agentic-paper-digest-skill

name	agentic-paper-digest-skill
description	Fetches and summarizes recent arXiv and Hugging Face papers with Agentic Paper Digest. Use when the user wants a paper digest, a JSON feed of recent papers, or to run the arXiv/HF pipeline. Use when this capability is needed.
metadata	{"author":"demerzels-lab"}

Agentic Paper Digest

When to use

• Fetch a recent paper digest from arXiv and Hugging Face.
• Produce JSON output for downstream agents.
• Run a local API server when a polling workflow is needed.

Prereqs

• Python 3 and network access.
• LLM access via OPENAI_API_KEY or an OpenAI-compatible provider via LITELLM_API_BASE + LITELLM_API_KEY.
• git is optional for bootstrap; otherwise curl/wget (or Python) is used to download the repo.

Get the code and install

• Preferred: run the bootstrap helper script. It uses git when available or falls back to a zip download.

bash "{baseDir}/scripts/bootstrap.sh"

• Override the clone location by setting PROJECT_DIR.

PROJECT_DIR="/Users/matanlevi/dev/agentic_paper_digest" bash "{baseDir}/scripts/bootstrap.sh"

Run (CLI preferred)

bash "{baseDir}/scripts/run_cli.sh"

• Pass through CLI flags as needed.

bash "{baseDir}/scripts/run_cli.sh" --window-hours 24 --sources arxiv,hf

Run (API optional)

bash "{baseDir}/scripts/run_api.sh"

• Trigger runs and read results.

curl -X POST http://127.0.0.1:8000/api/run
curl http://127.0.0.1:8000/api/status
curl http://127.0.0.1:8000/api/papers

• Stop the API server if needed.

bash "{baseDir}/scripts/stop_api.sh"

Outputs

• CLI --json prints run_id, seen, kept, window_start, and window_end.
• Data store: data/papers.sqlite3 (under PROJECT_DIR).
• API: POST /api/run, GET /api/status, GET /api/papers, GET/POST /api/topics, GET/POST /api/settings.

Configuration

Config files live in PROJECT_DIR/config. Environment variables can be set in the shell or via a .env file. The wrappers here auto-load .env from PROJECT_DIR (override with ENV_FILE=/path/to/.env).

Environment (.env or exported vars)

• OPENAI_API_KEY: required for OpenAI models (litellm reads this).
• LITELLM_API_BASE, LITELLM_API_KEY: use an OpenAI-compatible proxy/provider.
• LITELLM_MODEL_RELEVANCE, LITELLM_MODEL_SUMMARY: models for relevance and summarization.
• LITELLM_TEMPERATURE_RELEVANCE, LITELLM_TEMPERATURE_SUMMARY: lower for more deterministic output.
• WINDOW_HOURS, APP_TZ: recency window and timezone.
• ARXIV_CATEGORIES: comma-separated categories (default includes cs.CL,cs.AI,cs.LG,stat.ML,cs.CR).
• ARXIV_MAX_RESULTS, ARXIV_PAGE_SIZE, FETCH_TIMEOUT_S, MAX_CANDIDATES_PER_SOURCE: fetch limits and timeouts.
• ENABLE_PDF_TEXT=1: include first-page PDF text in summaries; requires PyMuPDF (pip install pymupdf).
• Path overrides: TOPICS_PATH, SETTINGS_PATH, AFFILIATION_BOOSTS_PATH, DATA_DIR.

Config files

• config/topics.json: list of topics with id, label, description, max_per_topic, and keywords. The relevance classifier must output topic IDs exactly as defined here. max_per_topic is also used to cap results in GET /api/papers when apply_topic_caps=1.
• config/settings.json: overrides default fetch limits (arxiv_max_results, arxiv_page_size, fetch_timeout_s, max_candidates_per_source). Updated via POST /api/settings.
• config/affiliations.json: list of {pattern, weight} boosts applied by substring match over affiliations. Weights add up and are capped at 1.0. Invalid JSON disables boosts, so keep the file strict JSON (no trailing commas).

Getting good results

• Keep topics focused and mutually exclusive so the classifier can choose the right IDs.
• Use a stronger model for summaries than for relevance if quality matters.
• Increase WINDOW_HOURS or ARXIV_MAX_RESULTS when results are sparse, or lower them if results are too noisy.
• Tune ARXIV_CATEGORIES to your research domains.
• Enable PDF text (ENABLE_PDF_TEXT=1) when abstracts are too thin.
• Use modest affiliation weights to bias ranking without swamping relevance.

Troubleshooting

• Port 8000 busy: run bash "{baseDir}/scripts/stop_api.sh" or pass --port to the API command.
• Empty results: increase WINDOW_HOURS or verify the API key in .env.
• Missing API key errors: export OPENAI_API_KEY or LITELLM_API_KEY in the shell before running.

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