biblioflow-nb

Notebook widget application for biblioflow bibliometric workflows.

biblioflow-nb provides a Jupyter/Colab-friendly widget UI that mirrors the core workflow of biblioflow-web without running FastAPI, React, or a local web server. All calculations are delegated to the core biblioflow package.

Quickstart

import biblioflow_nb as bfn

bfn.colab_setup()  # safe outside Google Colab
app = bfn.launch()

Launch with an existing dataset:

import biblioflow as bf
import biblioflow_nb as bfn

dataset = bf.load("records.ris")
app = bfn.launch(records=dataset)

Import from PubMed/PMC directly, or stage records first for screening:

import os
import biblioflow_nb as bfn

os.environ["BIBLIOFLOW_NCBI_EMAIL"] = "researcher@example.org"

app = bfn.app(display=False)
app.from_pubmed(query="bibliometrics AND reproducibility", limit=20)
app.from_pmc(query="open science", limit=20)

run = app.stage_pubmed(query="bibliometrics AND reproducibility", limit=20)
app.update_candidates([run["candidates"][0]["candidate_id"]], status="selected")
app.promote_candidates()
app.display()

The widget app also includes a Remote screening panel. API keys can be provided in the panel or through BIBLIOFLOW_NCBI_API_KEY; they are not stored in the session manifest.

Generic screening helpers are available for any records or local file:

app.stage_records([{"title": "Manual candidate"}], source="generic")
app.stage_file("records.ris", source="auto", format="auto")
app.stage_pmc(query="open science", limit=50)
app.update_candidates(["candidate-id"], status="maybe")
app.promote_candidates(include_statuses=("selected", "maybe"))

Development

cd packages/biblioflow-nb
PYTHONPATH=src:../biblioflow/src pytest --cov=biblioflow_nb --cov-fail-under=90
PYTHONPATH=src:../biblioflow/src python -m ruff check src tests
PYTHONPATH=src:../biblioflow/src python -m mypy src
poetry build