astrobib

A terminal-based literature manager for astrophysics research

astrobib is a personal astrophysics literature manager. It connects to the NASA/Harvard ADS to search and fetch papers, stores BibTeX in ~/.local/share/astrobib/library/, and generates refs.bib files for LaTeX manuscripts by scanning for cite keys.

Keywords follow the Unified Astronomy Thesaurus (UAT), the controlled vocabulary used by AAS journals.

Quick start

# Download the UAT concept hierarchy (one-time, ~2 MB)
astrobib uat update

# Launch the TUI
astrobib

# Set your ADS API token (https://ui.adsabs.harvard.edu/user/settings/token)
astrobib token

TUI key bindings

Core actions (shown in footer)

• i — Import highlighted/selected papers to library (ADS tabs)
• d — Remove highlighted paper from library
• p — Download PDF for highlighted paper
• o — Open cached PDF (all selected, or highlighted)
• / — Library: filter with query syntax (see Filtering the library). ADS tab: view/edit the tab's query
• S — Open new ADS search tab
• r — Refresh current ADS tab
• ? — Show this help
• q — Quit

Footer actions keep fixed positions; a greyed-out action is unavailable in the current context (wrong tab, no PDF cached, already imported, …).

More keys

• Space — Toggle selection of highlighted row
• y — Copy highlighted/selected cite key(s), shortest unambiguous form
• Y — Copy highlighted/selected cite key(s), full form with hash
• s — Star / unstar highlighted paper
• m — Add/remove highlighted or selected papers in the manuscript db
• M — Toggle manuscript-only view (hide personal-library-only papers)
• R — Browse references of highlighted paper (opens ADS tab)
• c — Browse citations of highlighted paper (opens ADS tab)
• e — Export selected papers to astrobib-export.bib
• B — Download PDF via system browser (watches ~/Downloads)
• X — Clear cached PDF (or cancel a browser download)
• u — Open UAT concept browser
• C — Configuration (ADS API token)
• [ / ] — Switch to previous / next tab
• Ctrl+W — Close current ADS tab
• + / - — Increase / decrease ADS result count (then r to reload)
• Escape — Clear filter
• z — Zoom detail panel

Copying text from the TUI

Terminal applications such as astrobib enable mouse reporting, so drag-selection is captured by the application rather than the terminal, which is why ⌘C often copies nothing. There are two workarounds:

• Press y to copy the highlighted (or Space-selected) cite keys directly to the system clipboard. This is the intended workflow for placing keys in a .tex file.
• For arbitrary text, hold ⌥ Option (macOS Terminal/iTerm2; Shift on most Linux terminals) while dragging: this bypasses mouse reporting and restores native selection, after which ⌘C works normally.

Filtering the library

Press / on the Library tab to filter the list as you type. The filter is a local query language modeled on ADS syntax, evaluated live against your library. Whitespace-separated terms all AND together, and each term is a case-insensitive partial match. Bare terms match across author, title, abstract, cite key, keywords, and year; prefix a field name to narrow the match. Examples:

sironi shock                        bare terms — match author, title, abstract, key, keywords, year
author:sironi                       author anywhere in the author list
author:^zrake                       first-author papers only (ADS ^ convention)
title:magnetar                      word in title
abs:"fast radio burst"              phrase in abstract
key:Zrake2020                       cite key
kw:"compact objects"                keyword
year:2020                           single year
year:2015-2020                      year range
year:2020-                          2020 or later (year:-2015 for 2015 or earlier)
"quoted phrase"                     exact phrase, any field
-abs:neutrino  -is:ms               a leading - negates any term
is:starred                          starred papers
is:ms                               manuscript-db members
is:pdf                              papers with a cached PDF

author:^zrake year:2019- is:pdf     terms combine with implicit AND

A partially typed query never produces an error: unknown fields are treated as bare text, so the list refines smoothly as you type.

With a filter active, pressing S opens an ADS search tab pre-filled with the equivalent ADS query; local-only terms (is:, key:, and negations) are dropped. This allows you to filter locally and escalate the same query to ADS in one keystroke.

