gcn-circular-llm 0.4.0

Extract structured astrophysical information from NASA GCN circulars using an LLM via DeepSeek.

GCN Circular LLM Parser (gcn-circular-llm)

A lightweight Python package for extracting structured astrophysical information from NASA GCN (Gamma-ray Coordinates Network) circulars using an LLM via any OpenAI-compatible API (DeepSeek, OpenAI, Minimax, etc.).

Features

• Fetch circulars for a given transient event from the NASA GCN archive
• Extract structured fields with an LLM:
  • Event coordinates (RA, Dec, system, error)
  • Redshift and host galaxy
  • Classification (e.g. Long GRB, SGRB, Supernova)
  • Flux / magnitude measurements with UTC timestamps and optional MJD
  • Observations and instrument references
  • A one-sentence summary per circular
• Post-extraction validation automatically checks completeness and fills gaps:
  • Cross-fills missing coordinates, redshift, event type from sibling circulars
  • Propagates flux measurement times across matching bands/instruments
  • Regex fallback extracts RA/Dec, redshift, and UTC timestamps from raw text
  • Flags circulars needing manual review in needs_review.json
• Organized output — all results land in output/<event>/ with JSON, CSV, full extraction log, and review file
• Export light-curve CSV that aggregates all measurements across circulars with automatic UTC/MJD cross-fill and standardized photometric band names

Installation

From PyPI (recommended)

pip install gcn-circular-llm

From source

git clone [e-mail]:LAujust/gcn_parser.git
cd gcn_parser
pip install .

Requirements

• Python >= 3.10
• An API key for any OpenAI-compatible LLM provider

Configuration

Set up your LLM provider via environment variables or a .env file.

Supported env vars

Env Var	Default	Description
LLM_API_KEY	(falls back to DEEPSEEK_API_KEY)	API key for your LLM provider
LLM_BASE_URL	https://api.deepseek.com	API base URL
LLM_MODEL	deepseek-v4-flash	Default model name

Provider examples

Create a .env file in your working directory (see .env.example for the template):

DeepSeek (default):

LLM_API_KEY=sk-...
# Uses default base URL and model — no additional config needed

OpenAI:

LLM_BASE_URL=https://api.openai.com/v1
LLM_API_KEY=sk-...
LLM_MODEL=gpt-4o

Minimax:

LLM_BASE_URL=https://api.minimax.chat/v1
LLM_API_KEY=your-key-here
LLM_MODEL=minimax-m2.5

For backward compatibility, DEEPSEEK_API_KEY is still supported as a fallback for LLM_API_KEY.

Usage

CLI

After installation, the gcn-parser command is available globally:

# Basic extraction — writes to output/GRB250101A/
gcn-parser GRB250101A

# Specify output directory
gcn-parser GRB250101A -d my_results/GRB250101A

# Use a different model
gcn-parser GRB250101A -m deepseek-v4-pro

# Use OpenAI directly (requires LLM_BASE_URL + LLM_API_KEY in .env)
gcn-parser GRB250101A -m gpt-4o

# Enable debug logging
gcn-parser GRB250101A -v

# List all options
gcn-parser --help

CLI options

Option	Description
event	Event identifier, e.g. GRB250101A or EP260321a
-d, --outdir	Output directory (default: output/<event>)
-m, --model	Override the default model (LLM_MODEL env var or deepseek-v4-flash)
-v, --verbose	Enable debug-level logging

Output directory structure (after a run):

output/GRB250101A/
  ├── GRB250101A.json      # Full extraction results with _filled_from annotations
  ├── GRB250101A.csv       # Light-curve CSV
  ├── extraction.log       # Timestamped log of the full run
  └── needs_review.json    # Circulars requiring manual inspection

You can also run it as a Python module:

python -m gcn_parser GRB250101A -d output/GRB250101A

Python API

Use the package programmatically in your own scripts:

from gcn_parser import (
    fetch_event_circulars,
    extract_circular,
    cross_fill,
    cross_fill_flux_time,
    check_completeness,
    regex_fallback,
    OutputManager,
)

# Fetch all circulars for an event
circulars = fetch_event_circulars("EP260321a")

# Extract each circular
results = []
for c in circulars:
    extraction = extract_circular(c["text"], model="deepseek-v4-flash")
    results.append({
        "gcn": c["gcn"],
        "extraction": extraction.model_dump(by_alias=True),
        "raw_text": c["text"],
    })

# Post-extraction validation
results = cross_fill(results)            # fill top-level fields from siblings
results = cross_fill_flux_time(results)  # propagate flux times across bands

for r in results:
    missing = check_completeness(r["extraction"])
    if missing:
        fb = regex_fallback(r["raw_text"])
        # apply fb["coordinates"], fb["redshift"], fb["utc_times"] ...

