updated name

mbarber · mbarber · commit 6d9af12582e5 · 2023-08-04T03:31:13.000Z
diff --git a/openprotein_python/__init__.py b/openprotein_python/__init__.py
@@ -1,13 +1,13 @@
-from openprotein._version import __version__
+from openprotein_python._version import __version__
 
-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
+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
 class OpenProtein(APISession):
     """
     The base class for accessing OpenProtein API functionality.
diff --git a/openprotein_python/_version.py b/openprotein_python/_version.py
@@ -1,2 +1,2 @@
-__version_tuple__ = version_tuple = (0, 1, 1, 'b3')
+__version_tuple__ = version_tuple = (0, 1, 1, 'b5')
 __version__ = version = '.'.join(str(x) for x in __version_tuple__)
diff --git a/openprotein_python/api/__init__.py b/openprotein_python/api/__init__.py
diff --git a/openprotein_python/api/data.py b/openprotein_python/api/data.py
@@ -3,10 +3,10 @@
 from typing import Optional, List
 from io import BytesIO
 
-from openprotein.models import AssayMetadata, AssayDataPage
-from openprotein.errors import APIError
-from openprotein.base import APISession
-import openprotein.config as config
+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
 
 
 def list_models(session: APISession, assay_id: str) -> List:
diff --git a/openprotein_python/api/design.py b/openprotein_python/api/design.py
@@ -1,12 +1,12 @@
 from typing import Optional
 import pydantic
 
-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 (
+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 (
     APIError,
     InvalidJob,
 )
diff --git a/openprotein_python/api/embedding.py b/openprotein_python/api/embedding.py
@@ -1,15 +1,15 @@
-from openprotein.base import APISession
-from openprotein.api.jobs import (
+from openprotein_python.base import APISession
+from openprotein_python.api.jobs import (
     Job,
     MappedAsyncJobFuture,
     PagedAsyncJobFuture,
     job_get,
     JobStatus,
 )
-from openprotein.errors import InvalidJob
-import openprotein.config as config
-from openprotein.api.jobs import load_job
-from openprotein.models import (
+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 (
     ModelDescription,
     TokenInfo,
     ModelMetadata,
diff --git a/openprotein_python/api/jobs.py b/openprotein_python/api/jobs.py
@@ -11,9 +11,9 @@
 import pydantic
 from pydantic import BaseModel
 
-from openprotein.errors import TimeoutException
-from openprotein.base import APISession
-import openprotein.config as config
+from openprotein_python.errors import TimeoutException
+from openprotein_python.base import APISession
+import openprotein_python.config as config
 
 
 class JobStatus(str, Enum):
diff --git a/openprotein_python/api/poet.py b/openprotein_python/api/poet.py
@@ -5,18 +5,18 @@
 import codecs
 import requests
 
-from openprotein.base import APISession
-from openprotein.api.jobs import (
+from openprotein_python.base import APISession
+from openprotein_python.api.jobs import (
     Job,
     AsyncJobFuture,
     StreamingAsyncJobFuture,
     job_get,
     job_args_get,
 )
-from openprotein.api.jobs import load_job #as base_load_job
-import openprotein.config as config
+from openprotein_python.api.jobs import load_job #as base_load_job
+import openprotein_python.config as config
 
-from openprotein.models import (
+from openprotein_python.models import (
     MSASamplingMethod,
     PoetInputType,
     PoetScoreJob,
@@ -27,7 +27,7 @@
     PoetSSPJob,
     PoetSSPResult,
 )
-from openprotein.errors import (
+from openprotein_python.errors import (
     InvalidParameterError,
     MissingParameterError,
     APIError,
diff --git a/openprotein_python/api/predict.py b/openprotein_python/api/predict.py
@@ -1,18 +1,18 @@
 from typing import Optional, List, Union
 import pydantic
 
-from openprotein.base import APISession
-from openprotein.api.jobs import AsyncJobFuture, Job
-from openprotein.models import (
+from openprotein_python.base import APISession
+from openprotein_python.api.jobs import AsyncJobFuture, Job
+from openprotein_python.models import (
     SequenceDataset,
     SequenceData,
     PredictJob,
     PredictSingleSiteJob,
     JobType,
 )
-from openprotein.errors import InvalidParameterError, APIError, InvalidJob
-from openprotein.api.train import TrainFuture
-from openprotein.api.jobs import load_job
+from openprotein_python.errors import InvalidParameterError, APIError, InvalidJob
+from openprotein_python.api.train import TrainFuture
+from openprotein_python.api.jobs import load_job
 
 
 def _create_predict_job(
diff --git a/openprotein_python/api/train.py b/openprotein_python/api/train.py
@@ -1,11 +1,11 @@
 from typing import Optional, List, Union
 import pydantic
-from openprotein.base import APISession
-from openprotein.api.jobs import AsyncJobFuture, Job
+from openprotein_python.base import APISession
+from openprotein_python.api.jobs import AsyncJobFuture, Job
 
