openprotein-python 0.1.1b8__tar.gz → 0.1.1b10__tar.gz

{openprotein_python-0.1.1b8 → openprotein_python-0.1.1b10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: openprotein-python
-Version: 0.1.1b8
+Version: 0.1.1b10
 Summary: OpenProtein Python interface.
 Home-page: https://docs.openprotein.ai/
 License: MIT
@@ -22,6 +22,9 @@ Requires-Dist: requests (>=2)
 Requires-Dist: tqdm (>=4)
 Description-Content-Type: text/markdown
 
+[![PyPI version](https://badge.fury.io/py/openprotein-python.svg)](https://pypi.org/project/openprotein-python/)
+[![Coverage](./apidocs/source/coverage.svg)](https://pypi.org/project/openprotein-python/)
+
 # openprotein-python
 Python interface for the OpenProtein.AI REST API.
 
@@ -36,7 +39,7 @@ pip install openprotein_python
 
 First, create a session using your login credentials.
 ```
-import openprotein
+import openprotein_python
 session = openprotein.connect(USERNAME, PASSWORD)
 ```
 

{openprotein_python-0.1.1b8 → openprotein_python-0.1.1b10}/README.md

@@ -1,3 +1,6 @@
+[![PyPI version](https://badge.fury.io/py/openprotein-python.svg)](https://pypi.org/project/openprotein-python/)
+[![Coverage](./apidocs/source/coverage.svg)](https://pypi.org/project/openprotein-python/)
+
 # openprotein-python
 Python interface for the OpenProtein.AI REST API.
 
@@ -12,7 +15,7 @@ pip install openprotein_python
 
 First, create a session using your login credentials.
 ```
-import openprotein
+import openprotein_python
 session = openprotein.connect(USERNAME, PASSWORD)
 ```
 

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/__init__.py

@@ -1,13 +1,13 @@
-from openprotein_python._version import __version__
+from openprotein._version import __version__
 
-from openprotein_python.base import APISession
-from openprotein_python.api.jobs import JobsAPI, Job
-from openprotein_python.api.data import DataAPI
-from openprotein_python.api.poet import PoetAPI
-from openprotein_python.api.embedding import EmbeddingAPI
-from openprotein_python.api.train import TrainingAPI
-from openprotein_python.api.design import DesignAPI
-from openprotein_python.api.predict import PredictAPI
+from openprotein.base import APISession
+from openprotein.api.jobs import JobsAPI, Job
+from openprotein.api.data import DataAPI
+from openprotein.api.poet import PoetAPI
+from openprotein.api.embedding import EmbeddingAPI
+from openprotein.api.train import TrainingAPI
+from openprotein.api.design import DesignAPI
+from openprotein.api.predict import PredictAPI
 class OpenProtein(APISession):
     """
     The base class for accessing OpenProtein API functionality.

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/_version.py

@@ -1,2 +1,2 @@
-__version_tuple__ = version_tuple = (0, 1, 1, 'b8')
+__version_tuple__ = version_tuple = (0, 1, 1, 'b10')
 __version__ = version = '.'.join(str(x) for x in __version_tuple__)

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/data.py

@@ -3,10 +3,10 @@ import pydantic
 from typing import Optional, List
 from io import BytesIO
 
-from openprotein_python.models import AssayMetadata, AssayDataPage
-from openprotein_python.errors import APIError
-from openprotein_python.base import APISession
-import openprotein_python.config as config
+from openprotein.models import AssayMetadata, AssayDataPage
+from openprotein.errors import APIError
+from openprotein.base import APISession
+import openprotein.config as config
 
 
 def list_models(session: APISession, assay_id: str) -> List:

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/design.py

@@ -1,12 +1,12 @@
 from typing import Optional
 import pydantic
 
-from openprotein_python.base import APISession
-from openprotein_python.api.jobs import AsyncJobFuture, Job
-import openprotein_python.config as config
-from openprotein_python.api.jobs import load_job
-from openprotein_python.models import DesignJobCreate, JobType, DesignResults
-from openprotein_python.errors import (
+from openprotein.base import APISession
+from openprotein.api.jobs import AsyncJobFuture, Job
+import openprotein.config as config
+from openprotein.api.jobs import load_job
+from openprotein.models import DesignJobCreate, JobType, DesignResults
+from openprotein.errors import (
     APIError,
     InvalidJob,
 )