# Write organized output
out = OutputManager("EP260321a")
out.attach_log()
out.write_json(results)
out.write_csv(results)
out.detach_log()

Output

JSON

Each circular produces an object with the following schema. Fields auto-filled from sibling circulars or regex carry a _filled_from annotation tracing their provenance:

[
  {
    "gcn": "GCN 12345",
    "extraction": {
      "event_type": "GRB",
      "coordinates": {
        "ra": "12:34:56.78",
        "dec": "+12:34:56.7",
        "system": "J2000",
        "error_arcsec": 1.2
      },
      "redshift": 0.5,
      "host_galaxy": "Host Galaxy Name",
      "classification": "Long GRB",
      "flux_magnitude": [
        {
          "value": 18.5,
          "err": null,
          "band": "r",
          "instrument": "ZTF",
          "utc": "2025-01-01T12:00:00Z",
          "mjd": null,
          "unit": "AB mag",
          "upper_limit": false
        }
      ],
      "observations": ["Swift/XRT follow-up"],
      "references": ["GCN 12344"],
      "confidence": "high",
      "summary": "...",
      "_filled_from": {
        "coordinates": "GCN 12346",
        "redshift": "GCN 12344"
      }
    }
  }
]

needs_review.json

Circulars that still have missing critical fields after cross-fill and regex fallback are listed with the reason and a snippet of the raw text:

[
  {
    "gcn": "GCN Circular 12347",
    "reason": "missing: flux_magnitude (empty)",
    "raw_text_snippet": "We report on the detection of..."
  }
]

CSV Light-Curve

The --csv option flattens all flux_magnitude entries across circulars into a single table. Before writing, the exporter performs two clean-up steps automatically:

1. UTC / MJD cross-fill — if one timestamp field is missing, it is computed from the other (UTC ↔ MJD conversion using the MJD epoch).
2. Band standardization — common aliases are normalized (e.g. r-band, R band, VT_R → r or R).

Column	Description
gcn_number	Source circular number
utc	Observation time in ISO-8601 UTC
mjd	Modified Julian Date (optional)
value	Numeric measurement
err	Measurement error; for upper limits, value is set to 0 and err stores the limit
unit	e.g. mag, AB mag, uJy, mJy/beam
band	Standardized photometric band or frequency
instrument	Telescope or instrument name

Rows are sorted chronologically (by UTC, with MJD as fallback).

Models & Rate Limiting

The default model is deepseek-v4-flash (via DeepSeek) with a default delay of 2s between batches. If you hit rate limits (429 Too Many Requests), the package automatically retries with exponential backoff.

For faster or higher-accuracy analysis, switch models:

# Use a different DeepSeek model
gcn-parser EP260321a -m deepseek-v4-pro

# Via OpenAI (set LLM_BASE_URL and LLM_API_KEY in .env first)
gcn-parser EP260321a -m gpt-4o

Suggested models

Model	Speed	Cost	Notes
deepseek-v4-flash	Fast	Low	Default; good balance of speed and accuracy
deepseek-v4-pro	Medium	Medium	Higher accuracy; supports thinking mode
gpt-4o	Fast	Low	Higher accuracy for complex circulars

Troubleshooting

Issue	Cause	Solution
429 Too Many Requests	Rate limit hit	Add delay between requests or switch to a different model
LLM returned an empty response	Model did not produce valid output	Retry with a different model (e.g. deepseek-v4-pro)
LLM_API_KEY is not set	Missing API key	Set LLM_API_KEY (or DEEPSEEK_API_KEY as fallback) in .env or export it. Get your key at https://platform.deepseek.com/api_keys
No circulars found	Event name typo or GCN has no circulars	Check the exact event name on gcn.nasa.gov

License

This project is licensed under the MIT License. See LICENSE for details.