release v0.5.1

Author: markgeejw

Makefile

@@ -1,4 +1,4 @@
-VERSION ?= 0.5.0
+VERSION ?= 0.5.2
 SHELL := /bin/bash
 
 .PHONY: releasehere

anaconda_build/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: openprotein-python
-  version: "0.5.0"
+  version: "0.5.2"
 
 source:
   path: ../
@@ -12,19 +12,19 @@ build:
 
 requirements:
   build:
-    - python >=3.10,<3.11
+    - python >=3.10
     - hatchling >=1.25.0,<2
   host:
-    - python >=3.10,<3.11
+    - python >=3.10
     - pip
     - hatchling >=1.25.0,<2
   run:
-    - python >=3.10,<3.11
+    - python >=3.10
     - requests >=2.32.3,<3
     - pydantic >=2.5,<3
     - tqdm >=4.66.5,<5
-    - pandas >=2.1.4,<3
-    - numpy >=2.1.1,<3
+    - pandas >=2.2.2,<3
+    - numpy >=1.9,<3
 
 about:
   home: https://www.openprotein.ai/

openprotein/__init__.py

@@ -1,14 +1,24 @@
+"""
+OpenProtein Python client.
+
+A pythonic interface for interacting with our cutting-edge protein engineering platform.
+
+isort:skip_file
+"""
+
 from openprotein._version import __version__
 from openprotein.app import (
-    SVDAPI,
-    AlignAPI,
     AssayDataAPI,
+    JobsAPI,
+    TrainingAPI,
     DesignAPI,
+    AlignAPI,
     EmbeddingsAPI,
     FoldAPI,
-    JobsAPI,
+    SVDAPI,
+    UMAPAPI,
     PredictorAPI,
-    TrainingAPI,
+    DesignerAPI,
 )
 from openprotein.app.models import Future
 from openprotein.base import APISession
@@ -19,15 +29,17 @@ class OpenProtein(APISession):
     The base class for accessing OpenProtein API functionality.
     """
 
-    _embedding = None
-    _svd = None
-    _fold = None
-    _align = None
-    _jobs = None
     _data = None
+    _jobs = None
     _train = None
     _design = None
+    _align = None
+    _embedding = None
+    _svd = None
+    _umap = None
+    _fold = None
     _predictor = None
+    _designer = None
 
     def wait(self, future: Future, *args, **kwargs):
         return future.wait(*args, **kwargs)
@@ -37,15 +49,6 @@ def wait(self, future: Future, *args, **kwargs):
     def load_job(self, job_id):
         return self.jobs.__load(job_id=job_id)
 
-    @property
-    def jobs(self) -> JobsAPI:
-        """
-        The jobs submodule gives access to functionality for listing jobs and checking their status.
-        """
-        if self._jobs is None:
-            self._jobs = JobsAPI(self)
-        return self._jobs
-
     @property
     def data(self) -> AssayDataAPI:
         """
@@ -55,6 +58,15 @@ def data(self) -> AssayDataAPI:
             self._data = AssayDataAPI(self)
         return self._data
 
+    @property
+    def jobs(self) -> JobsAPI:
+        """
+        The jobs submodule gives access to functionality for listing jobs and checking their status.
+        """
+        if self._jobs is None:
+            self._jobs = JobsAPI(self)
+        return self._jobs
+
     @property
     def train(self) -> TrainingAPI:
         """
@@ -64,6 +76,15 @@ def train(self) -> TrainingAPI:
             self._train = TrainingAPI(self)
         return self._train
 
+    @property
+    def design(self) -> DesignAPI:
+        """
+        The design submodule gives access to functionality for designing new sequences using models from train.
+        """
+        if self._design is None:
+            self._design = DesignAPI(self)
+        return self._design
+
     @property
     def align(self) -> AlignAPI:
         """
@@ -91,6 +112,15 @@ def svd(self) -> SVDAPI:
             self._svd = SVDAPI(self, self.embedding)
         return self._svd
 
+    @property
+    def umap(self) -> UMAPAPI:
+        """
+        The embedding submodule gives access to protein embedding models and their inference endpoints.
+        """
+        if self._umap is None:
+            self._umap = UMAPAPI(self)
+        return self._umap
+
     @property
     def predictor(self) -> PredictorAPI:
         """
@@ -101,13 +131,13 @@ def predictor(self) -> PredictorAPI:
         return self._predictor
 
