tamarind-cli 0.1.3__tar.gz → 0.2.0__tar.gz

tamarind_cli-0.2.0/.github/workflows/ci.yml

@@ -0,0 +1,67 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  package:
+    name: Build release artifacts
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - name: Build source and wheel distributions
+        run: uv build
+      - name: Reject local caches in the source distribution
+        run: >-
+          python -c "import glob, tarfile;
+          names = tarfile.open(glob.glob('dist/*.tar.gz')[0]).getnames();
+          assert not any('/.uv-cache/' in name or '/.venv/' in name for name in names)"
+      - name: Smoke-check the built wheel
+        run: uv run --isolated --no-project --with dist/*.whl tamarind --version
+
+  test:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+      - name: Install project and development dependencies
+        run: uv sync --extra dev
+      - name: Test
+        run: uv run pytest
+      - name: Lint
+        run: uv run ruff check .
+
+  cross-platform:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - name: Install project and development dependencies
+        run: uv sync --extra dev
+      - name: Test
+        run: uv run pytest

{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/.github/workflows/publish.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Build sdist + wheel
         run: uv build
       - name: Smoke-check the build
-        run: uv run --with dist/*.whl tamarind --version
+        run: uv run --isolated --no-project --with dist/*.whl tamarind --version
       - uses: actions/upload-artifact@v4
         with:
           name: dist

{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/.gitignore

@@ -6,6 +6,7 @@ build/
 dist/
 .pytest_cache/
 .ruff_cache/
+.uv-cache/
 .coverage
 htmlcov/
 .tamarind/

tamarind_cli-0.2.0/LICENSE

@@ -0,0 +1,201 @@
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
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+      the terms of any separate license agreement you may have executed
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+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
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+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
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+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
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{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: tamarind-cli
-Version: 0.1.3
+Version: 0.2.0
 Summary: Command-line interface for the Tamarind Bio platform — submit, monitor, and download protein/molecule jobs from your terminal or an AI agent.
 Project-URL: Homepage, https://tamarind.bio
 Project-URL: Documentation, https://app.tamarind.bio/api-docs
 Project-URL: Source, https://github.com/Tamarind-Bio/tamarind-cli
 Author: Tamarind Bio
-License: MIT
+License: Apache-2.0
+License-File: LICENSE
 Keywords: agents,alphafold,bioinformatics,boltz,cli,protein
 Requires-Python: >=3.10
 Requires-Dist: httpx>=0.27
@@ -20,6 +21,9 @@ Description-Content-Type: text/markdown
 
 # Tamarind CLI
 
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/downloads/)
+
 Command-line interface for the [Tamarind Bio](https://tamarind.bio) platform.
 Discover tools, submit and monitor protein / nucleic-acid / small-molecule jobs,
 and download results — from your terminal, a script, CI, or an AI coding agent
@@ -35,7 +39,8 @@ server](https://mcp.tamarind.bio) uses, so the two stay in lockstep. See
 uv tool install tamarind-cli      # or: pipx install tamarind-cli
 ```
 
-Or with the bootstrap installer (installs `uv` if needed):
+Or with the bootstrap installer (uses `uv`, `pipx`, or Python/pip already on
+your `PATH`):
 
 ```bash
 curl -fsSL https://app.tamarind.bio/cli/install.sh | sh
@@ -72,11 +77,12 @@ tamarind tools --search boltz
 
 # 2. Inspect its parameters and grab a runnable example
 tamarind schema boltz
-tamarind schema boltz --example > job.yaml
+tamarind schema boltz --example > job.yaml   # most tools ship an example; some don't
 
 # 3. Validate, then submit
 tamarind validate boltz --input job.yaml
-tamarind submit   boltz --input job.yaml --name my-run --wait --download ./out
+tamarind submit boltz --input job.yaml --name my-run \
+  --wait --timeout 3600 --download ./out
 