-from openprotein.models import TrainGraph, JobType, Jobplus, CVResults
-from openprotein.errors import InvalidParameterError, APIError, InvalidJob
-from openprotein.api.data import AssayDataset, AssayMetadata
+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
 
 
 def list_models(session: APISession, job_id: str) -> List:
diff --git a/openprotein_python/base.py b/openprotein_python/base.py
@@ -1,4 +1,4 @@
-import openprotein.config as config
+import openprotein_python.config as config
 
 import requests
 from urllib.parse import urljoin
@@ -7,7 +7,7 @@
 from requests.adapters import HTTPAdapter
 from requests.packages.urllib3.util.retry import Retry
 
-from openprotein.errors import APIError, InvalidParameterError, MissingParameterError, AuthError
+from openprotein_python.errors import APIError, InvalidParameterError, MissingParameterError, AuthError
 
 class BearerAuth(requests.auth.AuthBase):
     """
@@ -40,7 +40,7 @@ class APISession(requests.Session):
 
     def __init__(self, username:str,
                  password:str,
-                 backend:str = "https://dev.api.openprotein.ai/api/" ):
+                 backend:str = "https://api.openprotein.ai/api/" ):
         super().__init__()
         self.backend = backend
         self.verify = True
diff --git a/openprotein_python/config.py b/openprotein_python/config.py
diff --git a/openprotein_python/errors.py b/openprotein_python/errors.py
diff --git a/openprotein_python/fasta.py b/openprotein_python/fasta.py
diff --git a/openprotein_python/models.py b/openprotein_python/models.py
@@ -4,7 +4,7 @@
 from enum import Enum
 import numpy as np
 from pydantic import BaseModel, Field, validator
-from openprotein.api.jobs import Job, JobStatus
+from openprotein_python.api.jobs import Job, JobStatus
 
 class ModelDescription(BaseModel):
     citation_title: Optional[str] = None
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,26 +1,25 @@
 [tool.poetry]
-name = "openprotein-python"
-version = "0.1.1b4"
+name = "openprotein_python"
+version = "0.1.1b5"
 description = "OpenProtein Python interface."
+license = "MIT"
+readme = "README.md"
+homepage = "https://docs.openprotein.ai/"
 authors = ["OpenProtein <info@ne47.bio>"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+]
 
 [tool.poetry.dependencies]
 python = "^3.7"
-requests = "*"
-pydantic = "*"
-tqdm = "*"
-pandas = "*"
+requests = "^2.25"
+pydantic = "^1.8"
+tqdm = "^4.61"
+pandas = "^1.2"
 
 [tool.poetry.dev-dependencies]
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
-
-[[tool.poetry.source]]
-name = "testpypi"
-url = "https://test.pypi.org/simple"
-
-
-[project.urls]
-Homepage = "https://docs.openprotein.ai/"
diff --git a/tests/api/test_assay.py b/tests/api/test_assay.py
@@ -1,8 +1,8 @@
 import pytest
 from unittest.mock import MagicMock
-from openprotein.base import APISession
+from openprotein_python.base import APISession
 from datetime import datetime
-from openprotein.api.data import *
+from openprotein_python.api.data import *
 import io
 import pandas as pd
 from urllib.parse import urljoin
@@ -12,7 +12,7 @@
 import pydantic
 from unittest.mock import ANY
 import json
-from openprotein.base import BearerAuth
+from openprotein_python.base import BearerAuth
 
 
 class APISessionMock(APISession):
diff --git a/tests/api/test_base.py b/tests/api/test_base.py
@@ -1,6 +1,6 @@
 import pytest
 from unittest.mock import MagicMock, patch
-from openprotein.base import AuthError, APISession
+from openprotein_python.base import AuthError, APISession
 import io
 import requests
 import json
@@ -54,7 +54,7 @@ def test_APISession_authenticate_failed(response_mock_unauthenticated):
 
         assert "Unable to authenticate with given credentials" in str(exc.value) 
         APISession.post.assert_called_once_with(
-            'https://dev.api.openprotein.ai/api/v1/login/user-access-token',
+            'https://api.openprotein.ai/api/v1/login/user-access-token',
             params={'username': username, 'password': password}, timeout=3
         )
 