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/embedding.py

@@ -1,15 +1,15 @@
-from openprotein_python.base import APISession
-from openprotein_python.api.jobs import (
+from openprotein.base import APISession
+from openprotein.api.jobs import (
     Job,
     MappedAsyncJobFuture,
     PagedAsyncJobFuture,
     job_get,
     JobStatus,
 )
-from openprotein_python.errors import InvalidJob
-import openprotein_python.config as config
-from openprotein_python.api.jobs import load_job
-from openprotein_python.models import (
+from openprotein.errors import InvalidJob
+import openprotein.config as config
+from openprotein.api.jobs import load_job
+from openprotein.models import (
     ModelDescription,
     TokenInfo,
     ModelMetadata,

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/jobs.py

@@ -9,13 +9,19 @@ from enum import Enum
 
 import tqdm
 import pydantic
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
-from openprotein_python.errors import TimeoutException
-from openprotein_python.base import APISession
-import openprotein_python.config as config
+from openprotein.errors import TimeoutException
+from openprotein.base import APISession
+import openprotein.config as config
 
 
+
+class NewModel(BaseModel):
+    model_config = ConfigDict(
+        protected_namespaces=()
+    )
+
 class JobStatus(str, Enum):
     PENDING: str = "PENDING"
     RUNNING: str = "RUNNING"
@@ -34,7 +40,7 @@ class JobStatus(str, Enum):
 
 
 
-class Job(BaseModel):
+class Job(NewModel):
     status: JobStatus
     job_id: str
     job_type: str

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/poet.py

@@ -5,18 +5,18 @@ import csv
 import codecs
 import requests
 
-from openprotein_python.base import APISession
-from openprotein_python.api.jobs import (
+from openprotein.base import APISession
+from openprotein.api.jobs import (
     Job,
     AsyncJobFuture,
     StreamingAsyncJobFuture,
     job_get,
     job_args_get,
 )
-from openprotein_python.api.jobs import load_job #as base_load_job
-import openprotein_python.config as config
+from openprotein.api.jobs import load_job #as base_load_job
+import openprotein.config as config
 
-from openprotein_python.models import (
+from openprotein.models import (
     MSASamplingMethod,
     PoetInputType,
     PoetScoreJob,
@@ -27,7 +27,7 @@ from openprotein_python.models import (
     PoetSSPJob,
     PoetSSPResult,
 )
-from openprotein_python.errors import (
+from openprotein.errors import (
     InvalidParameterError,
     MissingParameterError,
     APIError,

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/predict.py

@@ -1,18 +1,18 @@
 from typing import Optional, List, Union
 import pydantic
 
-from openprotein_python.base import APISession
-from openprotein_python.api.jobs import AsyncJobFuture, Job
-from openprotein_python.models import (
+from openprotein.base import APISession
+from openprotein.api.jobs import AsyncJobFuture, Job
+from openprotein.models import (
     SequenceDataset,
     SequenceData,
     PredictJob,
     PredictSingleSiteJob,
     JobType,
 )
-from openprotein_python.errors import InvalidParameterError, APIError, InvalidJob
-from openprotein_python.api.train import TrainFuture
-from openprotein_python.api.jobs import load_job
+from openprotein.errors import InvalidParameterError, APIError, InvalidJob
+from openprotein.api.train import TrainFuture
+from openprotein.api.jobs import load_job
 
 
 def _create_predict_job(

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/api/train.py

@@ -1,11 +1,11 @@
 from typing import Optional, List, Union
 import pydantic
-from openprotein_python.base import APISession
-from openprotein_python.api.jobs import AsyncJobFuture, Job
+from openprotein.base import APISession
+from openprotein.api.jobs import AsyncJobFuture, Job
 
-from openprotein_python.models import TrainGraph, JobType, Jobplus, CVResults
-from openprotein_python.errors import InvalidParameterError, APIError, InvalidJob
-from openprotein_python.api.data import AssayDataset, AssayMetadata
+from openprotein.models import TrainGraph, JobType, Jobplus, CVResults
+from openprotein.errors import InvalidParameterError, APIError, InvalidJob
+from openprotein.api.data import AssayDataset, AssayMetadata
 
 
 def list_models(session: APISession, job_id: str) -> List:

