AtomDeepLit

简体中文

AtomDeepLit is a standalone Python CLI for literature intake. Paste paper URLs to retrieve public metadata, check for duplicates in Zotero, and review a batch before importing it. DeepSeek can suggest collections and reading priorities.

Quick start

Use Python 3.11 or newer. Run the commands below from the source directory, or install the atomdeeplit command with python -m pip install .. Enable local application access in Zotero Desktop under Settings → Advanced. Writing requires Zotero 10 or later.

python -X utf8 -m atomdeeplit preview --output plan.json

Paste URLs on separate lines or paste a block of Markdown links. Enter an empty line to finish. You can also pass URLs as arguments or use --file urls.txt. The preview shows titles, DOI or arXiv identifiers, possible duplicates, and candidate collections. Use --no-zotero for metadata lookup alone.

Optional DeepSeek suggestions

Copy config.example.toml to ~/.atomdeeplit/config.toml and set your research topics under focus. Use --config PATH before the subcommand to select another file.

# PowerShell 7
$env:DEEPSEEK_API_KEY = Read-Host -MaskInput 'DeepSeek API key'
python -X utf8 -m atomdeeplit preview --ai --output plan.json

With --ai, AtomDeepLit sends public titles, abstract excerpts, your focus topics, and a shortlist of collection names to DeepSeek. If the request fails, you can still review the saved plan manually. The plan records the error under ai_error.

Import reviewed items

python -X utf8 -m atomdeeplit apply plan.json --select 1,3 --priority 3 --use-suggestions

--select chooses which rows to import, and --priority marks rows with the configured priority tag. --use-suggestions applies the proposed collections. Use --collection 3=COLLKEY to override the collection for row 3. An item with no collection selection goes to My Library.

AtomDeepLit checks for duplicates again and displays the pending changes. Type APPLY to take a pre-write metadata snapshot and import the batch. Each batch is limited to 20 items.

When Zotero asks for access, choose Allow for the current write or Always Allow to reuse authorization for the same Zotero instance. Keep the command running while the dialog is open so AtomDeepLit can receive the response. AtomDeepLit saves a remembered key locally, protected by Windows DPAPI or owner-only file permissions on macOS and Linux. Each import still requires batch confirmation. To revoke remembered keys, use Clear Write Authorizations in Zotero's advanced settings.

Check PDF attachments

python -X utf8 -m atomdeeplit attachments receipt.json

This command checks attachments in the background. To look for missing PDFs, select the papers in Zotero and choose Find Available PDFs from the context menu. If a subscription PDF is available in your browser, download it there and attach it to the existing Zotero item.

Data and scope

• The CLI runs locally and uses public metadata sources. DeepSeek is optional. Zotero library access uses the local API.
• Keep plans, receipts, and metadata snapshots in a private directory. The metadata ZIP supports review of changes. Use Zotero's data-directory backup procedure for a full restore.
• This release covers URL intake, optional triage suggestions, and attachment checks. Automated PDF retrieval, Flexcil export, and AtomLeaf handoff are future work.

DeepSeek JSON output · Zotero local API · Zotero backup documentation