Local-first research software that carries a question from evidence to an auditable result.
Research graph · reproducible analysis · coding agents · provenance
Install · Setup guide · Quickstart · AI harnesses · Development · Contributing
Cly combines a scientific system of record with a multi-provider coding workspace. Research questions, sources, hypotheses, experiments, datasets, runs, metrics, claims, and review findings stay connected instead of being scattered across chats and folders.
Cly's research store and deterministic analysis run on the researcher's computer. Cly asks before opening local data and uses the existing authenticated session of an optional AI command-line harness; prompts and approved context sent to a harness are then governed by that provider's account and service terms. Raw analysis rows are not copied into Cly's project database.
- Guides a project through Question → Method → Evidence → Analysis → Claims → Review and identifies the first incomplete gate.
- Imports numeric CSV/TSV data and runs deterministic cross-validated binary classification or regression locally.
- Saves metrics, coefficients, dataset checksums, limitations, generated claims, evidence links, and provenance so a result survives restart.
- Connects sources and experiments to claims in an inspectable research graph.
- Audits reproducibility and integrity before a result is shared.
- Opens real coding projects and streams local agent chats through Codex, Claude Code, OpenCode, or Cursor.
- Exports project backups for recovery and review.
Download Cly from the Releases page. Under the latest release's Assets, choose the installer for your platform; the automatic Source code archives are for developers and do not contain an installable application.
- Apple Silicon Mac:
Cly-<version>-mac-arm64.dmg
The first downloadable desktop beta is for Apple Silicon (M-series) Macs. Intel Mac, Windows, and Linux installers will be added after their packaged builds have been independently validated.
On macOS, open the .dmg, drag Cly to Applications, then open it from
Applications. Current open-beta builds are not Developer ID signed or notarized,
so use Control-click Cly → Open the first time and confirm that you want to
open it. A clean install opens a blank guided setup with no demo projects. Use
Cly locally without signing in, or connect an existing Codex, Claude Code,
OpenCode, or Cursor account for agent features; then create a new project folder
or open a folder you already own. Cly does not yet support regulated or
sensitive data.
See the install and setup guide for platform-specific installation, local-data locations, backups, and the first project flow.
The command-line instructions below are only for developers and contributors working from source. They are not the end-user installation path.
Requirements: Git, Node.js 22.12 or newer, and pnpm 11.12. Python is not required for normal development or local analysis.
For macOS or Linux, the complete setup can be run as one command:
git clone https://github.com/Frostand/Cly.git && cd Cly && corepack enable && corepack prepare pnpm@11.12.0 --activate && pnpm install --frozen-lockfile && pnpm doctor && pnpm devOr run the same setup step by step:
git clone https://github.com/Frostand/Cly.git
cd Cly
corepack enable
corepack prepare pnpm@11.12.0 --activate
pnpm install --frozen-lockfile
pnpm doctor
pnpm devpnpm doctor checks the local toolchain and reports which optional AI harnesses are installed and signed in. Cly Research works without an AI harness.
- On first launch, choose local-only use or an optional AI provider, then select Create a new project or Open an existing folder and complete the setup guide.
- Enter the research question, working hypothesis, and scope.
- Add sources and connect them to a preliminary claim.
- Create an experiment and choose Run analysis.
- Select a CSV or TSV file, outcome, predictors, fold count, and seed.
- Review cross-validated performance, the baseline, coefficients, warnings, and generated result claim.
- Open Reproducibility, run the audit, and resolve the evidence gaps before sharing.
- Export a project backup from Settings → Privacy.
The supported local analysis boundary and an independent tester checklist are in Beta testing.
- Select Dev in the application switcher.
- Choose Open project and select a local repository.
- Open AI Providers, select an installed harness, and complete sign-in if needed.
- Start a chat, select a model, and review tool activity and file changes in the workspace.
Provider credentials remain in each provider's own CLI session; Cly does not collect or save them.
Install and authenticate at least one harness to use Cly Dev chat. Provider accounts and usage charges are managed by the provider, not Cly.
| Harness | Install | Sign in | Documentation |
|---|---|---|---|
| Codex | npm install -g @openai/codex |
codex login |
Codex CLI |
| Claude Code | npm install -g @anthropic-ai/claude-code |
claude |
Claude Code |
| OpenCode | npm install -g opencode-ai |
opencode auth login |
OpenCode CLI |
| Cursor | Install Cursor Agent CLI (agent or cursor-agent) |
<detected executable> login |
Cursor Agent CLI |
Cly checks both CLI availability and authentication. For Cursor it accepts only an agent executable whose help identifies it as Cursor, or cursor-agent, and checks <detected executable> status; installation alone is not treated as connected. Models come from each signed-in CLI's live discovery output. Provider/model failures and any labelled last-known catalog are surfaced in AI Providers, where setup commands can be copied and status refreshed.