@@ -68,6 +68,6 @@ def test_APISession_authenticate_successful(response_mock_authenticated):
 
         assert session.auth.token == token
         session.post.assert_called_once_with(
-            'https://dev.api.openprotein.ai/api/v1/login/user-access-token',
+            'https://api.openprotein.ai/api/v1/login/user-access-token',
             params={'username': username, 'password': password}, timeout=3
         )
diff --git a/tests/api/test_embeddings.py b/tests/api/test_embeddings.py
@@ -1,10 +1,10 @@
 import pytest
 from unittest.mock import MagicMock
-from openprotein.base import APISession
+from openprotein_python.base import APISession
 import io
 from urllib.parse import urljoin
-from openprotein.base import BearerAuth
-from openprotein.api.embedding import *
+from openprotein_python.base import BearerAuth
+from openprotein_python.api.embedding import *
 
 class ResponseMock:
     def __init__(self):
diff --git a/tests/api/test_poet.py b/tests/api/test_poet.py
@@ -1,16 +1,16 @@
 import pytest
 from unittest.mock import MagicMock
-from openprotein.base import APISession
+from openprotein_python.base import APISession
 from datetime import datetime
-from openprotein.api.poet import *
+from openprotein_python.api.poet import *
 import io
 from urllib.parse import urljoin
 
 from typing import List, Optional, Union
 from io import BytesIO
 from unittest.mock import ANY
 import json
-from openprotein.base import BearerAuth
+from openprotein_python.base import BearerAuth
 
 class ResponseMock:
     def __init__(self):
diff --git a/tests/api/test_predict.py b/tests/api/test_predict.py
@@ -1,9 +1,9 @@
 from unittest.mock import patch, MagicMock, ANY
-from openprotein.api.predict import PredictFuture, PredictAPI, get_prediction_results, get_single_site_prediction_results
-from openprotein.base import APISession
-from openprotein.api.train import TrainFuture
-from openprotein.models import SequenceDataset, SequenceData, AssayMetadata, Prediction, PredictJob, PredictSingleSiteJob
-from openprotein.api.jobs import Job
+from openprotein_python.api.predict import PredictFuture, PredictAPI, get_prediction_results, get_single_site_prediction_results
+from openprotein_python.base import APISession
+from openprotein_python.api.train import TrainFuture
+from openprotein_python.models import SequenceDataset, SequenceData, AssayMetadata, Prediction, PredictJob, PredictSingleSiteJob
+from openprotein_python.api.jobs import Job
 import pytest 
 from datetime import datetime 
 
diff --git a/tests/api/test_train.py b/tests/api/test_train.py
@@ -2,14 +2,14 @@
 from datetime import datetime
 from unittest.mock import MagicMock
 
-from openprotein.api.data import AssayDataset, AssayMetadata
-from openprotein.api.jobs import Job
-from openprotein.api.train import (TrainFuture, TrainingAPI, create_train_job,
+from openprotein_python.api.data import AssayDataset, AssayMetadata
+from openprotein_python.api.jobs import Job
+from openprotein_python.api.train import (TrainFuture, TrainingAPI, create_train_job,
                                    _create_train_job_br, _create_train_job_gp,
                                    get_training_results)
-from openprotein.base import APISession
-from openprotein.errors import InvalidParameterError
-from openprotein.models import TrainGraph
+from openprotein_python.base import APISession
+from openprotein_python.errors import InvalidParameterError
+from openprotein_python.models import TrainGraph
 
 
 @pytest.fixture
diff --git a/tests/e2e/test_embeddings_e2e.py b/tests/e2e/test_embeddings_e2e.py
@@ -25,9 +25,9 @@
 from protembed.datasets import pad_tensor_1d
 from protembed.factory import ProtembedModelLoader
 
-import openprotein
-from openprotein import OpenProtein
-from openprotein.api.embedding import SVDModel
+import openprotein_python
+from openprotein_python import OpenProtein
+from openprotein_python.api.embedding import SVDModel
 from tests.utils.svd import TorchLowRankSVDTransform
 
 
@@ -51,10 +51,10 @@ def load_model_and_alphabet_local(model_location, device):
 def session() -> OpenProtein:
     with open("secrets.config", "r") as f:
         config = json.load(f)
-    return openprotein.connect(
+    return openprotein_python.connect(
         config["username"],
         config["password"],
-        backend="https://dev.api.openprotein.ai/api/",
+        backend="https://api.openprotein.ai/api/",
     )
 
 

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`		`-__version_tuple__ = version_tuple = (0, 1, 1, 'b3')`
	`1`	`+__version_tuple__ = version_tuple = (0, 1, 1, 'b5')`
`2`	`2`	`__version__ = version = '.'.join(str(x) for x in __version_tuple__)`