tamarind-cli 0.1.0__py3-none-any.whl

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Files changed (20) hide show
  1. tamarind/__init__.py +16 -0
  2. tamarind/catalog.py +70 -0
  3. tamarind/cli/__init__.py +1 -0
  4. tamarind/cli/commands/__init__.py +1 -0
  5. tamarind/cli/commands/auth.py +90 -0
  6. tamarind/cli/commands/catalog.py +114 -0
  7. tamarind/cli/commands/files.py +113 -0
  8. tamarind/cli/commands/jobs.py +311 -0
  9. tamarind/cli/inputs.py +115 -0
  10. tamarind/cli/main.py +122 -0
  11. tamarind/cli/output.py +68 -0
  12. tamarind/config.py +152 -0
  13. tamarind/errors.py +59 -0
  14. tamarind/http.py +160 -0
  15. tamarind/jobs.py +106 -0
  16. tamarind/rest.py +192 -0
  17. tamarind_cli-0.1.0.dist-info/METADATA +131 -0
  18. tamarind_cli-0.1.0.dist-info/RECORD +20 -0
  19. tamarind_cli-0.1.0.dist-info/WHEEL +4 -0
  20. tamarind_cli-0.1.0.dist-info/entry_points.txt +2 -0
tamarind_cli-0.1.0.dist-info/METADATA ADDED
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+ Metadata-Version: 2.4
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+ Name: tamarind-cli
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+ Version: 0.1.0
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+ Summary: Command-line interface for the Tamarind Bio platform — submit, monitor, and download protein/molecule jobs from your terminal or an AI agent.
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+ Project-URL: Homepage, https://tamarind.bio
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+ Project-URL: Documentation, https://app.tamarind.bio/api-docs
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+ Project-URL: Source, https://github.com/Tamarind-Bio/tamarind-cli
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+ Author: Tamarind Bio
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+ License: MIT
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+ Keywords: agents,alphafold,bioinformatics,boltz,cli,protein
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+ Requires-Python: >=3.10
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+ Requires-Dist: httpx>=0.27
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+ Requires-Dist: pyyaml>=6.0
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+ Requires-Dist: typer>=0.12
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+ Provides-Extra: dev
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+ Requires-Dist: pytest>=8.0; extra == 'dev'
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+ Requires-Dist: respx>=0.21; extra == 'dev'
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+ Requires-Dist: ruff>=0.5; extra == 'dev'
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+ Description-Content-Type: text/markdown
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+
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+ # Tamarind CLI
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+
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+ Command-line interface for the [Tamarind Bio](https://tamarind.bio) platform.
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+ Discover tools, submit and monitor protein / nucleic-acid / small-molecule jobs,
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+ and download results — from your terminal, a script, CI, or an AI coding agent
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+ (Claude Code, Codex, …).
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+
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+ The CLI is a thin client over the same API the [Tamarind MCP
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+ server](https://mcp.tamarind.bio) uses, so the two stay in lockstep. See
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+ [`docs/architecture.md`](docs/architecture.md) for how drift is prevented.
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+
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+ ## Install
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+
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+ Once published to PyPI:
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+
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+ ```bash
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+ curl -fsSL https://install.tamarind.bio/cli/install.sh | sh
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+ # or:
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+ uv tool install tamarind-cli # or: pipx install tamarind-cli
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+ ```
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+
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+ Before then (or to track the repo directly), install from git:
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+
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+ ```bash
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+ uv tool install "git+https://github.com/Tamarind-Bio/tamarind-cli"
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+ # or: pipx install "git+https://github.com/Tamarind-Bio/tamarind-cli"
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+ ```
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+
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+ > Releasing: tag a GitHub Release and the [`publish.yml`](.github/workflows/publish.yml)
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+ > workflow builds and uploads to PyPI via Trusted Publishing (configure the
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+ > trusted publisher for `tamarind-cli` on PyPI first).
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+
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+ ## Authenticate
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+
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+ Get an API key from the Tamarind web app (Settings → API), then either:
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+
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+ ```bash
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+ export TAMARIND_API_KEY="sk_..." # best for agents / CI
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+ # or
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+ tamarind auth login # stores it in ~/.tamarind/config.json
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+ tamarind auth status
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+ ```
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+
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+ ## Quickstart
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+
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+ ```bash
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+ # 1. Find a tool
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+ tamarind tools --function structure-prediction --modality protein
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+ tamarind tools --search boltz
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+
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+ # 2. Inspect its parameters and grab a runnable example
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+ tamarind schema boltz
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+ tamarind schema boltz --example > job.yaml
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+
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+ # 3. Validate, then submit
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+ tamarind validate boltz --input job.yaml
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+ tamarind submit boltz --input job.yaml --name my-run --wait --download ./out
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+
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+ # 4. Monitor / fetch
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+ tamarind jobs
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+ tamarind status my-run
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+ tamarind results my-run --download ./out
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+ ```
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+
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+ Set individual fields inline instead of a file:
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+
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+ ```bash
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+ tamarind submit boltz \
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+ --set inputFormat=sequence \
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+ --set sequence=MKTVRQERLKSIVRIL... \
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+ --name quick-fold
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+ ```
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+
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+ ## Output for agents
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+
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+ Every command emits JSON when stdout is not a TTY, or with `--json`. Exit codes
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+ are stable: `0` ok, `3` auth, `4` not-found, `5` validation, `6` rate-limit.
