SciMinds Command Line Toolkit

A small smart CLI toolkit for academic work on macOS in a single command: sci

Install

curl -fsSL https://raw.githubusercontent.com/sciminds/sci/main/install.sh | sh

Written in Go because:

• Go is typed and compiled which makes it much faster than Python/JS and makes TDD with LLMs more reliable
• Easy to create single-file programs that work on any computer
• No complicated dev tooling: everything is pretty standardized in the ecosystem and distribution is just GitHub
• Eshin wanted to learn a new language

What can it do?

Getting started

Command	What it does
sci help	Interactive help TUI with demos for any command
sci learn	Interactive guides with terminal demos
sci doctor	Check that your Mac is set up correctly
sci update	Update sci to the latest version

Browse data files

Command	What it does
sci view <file>	Interactively browse any tabular data file (CSV, JSON, SQLite)

The interactive data viewer is powered by dbtui (internal/tui/dbtui/), also installable as a standalone binary: go install github.com/sciminds/cli/cmd/dbtui@latest.

Manage Python projects

Command	What it does
sci proj new	Create a new Python project
sci proj add	Add packages to the project
sci proj remove	Remove packages from the project
sci proj config	Refresh config files in your project
sci proj preview	Start a live preview server for documents
sci proj render	Build documents into HTML or PDF
sci proj run	Run a project task
sci py repl	Open a Python scratchpad
sci py marimo	Open a marimo notebook
sci py convert	Convert between marimo (.py), MyST (.md), and Quarto (.qmd)

Manage databases

Command	What it does
sci db create	Create an empty database
sci db info	Show database metadata and tables
sci db add	Import CSV files into a database
sci db rename	Rename a table in a database
sci db delete	Delete a table from a database
sci db reset	Delete and recreate an empty database

Cloud storage

Command	What it does
sci cloud setup	Authenticate with GitHub (requires sciminds org membership)
sci cloud put <file>	Upload a file to cloud storage
sci cloud get <name>	Download a shared file
sci cloud list	List all shared files
sci cloud remove <name>	Remove a shared file

Lab storage (sftp)

Command	What it does
sci lab setup	Configure SSH access to lab storage
sci lab ls	List remote directory contents
sci lab get	Download a file or directory from lab storage
sci lab put	Upload a file or directory to your lab space
sci lab browse	Open an SSH shell in lab storage

Manage tools (Homebrew & uv)

Command	What it does
sci tools list	List packages in the Brewfile
sci tools install	Install packages from the Brewfile, or add and install a new package
sci tools uninstall	Remove a package from the Brewfile and uninstall it
sci tools update	Update the Homebrew registry and upgrade outdated packages
sci tools reccs	Pick optional tools to install

Video/audio editing

Command	What it does
sci vid info	Show video info (resolution, duration, codec, fps, size)
sci vid cut	Trim a segment (e.g. 0:30 1:00)
sci vid compress	Shrink a video file (reduce file size)
sci vid convert	Convert to another format (mp4, webm, etc.)
sci vid gif	Convert to optimized GIF
sci vid resize	Scale video (720p, 1080p, 4k, 50%, W:H)
sci vid speed	Change playback speed (e.g. 2 = 2x faster)
sci vid mute	Remove audio from a video
sci vid extract-audio	Extract audio track to file
sci vid strip-subs	Remove subtitles from a video

Canvas LMS & GitHub Classroom

Command	What it does
sci cass setup	Save your Canvas API token (one-time)
sci cass init	Create a cass.yaml config for a course directory
sci cass pull	Fetch students, assignments, and submissions from Canvas/GitHub
sci cass status	Show sync status, pending changes, and discrepancies
sci cass diff	Show pending grade changes (local or --remote 3-way)
sci cass push	Push grade changes to Canvas
sci cass match	Interactively match GitHub usernames to Canvas students
sci cass revert	Discard unpushed grade edits
sci cass log	Show operation history
sci cass canvas modules	List, create, publish, or delete course modules
sci cass canvas assignments	List, create, publish, or delete assignments
sci cass canvas announce	List, post, or delete announcements
sci cass canvas files	List course files

Syncs course data to a local SQLite database (cass.db) with a git-like workflow: pull shows changelogs, diff shows pending grade changes, push sends grades to Canvas with conflict detection. GitHub Classroom is optional — works with Canvas-only courses.

