openprotein-python 0.2.3__tar.gz → 0.2.7__tar.gz

{openprotein_python-0.2.3 → openprotein_python-0.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: openprotein-python
-Version: 0.2.3
+Version: 0.2.7
 Summary: OpenProtein Python interface.
 Home-page: https://docs.openprotein.ai/
 License: MIT
@@ -14,6 +14,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3
 Requires-Dist: pandas (>=1)
 Requires-Dist: pydantic (>=1)
 Requires-Dist: requests (>=2)

{openprotein_python-0.2.3 → openprotein_python-0.2.7}/openprotein/api/embedding.py

@@ -1,6 +1,7 @@
 from openprotein.base import APISession
 from openprotein.api.jobs import (
     Job,
+    AsyncJobFuture,
     MappedAsyncJobFuture,
     PagedAsyncJobFuture,
     job_get,
@@ -504,7 +505,7 @@ class ProtembedModel:
         return SVDModel(self.session, metadata)
 
 
-class SVDModel:
+class SVDModel(AsyncJobFuture):
     """
     Class providing embedding endpoint for SVD models. \
         Also allows retrieving embeddings of sequences used to fit the SVD with `get`.
@@ -513,6 +514,7 @@ class SVDModel:
     def __init__(self, session: APISession, metadata: SVDMetadata):
         self.session = session
         self._metadata = metadata
+        self._job = None
 
     def __str__(self) -> str:
         return str(self.metadata)
@@ -563,6 +565,20 @@ class SVDModel:
     def get_job(self) -> Job:
         """Get job associated with this SVD model"""
         return job_get(self.session, self.id)
+    
+    def get(self):
+        # overload for AsyncJobFuture
+        return self
+    
+    @property
+    def job(self) -> Job:
+        if self._job is None:
+            self._job = self.get_job()
+        return self._job
+
+    @job.setter
+    def job(self, j):
+        self._job = j
 
     def get_inputs(self) -> List[bytes]:
         """

{openprotein_python-0.2.3 → openprotein_python-0.2.7}/openprotein/base.py

@@ -7,7 +7,7 @@ from typing import Union
 from requests.adapters import HTTPAdapter
 from requests.packages.urllib3.util.retry import Retry
 
-from openprotein.errors import APIError, InvalidParameterError, MissingParameterError, AuthError
+from openprotein.errors import HTTPError, APIError, AuthError
 
 class BearerAuth(requests.auth.AuthBase):
     """
@@ -37,13 +37,16 @@ class APISession(requests.Session):
     --------
     >>> session = APISession("username", "password")
     """
+    
 
     def __init__(self, username:str,
                  password:str,
-                 backend:str = "https://api.openprotein.ai/api/" ):
+                 backend:str = "https://api.openprotein.ai/api/",
+                 timeout:int = 180):
         super().__init__()
         self.backend = backend
         self.verify = True
+        self.timeout = timeout
 
         # Custom retry strategies
         #auto retry for pesky connection reset errors and others
@@ -55,6 +58,28 @@ class APISession(requests.Session):
         self.mount('https://', adapter)
         self.login(username, password)
 
+
+    def post(self, url, data=None, json=None, **kwargs):
+        r"""Sends a POST request. Returns :class:`Response` object.
+
+        :param url: URL for the new :class:`Request` object.
+        :param data: (optional) Dictionary, list of tuples, bytes, or file-like
+            object to send in the body of the :class:`Request`.
+        :param json: (optional) json to send in the body of the :class:`Request`.
+        :param \*\*kwargs: Optional arguments that ``request`` takes.
+        :rtype: requests.Response
+        """
+        timeout = self.timeout
+        if 'timeout' in kwargs:
+            timeout = kwargs.pop('timeout')
+  
+        return self.request("POST",
+                            url,
+                            data=data,
+                            json=json,
+                            timeout=timeout,
+                            **kwargs)
+    
     def login(self, username:str, password:str):
         """ 
         Authenticate connection to OpenProtein with your credentials.
@@ -71,28 +96,28 @@ class APISession(requests.Session):
     def _get_auth_token(self, username:str, password:str):
         endpoint = "v1/login/user-access-token"
         url = urljoin(self.backend, endpoint)
-        response = self.post(
-            url, params={"username": username, "password": password}, timeout=3
-        )
-        if response.status_code == 200:
-            result = response.json()
-            token = result["access_token"]
-            return BearerAuth(token)
-        else:
-            raise AuthError(
-                f"Unable to authenticate with given credentials: {response.status_code} : {response.text}"
+        try:
+            response = self.post(
+                url, params={"username": username, "password": password}, timeout=3
             )
+        except HTTPError as e:
+            # if an error occured during auth, we raise an AuthError with reference to the HTTPError
+            raise AuthError(
+                f"Authentication failed. Please check your credentials and connection."
+            ) from e
+
+        result = response.json()
+        token = result["access_token"]
+        return BearerAuth(token)    
 
     def request(
         self, method: Union[str, bytes], url: Union[str, bytes], *args, **kwargs
     ):
         full_url = urljoin(self.backend, url)
         response = super().request(method, full_url, *args, **kwargs)
-        # allow 400 to pass to get caught by autherror
-        if response.status_code not in [200, 201, 202, 400]:
-            raise APIError(
-                f"Request failed: \n\t status: {response.status_code} \n\t message: {response.text} "
-            )
+        if not response.ok:
+            # raise custom exception that prints better error message than requests.HTTPError
+            raise HTTPError(response)
         return response
 
 

{openprotein_python-0.2.3 → openprotein_python-0.2.7}/openprotein/errors.py

@@ -17,6 +17,15 @@ class APIError(Exception):
         self.message = message
         super().__init__(self.message)
 
+class HTTPError(APIError):
+    def __init__(self, response):
+        self.response = response
+        self.status_code = response.status_code
+        self.text = response.text
+        self.url = response.url
+        message = f"Status code {self.status_code}\non resource: {self.url}\n{self.text}"
+        super().__init__(message)
+
 class AuthError(Exception):
     """InvalidParameterError"""
     def __init__(self, message="Invalid authorization"):

{openprotein_python-0.2.3 → openprotein_python-0.2.7}/openprotein/models.py

@@ -69,7 +69,7 @@ class DesignMetadata(NewModel):
     y_var: Optional[float] = None
 
 class DesignSubscore(NewModel):
-    score: int
+    score: float
     metadata: DesignMetadata
 
 class DesignStep(NewModel):
@@ -78,7 +78,7 @@ class DesignStep(NewModel):
     sequence: str
     # scores: List[int]
     # subscores_metadata: List[List[DesignSubscore]]
-    initial_scores: List[int] = Field(
+    initial_scores: List[float] = Field(
         ..., alias="scores"
     )  # renaming 'scores' to 'initial_scores'  # noqa: E501
     scores: List[List[DesignSubscore]] = Field(

{openprotein_python-0.2.3 → openprotein_python-0.2.7}/pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "openprotein_python"
 packages = [{include = "openprotein"}]
-version = "0.2.3"
+version = "0.2.7"
 description = "OpenProtein Python interface."
 license = "MIT"
 readme = "README.md"