Cly does not install a standalone cly command. End users launch the desktop
application normally. Contributors use the repository's pnpm scripts, and Cly
Dev optionally calls a provider CLI that is already installed and authenticated
on the same computer.
| Command | Purpose |
|---|---|
pnpm doctor |
Verify Node.js, pnpm, Git, and optional provider CLI status. |
pnpm dev |
Start Electron and its Vite renderer in development mode. |
pnpm vite:build |
Build the renderer into dist/. |
pnpm start |
Run the source checkout in production mode; run pnpm vite:build first. |
pnpm test |
Run the Vitest unit and integration suite. |
pnpm test:e2e |
Run the Playwright Electron end-to-end suite. |
pnpm package:dir |
Build an unpacked application for the current platform. |
pnpm package:mac |
Build macOS .dmg and .zip artifacts on macOS. |
No .env file, API key, hosted database, or external service is required for
Cly Research or the normal source-development path. Provider credentials stay
in the provider's own CLI session. Release signing, notarization, update-feed,
and CI-only environment variables are configured by the production release
workflow and are not needed for local use.
Example production-mode source run:
pnpm install --frozen-lockfile
pnpm doctor
pnpm vite:build
pnpm startExample local packaged-app check:
pnpm package:dir
pnpm package:verify:contents
pnpm package:smoke -- --app release/mac-arm64/Cly.appThe content check discovers the current platform's default release/ output.
The smoke check requires the unpacked application path; replace the macOS path
above with release/win-unpacked/Cly.exe or the executable inside
release/linux-unpacked/ on those platforms.
Cly Core (local project store, research graph, context, permissions, provenance)
├── Cly Research (question, sources, experiments, analysis, claims, review)
└── Cly Dev (projects, files, terminal, diffs, multi-provider agent chat)
The capability inventory is the machine-checked beta boundary. Every production action has a real local service/API boundary and a test. Unsupported actions are omitted from production controls instead of appearing as previews or behaving like completed features.
The end-to-end local research loop, persistent research objects, CSV/TSV analysis, evidence linkage, audits, backups, and live Cly Dev provider chat are available now. Research Agent Sessions can start, stream, approve, stop, resume, restart, and recover authenticated Codex and Claude runs; models and reasoning levels come from live provider discovery. Runtime-owned events are shown in the session record, while fixture-backed browser/terminal/diff panes are absent from production.
Notebook import, code scanning, hosted sync relay, hosted research/data integrations, and automatic research-decision planning are not part of this beta. The Integrations route detects local Codex, Claude Code, OpenCode, and Cursor sessions plus installed editors; provider credentials remain in their own CLIs. Use de-identified, non-sensitive data and export a backup before testing. Please report defects through GitHub Issues.
pnpm install --frozen-lockfile
pnpm doctor
pnpm devRun the same quality gates used by CI:
pnpm lint
pnpm typecheck
pnpm capabilities:check
pnpm licenses:check
pnpm test
pnpm test:e2e
pnpm package:dir
pnpm package:verify:contents -- --app release/<platform-unpacked-path>
pnpm package:smoke -- --app release/<platform-unpacked-path>Production release jobs run the privacy, license, capability, unit, end-to-end, packaged-content, permission-metadata, signing, and unpacked-application launch checks on macOS, Windows, and Linux before publishing installers.
Useful commands:
pnpm package:mac # platform installer targets also exist for win and linuxpnpmis missing or the version is wrong: runcorepack enable, thencorepack prepare pnpm@11.12.0 --activate, and confirm withpnpm --version.- A provider is not detected or signed in: run
pnpm doctor, complete the provider's sign-in command from the table above, and restart Cly so the app receives the updated shellPATH. pnpm startopens without the current interface: runpnpm vite:buildfirst. Production mode serves the existingdist/directory.- Create reports that the folder already exists: choose Open an existing folder instead. Create intentionally makes a brand-new empty directory.
- An earlier beta project still appears: saved projects are preserved by design. Create another project for a blank workspace; reinstalling the app does not delete application data.
- A locally built macOS app is blocked: local builds are not automatically Developer ID signed or notarized. Use a published release, or Control-click the local app and choose Open for development testing.
For data locations, backups, and first-launch behavior, see the setup guide. For reproducible bug reports, use Settings → Diagnostics → Copy diagnostics and open a GitHub issue.
See Contributing, Security, the architecture, and the product roadmap.
Cly is licensed under Apache License 2.0. Third-party components retain their own licenses. Scoped attribution for inherited MIT-licensed material is preserved in NOTICE.md and licenses/DREAM_IDE-MIT.txt; it does not change Cly's Apache-2.0 license.