Zotero library management (Experimental)

Command	What it does
sci zot setup	Save your Zotero API key + library ID
sci zot search <query>	Search the local Zotero library
sci zot read <key>	Show full metadata for an item
sci zot list	List items / collections / tags
sci zot stats	Library size and field-coverage summary
sci zot export <key>	Export to CSL-JSON or minimal BibTeX
sci zot open <key>	Open the item's PDF attachment
sci zot add / update / delete	Create / patch / trash items via the Zotero Web API
sci zot collection / tag	Manage collections and tags
sci zot doctor	Run all hygiene checks (invalid → missing → orphans → duplicates)
sci zot missing / duplicates / invalid / orphans	Drill into individual hygiene reports

Reads the local zotero.sqlite (immutable, no contention with the running Zotero desktop app); writes go through the Zotero Web API. zot doctor --deep enables fuzzy duplicate detection and noisier orphan kinds.

Also installable as a standalone binary: go install github.com/sciminds/cli/cmd/zot@latest.

Ingest markdown into SQLite (Experimental)

Command	What it does
sci markdb ingest <dir>	Ingest a directory of .md files into SQLite
sci markdb search --db <db> <query>	Full-text search across files
sci markdb info --db <db>	Show database summary statistics
sci markdb diff <dir> --db <db>	Show what would change on next ingest
sci markdb export --db <db> --dir <dir>	Reconstruct markdown files from the database

Ingests any folder of markdown files with YAML front-matter into a single SQLite database. Front-matter keys become real SQL columns (dynamically discovered), wikilinks and markdown links are tracked in a links table, and FTS5 enables full-text search. Export reconstructs byte-identical files from the database.

Also installable as a standalone binary: go install github.com/sciminds/cli/cmd/markdb@latest.

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Releases

Every push to main triggers the Release workflow:

1. Check — fmt, vet, lint, test
2. Build — cross-compiles sci, dbtui, and markdb for darwin/linux × arm64/amd64
3. Publish — uploads all binaries to a rolling latest GitHub release

Binaries are named {tool}-{os}-{arch} (e.g. sci-darwin-arm64, dbtui-linux-amd64).

Updating: Users run sci update, which compares the compiled-in commit SHA against the latest release and atomically replaces the binary if a newer build is available.

Development

Prerequisites: Go 1.26+ and just (brew install just).

You'll also need asciicinema to create new terminal "casts" to place in internal/guide/casts/

This is also set up as a git pre-commit hook:

# Run the full check suite (fmt, vet, lint, test, build)
just ok

Launch auto-documentation site:

just docs

To try commands during development:

just run doctor       # same as: go run ./cmd/sci doctor
just run proj new     # etc.

Cloud auth infrastructure

sci cloud setup uses a GitHub OAuth device flow brokered by a Cloudflare Worker. The worker verifies sciminds GitHub org membership and returns shared R2 credentials.

Components:

1. GitHub OAuth App — sciminds org settings → OAuth Apps. Client ID is compiled into the CLI (internal/cloud/device.go). Must have "Enable Device Flow" checked.
2. Cloudflare Worker (worker/) — two endpoints: POST /auth/device and POST /auth/token. Deployed at sci-auth.sciminds.workers.dev.
3. R2 bucket — sci-public (public read, auth'd write).

Deploy / redeploy the worker:

cd worker
bun install
bunx wrangler deploy

Set or rotate worker secrets:

cd worker
bunx wrangler secret put GITHUB_CLIENT_SECRET
bunx wrangler secret put R2_ACCOUNT_ID
bunx wrangler secret put R2_ACCESS_KEY          # public bucket
bunx wrangler secret put R2_SECRET_KEY          # public bucket
bunx wrangler secret put R2_PUBLIC_URL           # e.g. https://pub-xxx.r2.dev

Each command prompts for the value interactively. Get these from the Cloudflare R2 dashboard → R2 → API Tokens.

List / delete secrets:

bunx wrangler secret list
bunx wrangler secret delete <NAME>

Adding a new bucket: Create the R2 bucket in Cloudflare, generate an API token scoped to it, set the corresponding R2_*_ACCESS_KEY / R2_*_SECRET_KEY worker secrets, and update worker/wrangler.toml vars if the bucket name differs.