deeporigin-sdk 5.0.0__tar.gz → 5.0.2__tar.gz

{deeporigin_sdk-5.0.0 → deeporigin_sdk-5.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deeporigin-sdk
-Version: 5.0.0
+Version: 5.0.2
 Summary: Deep Origin Platform SDK
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

{deeporigin_sdk-5.0.0 → deeporigin_sdk-5.0.2}/deeporigin_sdk.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deeporigin-sdk
-Version: 5.0.0
+Version: 5.0.2
 Summary: Deep Origin Platform SDK
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

deeporigin_sdk-5.0.2/src/VERSION

@@ -0,0 +1 @@
+5.0.2

{deeporigin_sdk-5.0.0 → deeporigin_sdk-5.0.2}/src/platform/files.py

@@ -22,6 +22,48 @@ _FILES_BASE = "/files"
 
 _MISSING_URL_FIELD = "Signed URL response missing 'url' field"
 
+# Signed-URL PUTs upload full file bodies; default httpx read timeout (5s) is too
+# short under concurrent upload_tree workers waiting on S3.
+_SIGNED_URL_UPLOAD_TIMEOUT = httpx.Timeout(
+    connect=10.0,
+    read=120.0,
+    write=300.0,
+    pool=10.0,
+)
+
+# Platform GET for presigned URLs can queue under many concurrent upload_tree workers.
+_SIGNED_URL_API_TIMEOUT = httpx.Timeout(
+    connect=10.0,
+    read=30.0,
+    write=10.0,
+    pool=10.0,
+)
+
+# Match httpx IteratorByteStream.CHUNK_SIZE for signed-URL PUT bodies.
+_SIGNED_URL_UPLOAD_CHUNK_SIZE = 65_536
+
+
+def _iter_local_file_chunks(
+    local_path: Path,
+    *,
+    chunk_size: int = _SIGNED_URL_UPLOAD_CHUNK_SIZE,
+) -> Iterator[bytes]:
+    """Yield fixed-size byte chunks from a local file for signed-URL PUTs.
+
+    Args:
+        local_path: Local file to read.
+        chunk_size: Maximum bytes per yielded chunk.
+
+    Yields:
+        Successive byte chunks until EOF.
+    """
+    with open(local_path, "rb") as file_obj:
+        while True:
+            chunk = file_obj.read(chunk_size)
+            if not chunk:
+                break
+            yield chunk
+
 
 class FileStream:
     """Streaming wrapper around an HTTP download response.
@@ -285,6 +327,7 @@ class Files:
         response = self._c.get_json(
             f"/files/{self._c.org_key}/signedUrl/{remote_path}",
             params=params,
+            timeout=_SIGNED_URL_API_TIMEOUT,
         )
 
         if "url" not in response:
@@ -297,17 +340,21 @@ class Files:
         local_path: Path,
         remote_path: str,
         *,
+        file_size: int | None = None,
         max_retries: int = 3,
         retry_backoff_factor: float = 1.0,
     ) -> str:
         """Upload a single file to a signed URL with retries.
 
-        Gets an upload signed URL for ``remote_path``, reads the file at
-        ``local_path``, and PUTs its contents directly to the signed URL.
+        On each attempt, requests a fresh upload signed URL for ``remote_path``,
+        streams the file at ``local_path`` in fixed-size chunks via HTTP PUT to
+        that URL, and retries on transient failures.
 
         Args:
             local_path: Local file to upload.
             remote_path: Remote path to request the signed URL for.
+            file_size: Optional precomputed ``st_size`` to avoid a duplicate stat
+                when ``upload_tree`` has already measured the file for sorting.
             max_retries: Maximum retry attempts on transient failures.
             retry_backoff_factor: Multiplier for exponential back-off between
                 retries.  Delay = retry_backoff_factor * 2^attempt.
@@ -318,18 +365,21 @@ class Files:
         Raises:
             httpx.HTTPStatusError: If the PUT fails after all retries.
         """
-        signed_url = self.signed_url(remote_path, upload=True)
-
-        file_content = local_path.read_bytes()
-
         last_exc: Exception | None = None
         for attempt in range(max_retries + 1):
             try:
-                with httpx.Client() as upload_client:
+                signed_url = self.signed_url(remote_path, upload=True)
+                headers = {"Content-Type": "application/octet-stream"}
+                if file_size is None:
+                    file_size = self._local_file_size(local_path)
+                if file_size > 0:
+                    headers["Content-Length"] = str(file_size)
+
+                with httpx.Client(timeout=_SIGNED_URL_UPLOAD_TIMEOUT) as upload_client:
                     resp = upload_client.put(
                         signed_url,
-                        content=file_content,
-                        headers={"Content-Type": "application/octet-stream"},
+                        content=_iter_local_file_chunks(local_path),
+                        headers=headers,
                     )
                     resp.raise_for_status()
                 return remote_path
@@ -344,6 +394,26 @@ class Files:
 
         raise last_exc  # type: ignore[misc]
 
+    @staticmethod
+    def _local_file_size(local_path: Path) -> int:
+        """Return ``st_size`` for a local file, or ``0`` when stat fails."""
+        try:
+            return local_path.stat().st_size
+        except OSError:
+            return 0
+
+    @staticmethod
+    def _sort_upload_pairs_by_size_desc(
+        upload_pairs: list[tuple[Path, str]],
+    ) -> list[tuple[Path, str, int]]:
+        """Return upload pairs with cached sizes, largest first."""
+        sized_pairs = [
+            (path, suffix, Files._local_file_size(path))
+            for path, suffix in upload_pairs
+        ]
+        sized_pairs.sort(key=lambda pair: pair[2], reverse=True)
+        return sized_pairs
+
     @staticmethod
     def _resolve_upload_pairs(
         local_path: str | Path | list[str | Path],
@@ -420,6 +490,7 @@ class Files:
             remote_dir += "/"
 
         upload_pairs = self._resolve_upload_pairs(local_path)
+        upload_pairs = self._sort_upload_pairs_by_size_desc(upload_pairs)
 
         results: list[str] = []
         errors: list[tuple[str, Exception]] = []
@@ -430,10 +501,11 @@ class Files:
                     self._put_to_signed_url,
                     fp,
                     f"{remote_dir}{suffix}",
+                    file_size=file_size,
                     max_retries=max_retries,
                     retry_backoff_factor=retry_backoff_factor,
                 ): fp
-                for fp, suffix in upload_pairs
+                for fp, suffix, file_size in upload_pairs
             }
 
             for future in tqdm(

{deeporigin_sdk-5.0.0 → deeporigin_sdk-5.0.2}/src/utils/constants.py

@@ -90,3 +90,10 @@ MOLPROPS_PROPERTY_KEYS: frozenset[str] = frozenset(
 
 MOLPROPS_DEFAULT_PROPERTIES: frozenset[str] = MOLPROPS_PROPERTY_KEYS
 """Default full ADMET bundle for :class:`~deeporigin.drug_discovery.molprops.Molprops`."""
+
+JOB_WATCH_BLOCK_ENV = "JOB_WATCH_BLOCK"
+"""Env var for blocking :meth:`~deeporigin.drug_discovery.notebook_watch_mixin.NotebookWatchMixin.watch`.
+
+When set to a truthy value (``1``, ``true``, ``yes``, ``on``), ``watch()`` blocks the
+notebook cell until the execution reaches a terminal state. Used by doc notebook CI
+(``scripts/build_docs.sh``) and ``nbconvert --execute``."""

deeporigin_sdk-5.0.0/src/VERSION

@@ -1 +0,0 @@
-5.0.0