tamarind-cli 0.1.0__tar.gz → 0.1.2__tar.gz

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tamarind-cli
-Version: 0.1.0
+Version: 0.1.2
 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
@@ -31,15 +31,17 @@ server](https://mcp.tamarind.bio) uses, so the two stay in lockstep. See
 
 ## Install
 
-Once published to PyPI:
-
 ```bash
-curl -fsSL https://install.tamarind.bio/cli/install.sh | sh
-# or:
 uv tool install tamarind-cli      # or: pipx install tamarind-cli
 ```
 
-Before then (or to track the repo directly), install from git:
+Or with the bootstrap installer (installs `uv` if needed):
+
+```bash
+curl -fsSL https://app.tamarind.bio/cli/install.sh | sh
+```
+
+To track the repo directly instead of the PyPI release:
 
 ```bash
 uv tool install "git+https://github.com/Tamarind-Bio/tamarind-cli"

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/README.md

@@ -11,15 +11,17 @@ server](https://mcp.tamarind.bio) uses, so the two stay in lockstep. See
 
 ## Install
 
-Once published to PyPI:
-
 ```bash
-curl -fsSL https://install.tamarind.bio/cli/install.sh | sh
-# or:
 uv tool install tamarind-cli      # or: pipx install tamarind-cli
 ```
 
-Before then (or to track the repo directly), install from git:
+Or with the bootstrap installer (installs `uv` if needed):
+
+```bash
+curl -fsSL https://app.tamarind.bio/cli/install.sh | sh
+```
+
+To track the repo directly instead of the PyPI release:
 
 ```bash
 uv tool install "git+https://github.com/Tamarind-Bio/tamarind-cli"

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "tamarind-cli"
-version = "0.1.0"
+version = "0.1.2"
 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"

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/src/tamarind/__init__.py

@@ -13,4 +13,11 @@ This package is a thin client over the Tamarind platform. Two surfaces:
   database directly.
 """
 
-__version__ = "0.1.0"
+from importlib.metadata import PackageNotFoundError, version as _pkg_version
+
+try:
+    # Single source of truth: the installed package version (pyproject.toml),
+    # so `tamarind --version` can never drift from the released version.
+    __version__ = _pkg_version("tamarind-cli")
+except PackageNotFoundError:  # running from a source tree with no install metadata
+    __version__ = "0.0.0+dev"

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/src/tamarind/cli/commands/files.py

@@ -75,16 +75,19 @@ def upload(
     """Upload a local file to your workspace (two-step presigned PUT)."""
     state = ctx.obj
     remote = name or path.name
+    content_type = "application/octet-stream"
     with state.rest_client() as client:
-        signed = rest.upload_file_url(client, filename=remote)
-    # The endpoint may return a non-dict error sentinel (e.g. -1) instead of an
-    # object; don't crash on .get — surface a clean error.
-    url = signed.get("signedUrl") if isinstance(signed, dict) else None
+        signed = rest.upload_file_url(client, filename=remote, content_type=content_type)
+    # The endpoint returns {uploadUrl, headUrl, key, bucket}; PUT the bytes to
+    # uploadUrl. Don't crash on a non-dict error body — surface a clean error.
+    url = signed.get("uploadUrl") if isinstance(signed, dict) else None
     if not url:
-        raise TamarindError("Upload did not return a signed URL.", detail=signed)
+        raise TamarindError("Upload did not return a presigned URL.", detail=signed)
     output.info(f"Uploading {path} → {remote}…", state.output)
+    # Content-Type must match what the presigned URL was signed with, or S3
+    # rejects the PUT with SignatureDoesNotMatch.
     with path.open("rb") as fh:
-        put = httpx.put(url, content=fh.read(), timeout=300.0)
+        put = httpx.put(url, content=fh.read(), headers={"Content-Type": content_type}, timeout=300.0)
     put.raise_for_status()
     output.emit(
         {"ok": True, "filename": remote, "bytes": path.stat().st_size},

