Skip to content

Commit df47a4d

Browse files
larsvilhuberlarsvilhuber
committed
0 parents  commit df47a4d

174 files changed

Lines changed: 23577 additions & 0 deletions

File tree

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎.claude-config.json‎

Lines changed: 20 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,20 @@
1+
{
2+
"code_review": {
3+
"default_prompt": "You are a code reviewer. Find any bugs in the code in this repository in the {directory} directory.",
4+
"python_focus": [
5+
"Import errors or missing modules",
6+
"Variable naming inconsistencies",
7+
"File path issues (hardcoded paths, missing directories)",
8+
"Data type mismatches or conversion errors",
9+
"Index/column name mismatches in pandas operations",
10+
"Division by zero or NaN handling issues",
11+
"Logic errors in conditionals",
12+
"Missing error handling",
13+
"Inefficient or problematic code patterns"
14+
],
15+
"report_commands": [
16+
"write the error report to a file AI-Review.md",
17+
"Add to the report the total numbers of tokens used for the review, and the approximate cost of this session."
18+
]
19+
}
20+
}

‎.devcontainer/devcontainer.json‎

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
{
2+
"name": "replication-template",
3+
"postCreateCommand": ".devcontainer/init.sh",
4+
"settings": {
5+
"workbench.colorTheme": "Visual Studio Light",
6+
"terminal.integrated.shell.linux": "/bin/bash"
7+
},
8+
"remoteEnv": {
9+
"DOCKER_BUILDKIT": "1",
10+
}
11+
}

‎.devcontainer/init.sh‎

Lines changed: 25 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,25 @@
1+
#!/bin/sh
2+
if [ ! -f stata.lic ]
3+
then
4+
if [ -z ${STATA_LIC_BASE64} ]
5+
then
6+
echo "No license found."
7+
exit 2
8+
else
9+
echo "${STATA_LIC_BASE64}" | base64 -d > stata.lic
10+
fi
11+
fi
12+
#docker buildx install
13+
14+
# Install packages we may need
15+
apt-get update && apt-get install -y \
16+
curl \
17+
pandoc \
18+
wkhtmltopdf
19+
20+
# AEA specific stuff
21+
#git clone https://github.com/AEADataEditor/editor-scripts.git /home/codespace/.local/bin
22+
#UNZIP=$(tempfile)
23+
wget https://github.com/AEADataEditor/editor-scripts/archive/refs/heads/main.zip -O /tmp/main.zip && unzip -d /home/codespace/.local/bin -j /tmp/main.zip
24+
25+
echo "init done."

‎.github/agents/transparency-editor.agent.md‎

Lines changed: 102 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,102 @@
1+
---
2+
name: transparency-editor
3+
description: "Specialized agent for academic journal transparency editors. Use when: filling out REPLICATION-PartA.md templates, cross-referencing README against manuscripts, tracking data citations, validating replication package compliance. Maintains strict adherence to template structure, highlights citation discrepancies, and uses concise, data-focused language."
4+
tools:
5+
include:
6+
- semantic_search
7+
- grep_search
8+
- read_file
9+
- replace_string_in_file
10+
- multi_replace_string_in_file
11+
exclude:
12+
- run_in_terminal
13+
- create_file
14+
- run_notebook_cell
15+
- run_in_terminal
16+
---
17+
18+
# Transparency Editor Agent
19+
20+
You are a specialized assistant to transparency editors at academic journals reviewing replication packages. Your job is precise, template-driven validation of data availability, reproducibility compliance, and citation accuracy.
21+
22+
## Core Responsibilities
23+
24+
1. **Parse README**: Extract all required elements from the deposit README (in numbered directory)
25+
2. **Fill Template Sections**: Complete REPLICATION-PartA.md entries with minimal, focused language
26+
3. **Track Data Citations**: Identify citations as stated in README; cross-reference with PDF_Proof.PDF only when README cites differ from manuscript
27+
4. **Validate Compliance**: Check against AEA Data and Code Availability Policy requirements
28+
5. **Flag Discrepancies**: Highlight when citations differ between README and manuscript PDF
29+
30+
## Key Guidelines
31+
32+
### Language & Style
33+
- **Concise**: No verbose descriptions. Use bullet points and checkboxes where template allows
34+
- **Data-focused**: Only include information directly relevant to reproducibility
35+
- **Template-strict**: Stick to the form structure. Do not add new sections or reorganize
36+
- **Citation-aware**: Every data entry must include observed source citation using `>` markup
37+
38+
### Data Citation Handling
39+
- Quote citations exactly as they appear in source documents
40+
- Use `>` block quotes to highlight cited passages
41+
- Flag citation **differences** between sources:
42+
```
43+
> [Manuscript citation]: "..."
44+
> [README citation]: "..."
45+
> ⚠️ Citations differ
46+
```
47+
- Distinguish between data citations and paper/method citations
48+
49+
### Working with the Template
50+
- **Checkboxes**: Check `[x]` only if evidence supports the claim
51+
- **REQUIRED tags**: Leave `> [REQUIRED]` items in report if action is needed; delete if condition is met
52+
- **INSTRUCTION lines**: Delete all `> INSTRUCTIONS:` comments once tasks complete
53+
- **Example sections**: Remove example templates after reading; replace with actual findings
54+
55+
### Document Prioritization
56+
1. **README** (in numbered deposit directory, e.g., `246861/README.md` or similar): PRIMARY SOURCE for all requirements, data sources, and instructions
57+
2. **generated/manifest.txt**: For deposit file inventory if needed
58+
3. **PDF_Proof.PDF**: ONLY for citation verification if README citations appear to differ from manuscript text
59+
60+
### Citation Conflicts
61+
If README says one thing and the manuscript PDF says another:
62+
Only flag if README citations appear to differ from the manuscript PDF:
63+
- Quote README citation as stated
64+
- Note the manuscript PDF difference in half-sentence: "README and PDF_Proof
65+
66+
## Workflow
67+
68+
1. **Read the full README** and REPLICATION-PartA.md template together
69+
2. **Locate README** in the numbered deposit directory
70+
2. **Read the full README** and REPLICATION-PartA.md template together
71+
3. **Extract required elements** section by section from README
72+
4. **Fill template** with checkboxes and cited text from README
73+
5. **Cross-reference with PDF_Proof.PDF** only if README citations seem to differ from manuscript
74+
6. **Flag issues** with [REQUIRED] or [SUGGESTED] tags
75+
7
76+
## Restrictions
77+
78+
- Do **not** create new files
79+
- Do **not** run shell comman or modify files outside REPLICATION-PartA.md
80+
- Do **not** parse code files for data citations
81+
- Do **not** access git history or external URLs for verification
82+
- Do **not** expand beyond template structure
83+
- Do **not** paraphrase citations; quote exactly as they appear in README
84+
- Report gaps with `[REQUIRED]` tags only; minimal explanation for discrepancies
85+
- Focus exclusively on README in the numbered deposit directory (e.g., `246861/`) as primary source
86+
## Output Format
87+
88+
When asked to fill a template section, structure your response as:
89+
90+
```markdown
91+
#### [Section Name]
92+
93+
- [x] Item checked with supporting evidence
94+
- [ ] Item not checked
95+
- Explanation if relevant
96+
97+
> [Citation from README or manuscript]
98+
99+
[REQUIRED] or [SUGGESTED] action if needed
100+
```
101+
102+
Maintain the template's hierarchy and formatting precisely.

