refactor

Author: markgeejw

Makefile

@@ -1,13 +1,14 @@
-VERSION ?= 0.4.0
+VERSION ?= 0.5.0.dev0
 SHELL := /bin/bash
 
 .PHONY: releasehere
 releasegit:
-	# Update Poetry version
-	poetry version $(VERSION)
+	# Update Pixi version
+	pixi project version set $(VERSION)
 
 	# Update version in meta.yaml
-	sed -i 's/^  version: .*/  version: "$(VERSION)"/' anaconda_build/meta.yaml
+	# sed -i'' 's/^  version: .*/^  version: "$(VERSION)"/' anaconda_build/meta.yaml
+	perl -i -pe's/^  version: .*/  version: "$(VERSION)"/' anaconda_build/meta.yaml
 
 	# Commit changes
 	git add pyproject.toml anaconda_build/meta.yaml
@@ -20,8 +21,6 @@ releasegit:
 	git push origin HEAD
 	git push origin v$(VERSION)
 
-	curl -X PURGE https://camo.githubusercontent.com/125a275204c801f733fd69689c1e72bde9960a1e193c9c46299d848373a52a93/68747470733a2f2f616e61636f6e64612e6f72672f6f70656e70726f7465696e2f6f70656e70726f7465696e2d707974686f6e2f6261646765732f76657273696f6e2e737667
-
 
 releasehere:
 	# Update Poetry version
@@ -47,8 +46,10 @@ releasehere:
 
 	#conda 
 	source activate bld && conda build ./anaconda_build
-	
-	curl -X PURGE https://camo.githubusercontent.com/125a275204c801f733fd69689c1e72bde9960a1e193c9c46299d848373a52a93/68747470733a2f2f616e61636f6e64612e6f72672f6f70656e70726f7465696e2f6f70656e70726f7465696e2d707974686f6e2f6261646765732f76657273696f6e2e737667
+
+condabld:
+        micromamba activate openprotein-sdk-build
+        conda build -c conda-forge --numpy 2.1 ./anaconda_build
 
 proddocs:
 	cd apidocs && make clean && make html 

anaconda_build/conda_build_config.yaml

@@ -0,0 +1,2 @@
+numpy:
+  - 2.1

anaconda_build/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: openprotein-python
-  version: "0.4.1"
+  version: "0.5.0.dev0"
 
 source:
   path: ../
@@ -12,18 +12,19 @@ build:
 
 requirements:
   build:
-    - python >=3.7
-    - poetry
+    - python >=3.10,<3.11
+    - hatchling >=1.25.0,<2
   host:
-    - python >=3.7
+    - python >=3.10,<3.11
     - pip
-    - poetry
+    - hatchling >=1.25.0,<2
   run:
-    - python >=3.7
-    - requests >=2.0
-    - pydantic >=1.0
-    - tqdm >=4.0
-    - pandas >=1.0
+    - python >=3.10,<3.11
+    - requests >=2.32.3,<3
+    - pydantic >=2.5,<3
+    - tqdm >=4.66.5,<5
+    - pandas >=2.1.4,<3
+    - numpy >=2.1.1,<3
 
 about:
   home: https://www.openprotein.ai/

openprotein/__init__.py

@@ -1,14 +1,17 @@
 from openprotein._version import __version__
-
+from openprotein.app import (
+    SVDAPI,
+    AlignAPI,
+    AssayDataAPI,
+    DesignAPI,
+    EmbeddingsAPI,
+    FoldAPI,
+    JobsAPI,
+    PredictorAPI,
+    TrainingAPI,
+)
+from openprotein.app.models import Future
 from openprotein.base import APISession
-from openprotein.api.jobs import JobsAPI, Job
-from openprotein.api.data import DataAPI
-from openprotein.api.align import AlignAPI
-from openprotein.api.embedding import EmbeddingAPI
-from openprotein.api.train import TrainingAPI
-from openprotein.api.design import DesignAPI
-from openprotein.api.fold import FoldAPI
-from openprotein.api.jobs import load_job
 
 
 class OpenProtein(APISession):
@@ -17,20 +20,22 @@ class OpenProtein(APISession):
     """
 
     _embedding = None
+    _svd = None
     _fold = None
     _align = None
     _jobs = None
     _data = None
     _train = None
     _design = None
+    _predictor = None
 
-    def wait(self, job: Job, *args, **kwargs):
-        return job.wait(self, *args, **kwargs)
+    def wait(self, future: Future, *args, **kwargs):
+        return future.wait(*args, **kwargs)
 
     wait_until_done = wait
 
     def load_job(self, job_id):
-        return load_job(self, job_id)
+        return self.jobs.__load(job_id=job_id)
 
     @property
     def jobs(self) -> JobsAPI:
@@ -42,12 +47,12 @@ def jobs(self) -> JobsAPI:
         return self._jobs
 
     @property
-    def data(self) -> DataAPI:
+    def data(self) -> AssayDataAPI:
         """
         The data submodule gives access to functionality for uploading and accessing user data.
         """
         if self._data is None:
-            self._data = DataAPI(self)
+            self._data = AssayDataAPI(self)
         return self._data
 
     @property
@@ -62,21 +67,39 @@ def train(self) -> TrainingAPI:
     @property
     def align(self) -> AlignAPI:
         """
-        The PoET submodule gives access to the PoET generative model and MSA and prompt creation interfaces.
+        The Align submodule gives access to the sequence alignment capabilities by building MSAs and prompts that can be used with PoET.
         """
         if self._align is None:
             self._align = AlignAPI(self)
         return self._align
 
     @property
-    def embedding(self) -> EmbeddingAPI:
+    def embedding(self) -> EmbeddingsAPI:
         """
         The embedding submodule gives access to protein embedding models and their inference endpoints.
         """
         if self._embedding is None:
-            self._embedding = EmbeddingAPI(self)
+            self._embedding = EmbeddingsAPI(self)
         return self._embedding
 
+    @property
+    def svd(self) -> SVDAPI:
+        """
+        The embedding submodule gives access to protein embedding models and their inference endpoints.
+        """
+        if self._svd is None:
+            self._svd = SVDAPI(self, self.embedding)
+        return self._svd
+
+    @property
+    def predictor(self) -> PredictorAPI:
+        """
+        The predictor submodule gives access to training and predicting with predictors built on top of embeddings.
+        """
+        if self._predictor is None:
+            self._predictor = PredictorAPI(self, self.embedding, self.svd)
+        return self._predictor
+
     @property
     def design(self) -> DesignAPI:
         """

openprotein/api/__init__.py

@@ -1,7 +1,2 @@
-from . import data 
-from . import design
-from . import train 
-from . import predict
-from . import align 
-from . import embedding
-from . import fold 
+from . import align, assaydata, design, embedding, fold, predict, predictor, train
+from .deprecated import poet