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/src/tamarind/rest.py

@@ -103,9 +103,18 @@ def get_result(
     return client.post_json("result", json=body)
 
 
-def upload_file_url(client: HTTPClient, *, filename: str) -> dict:
-    """POST /uploadFile — returns {signedUrl, filename}; PUT the bytes to signedUrl."""
-    return client.post_json("uploadFile", json={"filename": filename})
+def upload_file_url(
+    client: HTTPClient, *, filename: str, content_type: str = "application/octet-stream"
+) -> dict:
+    """POST /getPresignedUploadUrl — returns {uploadUrl, headUrl, key, bucket}.
+
+    PUT the file bytes directly to ``uploadUrl`` with a matching ``Content-Type``
+    header (the presigned signature covers the content type). This uploads
+    straight to S3, bypassing the API's request-body size limit.
+    """
+    return client.post_json(
+        "getPresignedUploadUrl", json={"filename": filename, "contentType": content_type}
+    )
 
 
 def cancel_job(

{tamarind_cli-0.1.0 → tamarind_cli-0.1.2}/tests/test_cli_commands.py

@@ -82,11 +82,46 @@ def test_schema_unknown_tool_exits_nonzero():
 
 
 @respx.mock
-def test_upload_handles_non_dict_sentinel(tmp_path):
-    # Staging /uploadFile can return a bare -1; the command must fail cleanly, not crash.
-    f = tmp_path / "x.txt"
-    f.write_text("hi")
-    respx.post(f"{API}uploadFile").mock(return_value=httpx.Response(200, text="-1"))
+def test_upload_gets_presigned_url_then_puts_to_s3(tmp_path):
+    # `files upload` is a two-step presigned PUT: POST /getPresignedUploadUrl to
+    # get a PUT-able uploadUrl, then PUT the bytes straight to S3 (not multipart
+    # through the API). The Content-Type on the PUT must match what was signed.
+    import json
+
+    f = tmp_path / "target.pdb"
+    f.write_bytes(b"ATOM      1  N   MET A   1\n")
+    upload_url = "https://s3.amazonaws.com/alphafold-dbs-tamarind/user%40x.com/target.pdb"
+
+    post_route = respx.post(f"{API}getPresignedUploadUrl").mock(
+        return_value=httpx.Response(
+            200,
+            json={"uploadUrl": upload_url, "headUrl": "https://h", "key": "user@x.com/target.pdb", "bucket": "b"},
+        )
+    )
+    put_route = respx.put(upload_url).mock(return_value=httpx.Response(200))
+
+    res = runner.invoke(app, ["files", "upload", str(f)], env=ENV)
+
+    assert res.exit_code == 0, res.stdout
+    assert post_route.called and put_route.called
+    # POST carried the filename + contentType the URL is signed with
+    body = json.loads(post_route.calls.last.request.content)
+    assert body == {"filename": "target.pdb", "contentType": "application/octet-stream"}
+    # PUT streamed the exact bytes with the matching Content-Type
+    put_req = put_route.calls.last.request
+    assert put_req.content == b"ATOM      1  N   MET A   1\n"
+    assert put_req.headers["content-type"] == "application/octet-stream"
+
+
+@respx.mock
+def test_upload_surfaces_clean_error_on_non_dict_response(tmp_path):
+    # An auth/sentinel failure (e.g. bare -1) must not crash on .get — it should
+    # raise a clean TamarindError and never attempt the PUT.
+    f = tmp_path / "target.pdb"
+    f.write_bytes(b"x")
+    respx.post(f"{API}getPresignedUploadUrl").mock(return_value=httpx.Response(200, json=-1))
     res = runner.invoke(app, ["files", "upload", str(f)], env=ENV)
     assert res.exit_code != 0
-    assert not isinstance(res.exception, AttributeError)
+    # A clean, typed error (the isinstance(dict) guard worked) — NOT an
+    # AttributeError from calling .get on an int.
+    assert isinstance(res.exception, TamarindError)