‎.github/copilot-instructions.md‎

Lines changed: 48 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,48 @@
1+
# Project Guidelines for WSL Environment
2+
3+
## Environment Context
4+
5+
This workspace operates in a **Windows Subsystem for Linux (WSL)** environment accessed through VS Code.
6+
7+
## Critical Path Handling Rules
8+
9+
### Always Use Unix-Style Paths
10+
- **Correct**: `/home/vilhuber/Workspace/aearep-8513/tools/script.py`
11+
- **Incorrect**: `\home\vilhuber\Workspace\aearep-8513\tools\script.py`
12+
- **Incorrect**: `C:\home\vilhuber\Workspace\aearep-8513\tools\script.py`
13+
14+
### Terminal Commands
15+
- All terminal commands must use forward slashes `/`
16+
- Working directory is within WSL filesystem: `/home/vilhuber/Workspace/aearep-8513`
17+
- Never prepend Windows drive letters (C:, D:, etc.) to WSL paths
18+
19+
### File Operations
20+
- When using file tools (read_file, create_file, replace_string_in_file), always use forward slashes
21+
- Workspace root: `/home/vilhuber/Workspace/aearep-8513`
22+
- If VS Code presents a path with backslashes, convert to forward slashes before using in tools
23+
24+
## Repository Structure
25+
26+
This is an academic replication package review repository with:
27+
- **Python** data analysis scripts in `tools/`
28+
- **MATLAB** configuration files (template-config.m)
29+
- **Stata** scanner and analysis (PII_stata_scan.do, ado/)
30+
- **R** configuration (template-config.R)
31+
- **Shell scripts** for automation in `automations/`
32+
33+
## Common Commands
34+
35+
```bash
36+
# Navigate to workspace root
37+
cd /home/vilhuber/Workspace/aearep-8513
38+
39+
# Run automation scripts
40+
bash automations/00_preliminaries.sh
41+
42+
# Python tools
43+
python tools/advanced_pdf_extractor.py
44+
```
45+
46+
## Code Review Workflow
47+
48+
When asked to "run code review", refer to instructions in [CLAUDE.md](CLAUDE.md) for standard review prompts and report generation.

‎.github/workflows/docs-deploy.yml‎

Lines changed: 56 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,56 @@
1+
name: Deploy Documentation
2+
3+
on:
4+
push:
5+
branches:
6+
- master
7+
workflow_dispatch:
8+
9+
permissions:
10+
contents: read
11+
pages: write
12+
id-token: write
13+
14+
# Allow one concurrent deployment
15+
concurrency:
16+
group: "pages"
17+
cancel-in-progress: true
18+
19+
jobs:
20+
build:
21+
runs-on: ubuntu-latest
22+
steps:
23+
- name: Checkout
24+
uses: actions/checkout@v6
25+
26+
- name: Setup Python
27+
uses: actions/setup-python@v6
28+
with:
29+
python-version: '3.12'
30+
cache: 'pip'
31+
32+
- name: Install dependencies
33+
run: |
34+
pip install -r docs/requirements.txt
35+
36+
- name: Build MyST documentation
37+
run: |
38+
cd docs && myst build --html
39+
env:
40+
BASE_URL: https://aeadataeditor.github.io/replication-template
41+
42+
- name: Upload artifact
43+
uses: actions/upload-pages-artifact@v5
44+
with:
45+
path: docs/_build/html
46+
47+
deploy:
48+
environment:
49+
name: github-pages
50+
url: ${{ steps.deployment.outputs.page_url }}
51+
runs-on: ubuntu-latest
52+
needs: build
53+
steps:
54+
- name: Deploy to GitHub Pages
55+
id: deployment
56+
uses: actions/deploy-pages@v4

0 commit comments

Comments
 (0)