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+
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+ ```bash
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+ tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'
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+ ```
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+
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+ ## Commands
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+
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+ | Group | Commands |
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+ |---|---|
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+ | Discover | `tools`, `modalities`, `functions`, `schema` |
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+ | Submit | `validate`, `submit`, `batch` |
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+ | Monitor | `jobs`, `status`, `wait`, `results`, `logs` |
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+ | Files | `files list`, `files upload`, `files delete`, `files folders` |
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+ | Lifecycle | `cancel`, `delete` |
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+ | Auth | `auth login`, `auth status`, `auth logout` |
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+
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+ Run `tamarind <command> --help` for full options.
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+
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+ ## Configuration
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+
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+ | Setting | Flag | Env var | Default |
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+ |---|---|---|---|
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+ | API key | `--api-key` | `TAMARIND_API_KEY` | — |
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+ | Job API base | `--api-base` | `TAMARIND_API_BASE` | `https://app.tamarind.bio/api/` |
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+ | Catalog base | `--catalog-base` | `TAMARIND_CATALOG_BASE` | `https://mcp.tamarind.bio` |
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+ | Profile | `--profile` | `TAMARIND_PROFILE` | `default` |
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+
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+ Profiles (key + endpoints) are stored in `~/.tamarind/config.json`. Use a
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+ profile to point at staging:
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+
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+ ```bash
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+ tamarind --profile staging --api-base https://staging.tamarind.bio/api/ auth login
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+ TAMARIND_PROFILE=staging tamarind tools
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+ ```
tamarind_cli-0.1.0.dist-info/RECORD ADDED
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+ tamarind/__init__.py,sha256=Wd1r2m8FMiy1PR5J6tamVNJ-0w2Ohs2KmfLYWfveTBI,707
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+ tamarind/catalog.py,sha256=5kJZsRmp7ot_cNf0aok36aPAlr7pL3JqUeTfyScWRS0,2364
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+ tamarind/config.py,sha256=5Z1xECYk3ydsB0ZNZftCuAK9-DMh2UXT5xeNpf2oRZY,4399
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+ tamarind/errors.py,sha256=RlqiQj6yCvXbHLfd_Ep7Nmn43nz9vj2cNDo6MZpmDoA,1437
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+ tamarind/http.py,sha256=gJmeK4d8YSKYnJakI-X-sJRe3CF2POi_AtbxowjfzjQ,5127
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+ tamarind/jobs.py,sha256=WgqNfhNZyjzYJj8JfQ7gxp1aFA2LNg26E-x6dv2vp0Y,3360
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+ tamarind/rest.py,sha256=uRu189DlI6ntcQy__dWQVMCUoAGHIT2JfIvNWIFkvSg,6074
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+ tamarind/cli/__init__.py,sha256=Lq30AODa0cmKz24VuAgXQ-CAXTQ8EkvP06oJymTgY3U,49
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+ tamarind/cli/inputs.py,sha256=wChHGxRju5aENyUcVHpcrb2TJ6SAHfuzeIOeefxFFhA,3536
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+ tamarind/cli/main.py,sha256=1zOhM5D4V5TTuRHeRDOZ8h0tZj66e4FnI7m9v9wzU2g,3905
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+ tamarind/cli/output.py,sha256=1SEcWNcEHFoJW1vtbH7RPdoAEwwS1RnYWQYTzCkq0i0,1997
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+ tamarind/cli/commands/__init__.py,sha256=Rb-d2e6JpWZ5pPUP-TjKMWGtNCwpZCMYc0GulfEXbRs,26
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+ tamarind/cli/commands/auth.py,sha256=mbm9Tr98PKNZmiflFCELfPq8jVgwnzudxKG7gyZtsDk,2784
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+ tamarind/cli/commands/catalog.py,sha256=tKfitlfitpXcvUfEUhRLBba3mRs7JA3XIE9pxLQjKc8,4644
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+ tamarind/cli/commands/files.py,sha256=Kunvn3VbEMvHS9epZGtpF4GcvzqYluBfhwUAFcgoi-g,4536
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+ tamarind/cli/commands/jobs.py,sha256=2-tIirj5p9MQdl0aK5RwZHsDZtxTNj3ngT1Sn9GN_mA,14728
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+ tamarind_cli-0.1.0.dist-info/METADATA,sha256=4hk89JwXFBXwU2VwPnqllB841nvXvacKimuS7vw8gIw,4123
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+ tamarind_cli-0.1.0.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
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+ tamarind_cli-0.1.0.dist-info/entry_points.txt,sha256=XIVPkDzkzJ2QSZIC4YeSqQl8AIkCg2Lgr5CSAlnobCY,51
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+ tamarind_cli-0.1.0.dist-info/RECORD,,
tamarind_cli-0.1.0.dist-info/WHEEL ADDED
@@ -0,0 +1,4 @@
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+ Wheel-Version: 1.0
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+ Generator: hatchling 1.30.1
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+ Root-Is-Purelib: true
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+ Tag: py3-none-any
tamarind_cli-0.1.0.dist-info/entry_points.txt ADDED
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+ [console_scripts]
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+ tamarind = tamarind.cli.main:run