 # 4. Monitor / fetch
 tamarind jobs
@@ -95,13 +101,40 @@ tamarind submit boltz \
 
 ## Output for agents
 
-Every command emits JSON when stdout is not a TTY, or with `--json`. Exit codes
-are stable: `0` ok, `3` auth, `4` not-found, `5` validation, `6` rate-limit.
+Every command emits JSON when stdout is not a TTY, or with `--json`. Result
+documents are written to stdout. Typed command, transport, and usage errors are
+written to stderr as
+`{"error":{"type":...,"message":...,"exitCode":...,"detail":...}}`; `detail`
+is omitted when unavailable. A domain verdict can deliberately combine a
+nonzero exit with a result document: invalid `validate` output remains on
+stdout with exit 5, and a terminal unsuccessful job remains on stdout with exit
+9 so callers can inspect its status. Exit codes are stable: `0` ok, `1`
+generic failure, `2` usage, `3` auth, `4` not-found, `5` validation, `6`
+rate-limit, `7` timeout (a bounded wait elapsed while the remote job may still
+run), `8` budget/quota exhaustion, and `9` remote job failure.
+
+For agent workflows, always put a deadline on blocking commands. `submit --wait`
+and `results --wait` accept `--timeout`; the standalone `wait` command remains
+the easiest way to reattach to a durable job name.
+
+Starting in 0.2, `results` requires `--download DIR` by default and never prints
+a presigned URL implicitly. This intentional safety boundary is why the release
+uses a new pre-1.0 minor version. The explicit `--show-url` escape hatch returns
+a credential-bearing, short-lived URL; do not use it in agent, CI, or shared logs.
+
+Not every tool ships a runnable example — `schema <tool> --example` exits non-zero
+(with a clear message) when one isn't available, so a `> job.yaml` redirect never
+silently produces an empty file. Destructive commands (`delete`, `files delete`)
+require `--yes`/`-y` when run non-interactively (piped or `--json`), so an agent
+never removes data without an explicit confirmation.
 
 ```bash
-tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'
+tamarind --json jobs | jq '.jobs[] | select(.JobStatus=="Running")'
 ```
 
+`--json`, `--profile`, and the endpoint/auth overrides are global options, so
+place them before the command name.
+
 ## Commands
 
 | Group | Commands |
@@ -109,7 +142,7 @@ tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'
 | Discover | `tools`, `modalities`, `functions`, `schema` |
 | Submit | `validate`, `submit`, `batch` |
 | Monitor | `jobs`, `status`, `wait`, `results`, `logs` |
-| Files | `files list`, `files upload`, `files delete`, `files folders` |
+| Files | `files list`, `files stats`, `files upload`, `files delete`, `files folders` |
 | Lifecycle | `cancel`, `delete` |
 | Auth | `auth login`, `auth status`, `auth logout` |
 
@@ -131,3 +164,15 @@ profile to point at staging:
 tamarind --profile staging --api-base https://staging.tamarind.bio/api/ auth login
 TAMARIND_PROFILE=staging tamarind tools
 ```
+
+## Links
+
+- [CLI docs](https://app.tamarind.bio/api-docs/cli) — the hosted quickstart and command reference
+- [MCP server](https://app.tamarind.bio/api-docs/mcp-server) — the hosted option for claude.ai, ChatGPT, and other MCP clients
+- [API key](https://app.tamarind.bio/api-docs/api-key) — get your key and review rate limits
+
+Questions or need help? Contact us at [info@tamarind.bio](mailto:info@tamarind.bio).
+
+## License
+
+Licensed under the [Apache License 2.0](LICENSE).

{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/README.md

@@ -1,5 +1,8 @@
 # Tamarind CLI
 
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/downloads/)
+
 Command-line interface for the [Tamarind Bio](https://tamarind.bio) platform.
 Discover tools, submit and monitor protein / nucleic-acid / small-molecule jobs,
 and download results — from your terminal, a script, CI, or an AI coding agent
@@ -15,7 +18,8 @@ server](https://mcp.tamarind.bio) uses, so the two stay in lockstep. See
 uv tool install tamarind-cli      # or: pipx install tamarind-cli
 ```
 