ADS query syntax

The search box (S) passes your query straight to the ADS search API, so the full ADS/Solr query language is available. Pasting an ADS abstract URL imports that paper directly instead of searching. Examples:

relativistic jets                              plain text — searches everything
author:"zrake"                                 papers by an author
author:"^zrake"                                first-author papers only
author:"spitkovsky" author:"sironi"            both authors on the same paper
abs:"fast radio burst"                         phrase in abstract, title, or keywords
title:"magnetar"                               word in title only
year:2024                                      single year
year:2015-2020                                 year range
bibstem:ApJL                                   one journal (ApJ, MNRAS, PRL, arXiv, …)
arxiv_class:astro-ph.HE                        arXiv category
object:"SN 2023ixf"                            papers about a named object (via SIMBAD)
citation_count:[100 TO *]                      highly cited papers
property:refereed                              refereed only

author:"^zrake" year:2019-2024 bibstem:ApJ     terms combine with implicit AND
abs:"kilonova" NOT abs:"neutrino"              exclude a term
(abs:"jet" OR abs:"outflow") year:2023         boolean grouping

references(bibcode:"2020ApJ...900...12S")      papers this one cites (or press R)
citations(bibcode:"2020ApJ...900...12S")       papers citing this one (or press c)
citations(author:"^zrake")                     everything citing your first-author papers
similar(bibcode:"2020ApJ...900...12S")         textually similar papers
trending(abs:"gravitational waves")            what readers of this topic read now
useful(abs:"pulsar timing")                    methods/tools papers cited by this field

Cite keys

astrobib's key policy separates what the databases store from what a manuscript types, so keys can be collision-proof in one place and clean in the other.

Database keys are content-derived. Every stored entry is keyed AuthorYYYYhhhhh: the first author's surname, the year, and five hash characters computed from the paper's arXiv ID (or, failing that, its ADS bibcode), e.g. Zrake2020axbxt. The key depends only on the paper's identity, so:

• the same paper receives the same key regardless of who imports it, or when, so personal libraries and manuscript databases merge without coordination
• two different Smith 2020 papers can never collide
• re-importing a paper is detected as a duplicate rather than creating a second entry
• the key remains stable across the arXiv-to-journal transition (the hash is computed from the arXiv ID when one exists)

Database .bib files are always stored under their full key, one file per paper.

Manuscripts cite by any unambiguous prefix. In your .tex you may write the full key or any prefix that matches exactly one database key; in practice, \citep{Zrake2020}. The generated refs.bib keys each entry by the string actually cited, so BibTeX sees exactly what the manuscript says and the hash suffix never appears in your prose. (Classic BibTeX has no key-alias mechanism, so this aliasing happens at the refs.bib boundary, which astrobib owns.)

Ambiguity is detected, not guessed. If a prefix matches several keys (for example, after a second Zrake 2020 paper is imported), no candidate is chosen silently: the Manuscript tab shows the cite as magenta ≈ ambiguous with the candidates listed, and astrobib refs prints them and exits nonzero. Lengthening the key by a character or two resolves the ambiguity.

Displayed keys are the shortest unambiguous form. The TUI and CLI show short keys wherever possible, and astrobib import emits its cite-key replacement commands using short keys, so hash characters appear only when they are needed to disambiguate.

Manuscript databases

A manuscript can carry its own bib database: a bib/ directory inside the manuscript's git repository, holding one .bib file per cited paper. There is no registration step: launching astrobib from inside the repository (any directory with bib/ alongside .git) activates it, indicated by ms: <name> in the header. Coauthors who clone the repository get the same database automatically; coauthors without astrobib use the committed refs.bib.

While a manuscript db is active:

• The library view merges your personal library with the manuscript db; the ◆ column marks manuscript members (M hides everything else)
• Importing from ADS (i) writes to both the personal library and the manuscript db
• m toggles manuscript membership for existing library entries

astrobib never runs git on the manuscript repository; bib files are committed as part of your normal work on the paper.

Removal from the manuscript db is never destructive: if it holds the only copy of an entry (imported --ms-only, or added by a coauthor), removing it via m or refs --prune first copies it into your personal library.

The Manuscript tab

A Manuscript tab appears next to Library, showing the union of cite keys found in the .tex sources and entries in bib/, color-coded:

• ◆ normal — cited and in bib/: healthy
• ○ yellow — cited, in your personal library but not bib/: press m to add
• ✗ red — cited but found nowhere: fix the key, or S to search ADS (pre-filled)
• ≈ magenta — cite key is an ambiguous prefix of several entries: lengthen it
• · cyan — in bib/ but cited by nothing: press m to remove

Cite keys in the .tex may be any unambiguous prefix of a database key (\citep{Zrake2020}), and refs.bib is keyed by the cited string; see Cite keys.

