-genai-agentic-coding-example.git
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cd practical-genai-agentic-coding-example
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```
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‎docs/paths/r/index.md‎

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You need Git and a terminal. If you already have the exercise repository, open a terminal in its root. Otherwise, clone it first:
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```bash
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git clone https://github.com/ilarsf/practical-genai-agentic-coding-example.git
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git clone https://github.com/FritscheLab/practical-genai-agentic-coding-example.git
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cd practical-genai-agentic-coding-example
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```
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