omnisci

omnisci: DeepSeek is the scientist, the CLIs are the instruments

Do the science in the current CLI session. The python here does only what a model must not do by hand: render raw data into something viewable, run analysis code, fetch real references, assemble LaTeX, and enforce the gates. These CLIs never call another model API. DeepSeek V4 Flash remains the scientist and author. Because the official DeepSeek endpoint accepts text only, the CLI's view_image sends pixels to its fixed, vision-capable sidecar and returns only the factual observation to DeepSeek. This follows OmniScientist's own text-backbone plus VISION_SIDECAR design.

Where the commands live

The CLIs ship inside this skill and the launcher sets OMNISCI. Confirm it once and use it in every command:

test -n "$OMNISCI" && test -f "$OMNISCI/evidence_cli.py"
python3 $OMNISCI/evidence_cli.py --help            # confirm before going further

--task takes a case directory (absolute paths always work), or a bare name that resolves under $OMNISCI_CASES or the engine's bundled examples/. Every other path you pass (a script, a figure, a .tex, a sections.json) is resolved relative to the case directory.

Every command echoes the case it resolved. Check it on your first call. A bare name can land on a bundled example that already holds someone else's recorded runs, and the gate would then happily ground your paper's numbers against their ledger. When the case is the user's own folder, pass its absolute path.

Three state-changing steps are OmniScientist tools, not shell commands: omnisci_record, omnisci_bib, and omnisci_compile. Call them through the tool protocol. They run the packaged CLIs with argument arrays and return receipts that the final delivery verifier binds to the current files. A bash call to the same Python CLI may help diagnose a failure, but it cannot satisfy final delivery.

Before the loop: is there a case?

A case is a directory holding a series.json. Bundled demos have one. A real user almost never does: they have a folder of images, recordings or volumes, and a question. Build the case first, from their folder: