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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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# 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.
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).
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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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-[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.
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