sourcelens

sourcelens collects the latest research on any topic into one chronological catalogue. It searches PubMed, Europe PMC, arXiv and OpenAlex, downloads the open-access full texts, finds the code and packages the papers link to, and exports references for Zotero or LaTeX. Run it again later and it adds only what is new; notes you write in the catalogue are never overwritten.

Website: https://bhagesh-h.github.io/sourcelens/

Install

Python (3.10 or newer):

pip install sourcelens

Go binary (Linux and macOS, one file, no dependencies). Download it from the latest release, or:

curl -fLo sourcelens https://github.com/bhagesh-h/sourcelens/releases/latest/download/sourcelens_linux_amd64
chmod +x sourcelens && mv sourcelens ~/.local/bin/

For other systems replace linux_amd64 with linux_arm64, darwin_arm64 (Apple silicon) or darwin_amd64 (Intel Mac). With Go installed: go install github.com/bhagesh-h/sourcelens/cmd/sourcelens@latest.

Both have the same commands. To convert PDFs to text, the Go binary needs poppler (apt install poppler-utils, brew install poppler).

Use

sourcelens config set contact_email you@example.org    # once; Crossref, OpenAlex, NCBI and Unpaywall ask for it
sourcelens "CRISPR base editing"                        # start a catalogue; run again later to add what is new
sourcelens query --topic "CRISPR base editing" --range 1m
sourcelens export --topic "CRISPR base editing" --format BIB --out crispr.bib

Commas, semicolons and OR separate alternatives, every word of an alternative is required, and double quotes keep a phrase together: sourcelens '"base editing", "prime editing"'.

Each topic gets a folder such as ~/sourcelens/crispr-base-editing/, with progress.csv as the main table. sourcelens config set output DIR changes the folder, and sourcelens help lists every command.

Documentation

• Install options: pipx, PDF extras, Docker, Python or Go
• Usage: how a topic becomes a search, every command and option
• Outputs: the catalogue folder and the columns of progress.csv
• Configuration: settings and catalogue configuration
• Sources and limitations
• Development and publishing
• Default topic: aging clocks

License

GPL-3.0. See LICENSE.