     @property
-    def design(self) -> DesignAPI:
+    def designer(self) -> DesignerAPI:
         """
-        The design submodule gives access to functionality for designing new sequences using models from train.
+        The designer submodule gives access to functionality for designing new sequences using models from predictor train.
         """
-        if self._design is None:
-            self._design = DesignAPI(self)
-        return self._design
+        if self._designer is None:
+            self._designer = DesignerAPI(self)
+        return self._designer
 
     @property
     def fold(self) -> FoldAPI:

openprotein/api/__init__.py

@@ -1,2 +1 @@
 from . import align, assaydata, design, embedding, fold, predict, predictor, train
-from .deprecated import poet

openprotein/api/align.py

@@ -1,37 +1,15 @@
-import codecs
-import csv
 import io
 import random
 from typing import BinaryIO, Iterator
 
 import openprotein.config as config
 import requests
 from openprotein.base import APISession
+from openprotein.csv import csv_stream
 from openprotein.errors import APIError, InvalidParameterError, MissingParameterError
 from openprotein.schemas import Job, MSASamplingMethod, PoetInputType
 
 
-def csv_stream(response: requests.Response) -> Iterator[list[str]]:
-    """
-    Returns a CSV reader from a requests.Response object.
-
-    Parameters
-    ----------
-    response : requests.Response
-        The response object to parse.
-
-    Returns
-    -------
-    csv.reader
-        A csv reader object for the response.
-    """
-    raw_content = response.raw  # the raw bytes stream
-    content = codecs.getreader("utf-8")(
-        raw_content
-    )  # force the response to be encoded as utf-8
-    return csv.reader(content)
-
-
 def get_align_job_inputs(
     session: APISession,
     job_id: str,

openprotein/api/deprecated/poet.py

@@ -5,7 +5,11 @@
 from openprotein import config
 from openprotein.base import APISession
 from openprotein.errors import APIError, InvalidParameterError, MissingParameterError
-from openprotein.schemas import PoetGenerateJob, PoetScoreJob, PoetSSPJob
+from openprotein.schemas.deprecated.poet import (
+    PoetGenerateJob,
+    PoetScoreJob,
+    PoetSSPJob,
+)
 
 
 def poet_score_post(

openprotein/api/design.py

@@ -1,8 +1,12 @@
 from openprotein.base import APISession
-from openprotein.schemas import DesignJobCreate, DesignResults, Job
+from openprotein.schemas import (
+    WorkflowDesign,
+    WorkflowDesignJob,
+    WorkflowDesignJobCreate,
+)
 
 
-def create_design_job(session: APISession, design_job: DesignJobCreate):
+def create_design_job(session: APISession, design_job: WorkflowDesignJobCreate):
     """
     Send a POST request for protein design job.
 
@@ -13,7 +17,7 @@ def create_design_job(session: APISession, design_job: DesignJobCreate):
     design_job : DesignJobCreate
         The details of the design job to be created, with the following parameters:
         - assay_id: The ID for the assay.
-        - criteria: A list of CriterionItem lists for evaluating the design.
+        - criteria: Criteria for evaluating the design.
         - num_steps: The number of steps in the genetic algo. Default is 8.
         - pop_size: The population size for the genetic algo. Default is None.
         - n_offsprings: The number of offspring for the genetic algo. Default is None.
@@ -24,13 +28,13 @@ def create_design_job(session: APISession, design_job: DesignJobCreate):
 
     Returns
     -------
-    Job
+    WorkflowDesignJob
         The created job as a Job instance.
     """
     params = design_job.model_dump(exclude_none=True)
     # print(f"sending design: {params}")
     response = session.post("v1/workflow/design/genetic-algorithm", json=params)
-    return Job.model_validate(response.json())
+    return WorkflowDesignJob.model_validate(response.json())
 
 
 def get_design_results(
@@ -39,7 +43,7 @@ def get_design_results(
     step: int | None = None,
     page_size: int | None = None,
     page_offset: int | None = None,
-) -> DesignResults:
+) -> WorkflowDesign:
     """
     Retrieves the results of a Design job.
 
@@ -60,7 +64,7 @@ def get_design_results(
 
     Returns
     -------
-    DesignJob
+    WorkflowDesignJob
         The job object representing the Design job.
 
     Raises
@@ -79,4 +83,4 @@ def get_design_results(
 
     response = session.get(endpoint, params=params)
 
-    return DesignResults.model_validate(response.json())
+    return WorkflowDesign.model_validate(response.json())