/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.
homepage: https://github.com/matanle51/agentic_paper_digest
compatibility: Requires Python 3, network access, and either git or curl/wget for bootstrap. LLM access via OPENAI_API_KEY or LITELLM_API_KEY (OpenAI-compatible).
metadata: {"clawdbot":{"requires":{"anyBins":["python3","python"]}}}

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="$HOME/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 (summary defaults to relevance model if unset).
• `LITELLM_TEMPERATURE_RELEVANCE`, `LITELLM_TEMPERATURE_SUMMARY`: lower for more deterministic output.
• `LITELLM_MAX_RETRIES`: retry count for LLM calls.
• `LITELLM_DROP_PARAMS=1`: drop unsupported params to avoid provider errors.
• `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_API_BASE`, `HF_API_BASE`: override source endpoints if needed.
• `ARXIV_MAX_RESULTS`, `ARXIV_PAGE_SIZE`: arXiv paging limits.
• `MAX_CANDIDATES_PER_SOURCE`: cap candidates per source before LLM filtering.
• `FETCH_TIMEOUT_S`, `REQUEST_TIMEOUT_S`: source fetch and per-request timeouts.
• `ENABLE_PDF_TEXT=1`: include first-page PDF text in summaries; requires `PyMuPDF` (`pip install pymupdf`).
• `DATA_DIR`: location for `papers.sqlite3`.
• `CORS_ORIGINS`: comma-separated origins allowed by the API server (UI use).
• Path overrides: `TOPICS_PATH`, `SETTINGS_PATH`, `AFFILIATION_BOOSTS_PATH`.

**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` also caps results in `GET /api/papers` when `apply_topic_caps=1`.
• `config/settings.json`: overrides 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).

Mandatory workflow (follow step-by-step)

1. **You first MUST open and read the configuration from the github repo: https://github.com/matanle51/agentic_paper_digest you downloaded**:

• Load `config/topics.json`, `config/settings.json`, and `config/affiliations.json` (if present).
• Note current topic IDs, caps, and fetch limits before asking the user to change them.

2. **ASK THE USER TO PROVIDE IT'S PREFERENCES ABOUT THE FOLLOWING (HELP THE USER)**:

• **Topics of interest** → update `config/topics.json` (`topics[].id/label/description/keywords`, `max_per_topic`).

Show current defaults and ask whether to keep or change them.

• **Time window (hours)** → set `WINDOW_HOURS` (or pass `--window-hours` to CLI) **only if the user cares**; otherwise keep default to 24h.
• ASK THE USER TO FILL THE FOLLOWING PARAMETERS (explain the user why are their intent): `ARXIV_CATEGORIES`, `ARXIV_MAX_RESULTS`, `ARXIV_PAGE_SIZE`, `MAX_CANDIDATES_PER_SOURCE`.

Ask whether to keep defaults and show the current values.

• **Model/provider** → set `OPENAI_API_KEY` *or* `LITELLM_API_KEY` (+ `LITELLM_API_BASE` if proxy), and set `LITELLM_MODEL_RELEVANCE`/`LITELLM_MODEL_SUMMARY`.
• **Do NOT ask by default**: timezone, quality vs cost, timeouts, PDF text, affiliation biasing, sources list. Use defaults unless the user requests changes.

3. **Confirm workspace path**: Ask where to clone/run. Default to `PROJECT_DIR="$HOME/agentic_paper_digest"` if the user doesn’t care. Never hardcode `/Users/...` paths. 4. **Bootstrap the repo**: Run the bootstrap script (unless the repo already exists and the user says to skip). 5. **