-Or with the bootstrap installer (installs `uv` if needed):
+Or with the bootstrap installer (uses `uv`, `pipx`, or Python/pip already on
+your `PATH`):
 
 ```bash
 curl -fsSL https://app.tamarind.bio/cli/install.sh | sh
@@ -52,11 +56,12 @@ tamarind tools --search boltz
 
 # 2. Inspect its parameters and grab a runnable example
 tamarind schema boltz
-tamarind schema boltz --example > job.yaml
+tamarind schema boltz --example > job.yaml   # most tools ship an example; some don't
 
 # 3. Validate, then submit
 tamarind validate boltz --input job.yaml
-tamarind submit   boltz --input job.yaml --name my-run --wait --download ./out
+tamarind submit boltz --input job.yaml --name my-run \
+  --wait --timeout 3600 --download ./out
 
 # 4. Monitor / fetch
 tamarind jobs
@@ -75,13 +80,40 @@ tamarind submit boltz \
 
 ## Output for agents
 
-Every command emits JSON when stdout is not a TTY, or with `--json`. Exit codes
-are stable: `0` ok, `3` auth, `4` not-found, `5` validation, `6` rate-limit.
+Every command emits JSON when stdout is not a TTY, or with `--json`. Result
+documents are written to stdout. Typed command, transport, and usage errors are
+written to stderr as
+`{"error":{"type":...,"message":...,"exitCode":...,"detail":...}}`; `detail`
+is omitted when unavailable. A domain verdict can deliberately combine a
+nonzero exit with a result document: invalid `validate` output remains on
+stdout with exit 5, and a terminal unsuccessful job remains on stdout with exit
+9 so callers can inspect its status. Exit codes are stable: `0` ok, `1`
+generic failure, `2` usage, `3` auth, `4` not-found, `5` validation, `6`
+rate-limit, `7` timeout (a bounded wait elapsed while the remote job may still
+run), `8` budget/quota exhaustion, and `9` remote job failure.
+
+For agent workflows, always put a deadline on blocking commands. `submit --wait`
+and `results --wait` accept `--timeout`; the standalone `wait` command remains
+the easiest way to reattach to a durable job name.
+
+Starting in 0.2, `results` requires `--download DIR` by default and never prints
+a presigned URL implicitly. This intentional safety boundary is why the release
+uses a new pre-1.0 minor version. The explicit `--show-url` escape hatch returns
+a credential-bearing, short-lived URL; do not use it in agent, CI, or shared logs.
+
+Not every tool ships a runnable example — `schema <tool> --example` exits non-zero
+(with a clear message) when one isn't available, so a `> job.yaml` redirect never
+silently produces an empty file. Destructive commands (`delete`, `files delete`)
+require `--yes`/`-y` when run non-interactively (piped or `--json`), so an agent
+never removes data without an explicit confirmation.
 
 ```bash
-tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'
+tamarind --json jobs | jq '.jobs[] | select(.JobStatus=="Running")'
 ```
 
+`--json`, `--profile`, and the endpoint/auth overrides are global options, so
+place them before the command name.
+
 ## Commands
 
 | Group | Commands |
@@ -89,7 +121,7 @@ tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'
 | Discover | `tools`, `modalities`, `functions`, `schema` |
 | Submit | `validate`, `submit`, `batch` |
 | Monitor | `jobs`, `status`, `wait`, `results`, `logs` |
-| Files | `files list`, `files upload`, `files delete`, `files folders` |
+| Files | `files list`, `files stats`, `files upload`, `files delete`, `files folders` |
 | Lifecycle | `cancel`, `delete` |
 | Auth | `auth login`, `auth status`, `auth logout` |
 
@@ -111,3 +143,15 @@ profile to point at staging:
 tamarind --profile staging --api-base https://staging.tamarind.bio/api/ auth login
 TAMARIND_PROFILE=staging tamarind tools
 ```
+
+## Links
+
+- [CLI docs](https://app.tamarind.bio/api-docs/cli) — the hosted quickstart and command reference
+- [MCP server](https://app.tamarind.bio/api-docs/mcp-server) — the hosted option for claude.ai, ChatGPT, and other MCP clients
+- [API key](https://app.tamarind.bio/api-docs/api-key) — get your key and review rate limits
+
+Questions or need help? Contact us at [info@tamarind.bio](mailto:info@tamarind.bio).
+
+## License
+
+Licensed under the [Apache License 2.0](LICENSE).

