study-file-organization - SKILL.md Agent Skill

name: study-file-organization description: Directory structure, naming conventions, and git workflow for organizing studies.

Study File Organization & Rules

Complete reference for how to organize files, directories, and git workflow when running studies.

Directory Layout

All work lives in sessions/. Inside sessions, files are organized by topic (a general area of study). Each topic gets a directory with a descriptive alias derived from the user's request.

Example: "I want to study status quo bias among older people" → topic_status-quo-bias-age

If the directory already has topic folders, make sure your topic name is unique.

Within each topic, create one or more studies — self-contained collections of files that do something (create an agent list, run a simulation, etc.). Studies are named with snake-case post-fix indices: _a, _b, etc.

sessions/
  topic_<alias>/
    README.md
    .git
    study_a/
    study_b/
    study_c/

Creating a Study

Use the create_study_project.py tool to scaffold the structure:

python create_study_project.py sessions/topic_<alias>/<study_name>

This produces:

.git
README.md
requirements.txt
Makefile
refs/
DOCKERFILE
data/
  raw/
    .gitkeep
  cooked/
    .gitkeep
  uploaded/
    .gitkeep
edsl_jobs/
  job_a/
    study_agent_list.py
    study_scenario_list.py
    study_model_list.py
    run_job.py
  job_b/
    …
analysis/
computed_objects/
writeup/
  planning.md
  report.md
  report.css
  appendix.md
  tables/
  plots/
  numbers/

Report Formatting

CSS: Copy the Expected Parrot branded stylesheet into every study's writeup directory:

cp /Users/johnhorton/tools/ep/macaw/ep-agent/report.css <study_root>/writeup/report.css

The Makefile's report.html target must use --css=report.css to apply this stylesheet. Use this template for the report targets:

# --- Report ---
writeup/report.html: writeup/report.md PLOTS TABLES
    cd writeup && pandoc report.md -o report.html --standalone --css=report.css

writeup/report.pdf: writeup/report.md PLOTS TABLES
    cd writeup && pandoc report.md -o report.pdf --pdf-engine=xelatex

report: writeup/report.html writeup/report.pdf

No duplicate title: The report.md file uses a YAML frontmatter block with title: and date:. Pandoc renders the title as an H1 heading automatically. Do NOT also include an # H1 heading in the body — this causes the title to appear twice. Start the body with ## Summary or another H2.

Correct format:

---
title: "My Study Title"
date: 2026-01-15
---

## Summary

The body starts here with an H2...

Wrong format (title appears twice):

---
title: "My Study Title"
date: 2026-01-15
---

# My Study Title

## Summary
...

Rules

Always create this file structure for each study and do a git init. Also create checklist.md (see skills/study-checklist/SKILL.md).
Use README.md as your lab notebook — write what you did at each step:
```
PURPOSE
Author
Timestamp
LOG Entries
```
Git-add every new file immediately after creating it.
All file interactions are git-mediated. At good stopping points, create a detailed git commit.

IMPORTANT: The Makefile runs EDSL scripts from edsl_jobs/ (cd edsl_jobs && python ...). All git commands must be run from the study root (the directory containing the Makefile). Always cd back to the study root and verify your working directory before any git add / git commit.
Do not run Python files directly. Write scripts into analysis/ and wire them into the Makefile. Use make targets to execute them (e.g., make plots, make writeup/report.html). Analysis scripts create plots/tables written to writeup/tables or writeup/plots.
Snake-case names for outputs. Name scripts after what they produce:
- table_growth_over_time.py → writeup/tables/growth_over_time.csv
- plot_growth_over_time.py → writeup/plots/growth_over_time.png
- Each has a corresponding Makefile recipe.
PLOT and TABLES phony targets in the Makefile are dependencies for the overall report.
Follow-up studies use git subtree to pull predecessors into refs/.

IMPORTANT: Both repos must have at least one commit before adding a subtree.

Step-by-step:
1. Ensure the predecessor has at least one commit: git -C <path_to_predecessor> log --oneline -1
2. Create the new study and make an initial commit
3. From inside the new study's git repo:
```
git subtree add --prefix=refs/<predecessor_study_name> <absolute_path_to_predecessor> main --squash
```
4. Verify: ls refs/<predecessor_study_name>/
5. If any step fails, log the error to errors.jsonl (see skills/error-logging/SKILL.md) immediately, then fix and retry
Intermediate datasets (transformed raw data, fitted models, etc.) go in computed_objects/.
Add packages to requirements.txt as needed.
EDSL code goes in the edsl_jobs/ directory. Read skills/edsl-study-files/SKILL.md for the standard file templates and export conventions.
User-uploaded data goes in data/uploads. Data is also added to the repo unless too large.
Use the SearchExpectedParrot tool to search Expected Parrot for EDSL objects. Use it directly instead of writing Python scripts with Coop().list().
Single report file rule: Only ONE report markdown in writeup/ — that is report.md. To elaborate on results or extend the report, edit report.md rather than creating new files. Allowed .md files in writeup/: report.md, survey.md (auto-generated), planning.md (working notes), appendix.md (supplementary material). After any analysis run, run python check_writeup.py <study_dir> to verify compliance.