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/base.py

@@ -1,4 +1,4 @@
-import openprotein_python.config as config
+import openprotein.config as config
 
 import requests
 from urllib.parse import urljoin
@@ -7,7 +7,7 @@ from typing import Union
 from requests.adapters import HTTPAdapter
 from requests.packages.urllib3.util.retry import Retry
 
-from openprotein_python.errors import APIError, InvalidParameterError, MissingParameterError, AuthError
+from openprotein.errors import APIError, InvalidParameterError, MissingParameterError, AuthError
 
 class BearerAuth(requests.auth.AuthBase):
     """

{openprotein_python-0.1.1b8/openprotein_python → openprotein_python-0.1.1b10/openprotein}/models.py

@@ -3,21 +3,21 @@ from typing import Optional, List, Union, Dict, Literal
 from datetime import datetime
 from enum import Enum
 import numpy as np
-from pydantic import BaseModel, Field, validator
-from openprotein_python.api.jobs import Job, JobStatus
+from pydantic import BaseModel, Field, validator, ConfigDict
+from openprotein.api.jobs import Job, JobStatus, NewModel
 
-class ModelDescription(BaseModel):
+class ModelDescription(NewModel):
     citation_title: Optional[str] = None
     doi: Optional[str] = None
     summary: str
 
-class TokenInfo(BaseModel):
+class TokenInfo(NewModel):
     id: int
     token: str
     primary: bool
     description: str
 
-class ModelMetadata(BaseModel):
+class ModelMetadata(NewModel):
     model_id: str
     description: ModelDescription
     max_sequence_length: Optional[int] = None
@@ -27,7 +27,7 @@ class ModelMetadata(BaseModel):
     output_tokens: List[str]
     token_descriptions: List[List[TokenInfo]]
 
-class EmbeddedSequence(BaseModel):
+class EmbeddedSequence(NewModel):
     class Config:
         arbitrary_types_allowed = True
 
@@ -52,7 +52,7 @@ class SVDJob(Job):
     pass
 
 
-class SVDMetadata(BaseModel):
+class SVDMetadata(NewModel):
     id: str
     status: JobStatus
     created_date: Optional[datetime] = None
@@ -64,15 +64,15 @@ class SVDMetadata(BaseModel):
     def is_done(self):
         return self.status.done()
     
-class DesignMetadata(BaseModel):
+class DesignMetadata(NewModel):
     y_mu: Optional[float] = None
     y_var: Optional[float] = None
 
-class DesignSubscore(BaseModel):
+class DesignSubscore(NewModel):
     score: int
     metadata: DesignMetadata
 
-class DesignStep(BaseModel):
+class DesignStep(NewModel):
     step: int
     sample_index: int
     sequence: str
@@ -88,7 +88,7 @@ class DesignStep(BaseModel):
     umap2: float
 
 
-class DesignResults(BaseModel):
+class DesignResults(NewModel):
     status: str
     job_id: str
     created_date: str
@@ -106,20 +106,20 @@ class DirectionEnum(str, Enum):
     eq = "="
 
 
-class Criterion(BaseModel):
+class Criterion(NewModel):
     target: float
     weight: float
     direction: str
 
 
-class ModelCriterion(BaseModel):
+class ModelCriterion(NewModel):
     criterion_type: Literal["model"]
     model_id: str
     measurement_name: str
     criterion: Criterion
 
 
-class NMutationCriterion(BaseModel):
+class NMutationCriterion(NewModel):
     criterion_type: Literal["n_mutations"]
     # sequences: Optional[List[str]]
 
@@ -127,7 +127,7 @@ class NMutationCriterion(BaseModel):
 CriterionItem = Union[ModelCriterion, NMutationCriterion]
 
 
-class DesignJobCreate(BaseModel):
+class DesignJobCreate(NewModel):
     assay_id: str
     criteria: List[List[CriterionItem]]
     num_steps: Optional[int] = 8
@@ -173,34 +173,34 @@ class Jobplus(Job):
     sequence_length: Optional[int] = None
 
 
-class TrainStep(BaseModel):
+class TrainStep(NewModel):
     step: int
     loss: float
     tag: str
     tags: dict
 
 
-class TrainGraph(BaseModel):
+class TrainGraph(NewModel):
     traingraph: List[TrainStep]
     created_date: datetime
     job_id: str
 
 
-class SequenceData(BaseModel):
+class SequenceData(NewModel):
     sequence: str
 