{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/docs/architecture.md

@@ -10,11 +10,15 @@ the CLI and the MCP from drifting as the platform evolves.
 ### 1. Job/file REST surface — source of truth: the OpenAPI spec
 
 `submit`, `validate`, `batch`, `jobs`, `status`/`wait`, `results`, `files`,
-`cancel`, `delete` map 1:1 onto operations in `openapi-mcp.yaml` — the same
-spec the MCP server is generated from (`FastMCP.from_openapi`). The CLI's
-[`rest.py`](../src/tamarind/rest.py) is a literal, logic-free mapping of that
-spec. Because both clients derive from one spec, a contract test can fail CI if
-they diverge.
+`cancel`, and `delete` map onto operations in `openapi-mcp.yaml` — the same
+server contract used to generate the MCP surface. The CLI's
+[`rest.py`](../src/tamarind/rest.py) is intentionally a small mapping of those
+operations.
+
+The CLI mapping is still client code and can drift. Unit tests cover request and
+response shapes, and authenticated no-spend smoke tests should exercise auth,
+catalog lookup, schema lookup, and validation before a release. Changes to the
+server contract should update the CLI tests in the same change or release train.
 
 These calls go directly to the job API (`https://app.tamarind.bio/api/`) with
 the `x-api-key` header.
@@ -37,10 +41,9 @@ detail that can change without any client change and without drift.
 
 A from-scratch client in another language would re-encode the request shapes and
 the catalog logic — two copies that drift the moment the platform changes.
-Keeping the CLI a thin, spec-derived Python client that shares the OpenAPI
-contract (and, server-side, the catalog module) with the MCP makes drift a
-structural impossibility plus a CI-enforced check, rather than something to
-remember.
+Keeping the CLI thin and anchored to the same OpenAPI contract (and,
+server-side, the same catalog module) reduces drift and makes it testable. It
+does not eliminate the need for compatibility tests and coordinated releases.
 
 ## Configuration indirection
 

{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/pyproject.toml

@@ -1,10 +1,10 @@
 [project]
 name = "tamarind-cli"
-version = "0.1.3"
+version = "0.2.0"
 description = "Command-line interface for the Tamarind Bio platform — submit, monitor, and download protein/molecule jobs from your terminal or an AI agent."
 readme = "README.md"
 requires-python = ">=3.10"
-license = { text = "MIT" }
+license = { text = "Apache-2.0" }
 authors = [{ name = "Tamarind Bio" }]
 keywords = ["bioinformatics", "protein", "alphafold", "boltz", "cli", "agents"]
 dependencies = [

{tamarind_cli-0.1.3 → tamarind_cli-0.2.0}/src/tamarind/cli/commands/auth.py

@@ -7,7 +7,7 @@ from typing import Optional
 import typer
 
 from ... import rest
-from ...config import mask_key, save_profile
+from ...config import save_profile
 from ...errors import AuthError
 from ...http import HTTPClient
 from .. import output
@@ -56,23 +56,19 @@ def login(
 
 @app.command()
 def status(ctx: typer.Context) -> None:
-    """Show the active profile, endpoints, and whether the key works."""
+    """Show the active profile and whether its key works."""
     state = ctx.obj
     cfg = state.config()
     verified = cfg.has_key and _check_key(cfg.api_base, cfg.api_key)
     result = {
         "profile": cfg.profile,
-        "apiKey": mask_key(cfg.api_key),
         "hasKey": cfg.has_key,
         "verified": verified,
-        "apiBase": cfg.api_base,
-        "catalogBase": cfg.catalog_base,
     }
     human = (
         f"profile:      {cfg.profile}\n"
-        f"api key:      {mask_key(cfg.api_key)} ({'verified' if verified else 'not verified'})\n"
-        f"job api:      {cfg.api_base}\n"
-        f"catalog api:  {cfg.catalog_base}"
+        f"api key:      {'configured' if cfg.has_key else 'not configured'} "
+        f"({'verified' if verified else 'not verified'})"
     )
     output.emit(result, state.output, human=human)