If main.tex exists, it is the sole root document and other top-level .tex files (old drafts, notes) are ignored; otherwise every top-level .tex file is a root. Roots are expanded recursively through \input/\include, so multi-file papers are fully scanned.

The tab watches the .tex sources and bib/ (2 s poll) and refreshes itself as you write. refs.bib is regenerated automatically from the cited entries in bib/ whenever its content would change. Nothing is copied or removed automatically; membership changes always go through m (or astrobib refs / --prune on the command line). The status bar summarizes health: 42 cited · 2 missing · 5 uncited.

Keep the database in sync with what the paper actually cites:

cd ~/Work/Papers/my-paper
astrobib refs             # scan .tex, pull cited entries in from personal
                          # library, report unknowns, write refs.bib
astrobib refs --prune     # also drop entries nothing cites anymore

CLI reference

Adding papers

# Search ADS
astrobib search --ads "magnetohydrodynamical simulations"

# Add by ADS bibcode
astrobib add 2020ApJ...900...12S

# Add with extra keywords
astrobib add 2020ApJ...900...12S --keywords "Magnetohydrodynamical simulations"

Sharing papers

Export selected papers from the TUI (Space to select, e to export) and share the resulting astrobib-export.bib file. The recipient can import it:

astrobib import shared-papers.bib

Because keys are content-derived (see Cite keys), the same paper always gets the same key regardless of who added it, so shared files merge cleanly and duplicates are detected on import.

Importing a foreign .bib file

astrobib import accepts any .bib file, for example the bibliography of another paper with arbitrary cite keys. Every entry is resolved against ADS (by arXiv ID, DOI, or exact title + first author + year) and imported with canonical ADS BibTeX and a regenerated astrobib cite key. Entries whose key already matches their content-derived astrobib key (i.e. bibdata from an astrobib export) are recognized automatically and imported directly, with no ADS round-trip. Entries that cannot be resolved to exactly one ADS record are skipped with a warning. Entries already present are kept as-is (pass --verify to be prompted to replace them). After importing, astrobib prints copy-pasteable perl -pi -e commands that rewrite the old cite keys to the new ones in your .tex files.

Inside a manuscript repo, add and import write to both the personal library and the manuscript database (matching the TUI); use a flag to restrict:

astrobib import other-paper.bib                  # personal + manuscript db
astrobib import --personal-only other-paper.bib  # personal library only
astrobib import --ms-only other-paper.bib        # manuscript db only

CLI read commands (list, show, search, export, pdf) see the same merged personal + manuscript view as the TUI, with the same indicators: ↓ PDF cached, ◆ in manuscript db, ★ starred.

Generating refs.bib for a manuscript

Run this from inside the manuscript directory:

astrobib export                  # scans all .tex files in cwd
astrobib export paper.tex        # explicit file
astrobib export -o refs.bib      # explicit output path

The tool scans for \cite, \citep, \citet, and related commands, looks each key up in the library, and writes a refs.bib containing only the entries that are actually cited.

ADS token

astrobib token                   # show current token or prompt to enter one
astrobib token <your-token>      # set token directly
astrobib quota                   # check ADS API rate limit usage

The token can also be set via the ADS_API_TOKEN environment variable.

UAT commands

astrobib uat update              # download / refresh UAT cache
astrobib uat search hydrodynamics
astrobib uat show "Hydrodynamics"
astrobib uat browse              # standalone TUI browser

Other commands

astrobib show <key>              # print BibTeX entry
astrobib open <key>              # open PDF (fetched from arXiv if needed)
astrobib list                    # list all papers
astrobib list --keyword "Compact objects"
astrobib keywords                # list all keywords in the library

Library layout

Papers are stored in ~/.local/share/astrobib/library/bib/, one .bib file per paper. The directory is created automatically on first use.

Cite keys have the form AuthorYYYYhhhhh where hhhhh is the first 5 hex characters of the SHA-256 of the arXiv ID (or ADS bibcode for non-arXiv papers). This makes keys collision-resistant and stable across the arXiv→journal publishing transition.

PDF handling

PDFs are ephemeral and are never stored in the library. When you open a paper (o in the TUI or astrobib open <key>), astrobib:

1. Checks ~/.cache/astrobib/pdfs/<key>.pdf
2. If absent, fetches from https://arxiv.org/pdf/<eprint>
3. Caches and opens in the system PDF viewer

The cache can be deleted freely; everything is re-fetchable.