 
-class SequenceDataset(BaseModel):
+class SequenceDataset(NewModel):
     sequences: List[str]
 
 
-class JobDetails(BaseModel):
+class JobDetails(NewModel):
     job_id: str
     job_type: str
     status: str
 
 
-class AssayMetadata(BaseModel):
+class AssayMetadata(NewModel):
     assay_name: str
     assay_description: str
     assay_id: str
@@ -212,12 +212,12 @@ class AssayMetadata(BaseModel):
     sequence_length: Optional[int] = None
 
 
-class AssayDataRow(BaseModel):
+class AssayDataRow(NewModel):
     mut_sequence: str
     measurement_values: List[Union[float, None]]
 
 
-class AssayDataPage(BaseModel):
+class AssayDataPage(NewModel):
     assaymetadata: AssayMetadata
     page_size: int
     page_offset: int
@@ -243,7 +243,7 @@ class MSASamplingMethod(str, Enum):
 
 
 
-class PromptPostParams(BaseModel):
+class PromptPostParams(NewModel):
     msa_id: str
     num_sequences: Optional[int] = Field(None, ge=0, lt=100)
     num_residues: Optional[int] = Field(None, ge=0, lt=24577)
@@ -255,7 +255,7 @@ class PromptPostParams(BaseModel):
     num_ensemble_prompts: int = 1
     random_seed: Optional[int] = None
 
-#class PoetSiteResult(BaseModel):
+#class PoetSiteResult(NewModel):
 #    # obsolete
 #    sequence: bytes
 #    score: List[float]
@@ -277,7 +277,7 @@ class PoetInputType(str, Enum):
     PROMPT = "PROMPT"
 
 
-class PoetScoreResult(BaseModel):
+class PoetScoreResult(NewModel):
     sequence: bytes
     score: List[float]
     name: Optional[str] = None
@@ -291,7 +291,7 @@ class PoetScoreJob(Job):
     result: Optional[List[PoetScoreResult]] = None
     n_completed: Optional[int] = None
 
-class PoetSSPResult(BaseModel):
+class PoetSSPResult(NewModel):
     sequence: bytes
     score: List[float]
     name: Optional[str] = None
@@ -312,7 +312,7 @@ class PoetSSPJob(PoetScoreJob):
     result: Optional[List[PoetSSPResult]] = None
     n_completed: Optional[int] = None
 
-class Prediction(BaseModel):
+class Prediction(NewModel):
     """Prediction details."""
 
     model_id: str
@@ -320,7 +320,7 @@ class Prediction(BaseModel):
     properties: Dict[str, Dict[str, float]]
 
 
-class PredictJobBase(BaseModel):
+class PredictJobBase(NewModel):
     """Shared properties for predict job outputs."""
 
     # might be none if just fetching
@@ -329,7 +329,7 @@ class PredictJobBase(BaseModel):
     status: str
 
 
-class DesignJob(BaseModel):
+class DesignJob(NewModel):
     job_id: Optional[str] = None
     job_type: str
     status: str
@@ -338,7 +338,7 @@ class DesignJob(BaseModel):
 class PredictJob(PredictJobBase):
     """Properties about predict job returned via API."""
 
-    class SequencePrediction(BaseModel):
+    class SequencePrediction(NewModel):
         """Sequence prediction."""
 
         sequence: str
@@ -350,7 +350,7 @@ class PredictJob(PredictJobBase):
 class PredictSingleSiteJob(PredictJobBase):
     """Properties about single-site prediction job returned via API."""
 
-    class SequencePrediction(BaseModel):
+    class SequencePrediction(NewModel):
         """Sequence prediction."""
 
         position: int
@@ -361,7 +361,7 @@ class PredictSingleSiteJob(PredictJobBase):
     result: Optional[List[SequencePrediction]] = None
 
 
-class CVItem(BaseModel):
+class CVItem(NewModel):
     row_index: int
     sequence: str
     measurement_name: str

{openprotein_python-0.1.1b8 → openprotein_python-0.1.1b10}/pyproject.toml

@@ -1,6 +1,7 @@
 [tool.poetry]
 name = "openprotein_python"
-version = "0.1.1b8"
+packages = [{include = "openprotein"}]
+version = "0.1.1b10"
 description = "OpenProtein Python interface."
 license = "MIT"
 readme = "README.md"