Merge pull request #135 from OpenProteinAI/develop

Release python v0.8.0

Author: markgeejw

pixi.lock

@@ -25,7 +25,7 @@ dependencies = [
   "sphinx-notfound-page>=1.1.0,<1.2.0",
   "sphinx-panels>=0.4.1,<0.5.0",
   # autodoc
-  "openprotein-python",
+  "openprotein-python==0.8.0",
 ]
 
 [build-system]
@@ -41,7 +41,7 @@ platforms = ["osx-arm64"]
 [dependency-groups]
 dev = [
   "sphinx-autobuild",
-  "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private@develop",
+  "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private@3f9ccbc1a7651d5a084d1520b13f1d4c9198f380",
 ]
 
 [tool.pixi.environments]

pyproject.toml

@@ -7,10 +7,6 @@ Some tools (e.g. PoET, AlphaFold2) require an MSA to be generated. The tools bel
    :members:
    :inherited-members:
 
-.. autoclass:: openprotein.align.PromptFuture
-   :members:
-   :inherited-members:
-
 .. autoclass:: openprotein.align.MSAFuture
    :members:
    :inherited-members:

source/python-api/api-reference/align.rst

@@ -7,82 +7,124 @@ Property Regression Models
 
 Data
 ^^^^
+
+Upload and store your datasets on our platform to use with your protein engineering tasks.
+
 .. autosummary::
 
    openprotein.data.DataAPI
    openprotein.data.AssayDataset
 
-..
-    Train
-    ^^^^^
-    .. autosummary::
+Align
+-----
 
-    openprotein.api.train.TrainingAPI
-    openprotein.api.train.TrainFuture
-    openprotein.api.predict.PredictFuture
+Align your protein sequences or look up multiple sequence alignments.
 
-Predictor
-^^^^^^^^^
 .. autosummary::
 
-   openprotein.predictor.PredictorAPI
-   openprotein.predictor.PredictorModel
+   openprotein.align.AlignAPI
+   openprotein.align.MSAFuture
+
+Prompt
+------
+
+Create prompts using sequences and structures to condition our proprietary high-performance PoET foundation models.
 
-Design
-^^^^^^
 .. autosummary::
 
-   openprotein.design.DesignAPI
-   openprotein.design.DesignFuture
+   openprotein.prompt.PromptAPI
+   openprotein.prompt.Prompt
+   openprotein.prompt.Query
 
 
 Foundation models 
 -----------------
 
-Endpoints
-^^^^^^^^^
+Use foundation models to produce embeddings and logits with your protein sequences.
+
 .. autosummary::
 
    openprotein.embeddings.EmbeddingsAPI
 
 
 Models
 ^^^^^^
+
+The foundation models on our platform are classed appropriately to identify the models and group their functionality.
+
 .. autosummary::
 
-   openprotein.embeddings.OpenProteinModel
-   openprotein.embeddings.ESMModel
    openprotein.embeddings.PoET2Model
    openprotein.embeddings.PoETModel
-   openprotein.embeddings.SVDModel
-   openprotein.embeddings.UMAPModel
+   openprotein.embeddings.OpenProteinModel
+   openprotein.embeddings.ESMModel
 
 Results
 ^^^^^^^
+
+The models produce asynchronous results which are modeled as futures which can be awaited.
+
 .. autosummary::
 
    openprotein.embeddings.EmbeddingsResultFuture
    openprotein.embeddings.EmbeddingsScoreFuture
    openprotein.embeddings.EmbeddingsGenerateFuture
 
-Align
------
+Transform
+---------
+
+Transform and reduce your embeddings for use with visualization and training workflows.
 
+SVD
+^^^
 .. autosummary::
 
-   openprotein.align.AlignAPI
-   openprotein.align.PromptFuture
-   openprotein.align.MSAFuture
+   openprotein.svd.SVDAPI
+   openprotein.svd.SVDModel
+
+UMAP
+^^^^
+.. autosummary::
+
+   openprotein.umap.UMAPAPI
+   openprotein.umap.UMAPModel
+
+Predictor
+---------
+
+Train predictors from your assay datasets and use them to make predictions on novel sequences.
+
+.. autosummary::
+
+   openprotein.predictor.PredictorAPI
+   openprotein.predictor.PredictorModel
+   openprotein.predictor.PredictionResultFuture
+
+Design
+------
+
+Design novel protein sequences based on your assay datasets and trained models, optimizing toward your design criteria.
+
+.. autosummary::
+
+   openprotein.design.DesignAPI
+   openprotein.design.DesignFuture
 
 Fold
 ----
 
+Make structure predictions on your protein sequences.
+
 .. autosummary::
 
    openprotein.fold.FoldAPI
    openprotein.fold.ESMFoldModel
    openprotein.fold.AlphaFold2Model
+   openprotein.fold.Boltz2Model
+   openprotein.fold.Boltz1xModel
+   openprotein.fold.Boltz1Model
    openprotein.fold.FoldResultFuture
+   openprotein.fold.FoldComplexResultFuture
 
 
 .. toctree::
@@ -91,8 +133,11 @@ Fold
 
    basics
    data
+   align 
+   prompt
+   embedding
+   svd
+   umap
    predictor
    design
-   embedding
-   align 
    fold

source/python-api/api-reference/index.rst

@@ -0,0 +1,16 @@
+openprotein.prompt
+=====================
+
+Create prompts to be used with PoET models, along with queries which opens up use-cases like inverse folding with PoET-2. 
+
+.. autoclass:: openprotein.prompt.PromptAPI
+   :members:
+   :inherited-members:
+
+.. autoclass:: openprotein.prompt.Prompt
+   :members:
+   :inherited-members:
+
+.. autoclass:: openprotein.prompt.Query
+   :members:
+   :inherited-members:

source/python-api/api-reference/prompt.rst

@@ -0,0 +1,14 @@
+openprotein.svd
+===============
+
+Fit SVD models on top of our protein language models to produce reduced embeddings, which can be used to train predictors!
+
+Endpoints
+-----------
+.. autoclass:: openprotein.svd.SVDAPI
+   :members:
+   :undoc-members:
+
+.. autoclass:: openprotein.svd.SVDModel
+   :members:
+   :undoc-members:

source/python-api/api-reference/svd.rst

@@ -0,0 +1,14 @@
+openprotein.umap
+================
+
+Fit and transform your embeddings using UMAP to help visualize your embeddings.
+
+Endpoints
+-----------
+.. autoclass:: openprotein.umap.UMAPAPI
+   :members:
+   :undoc-members:
+
+.. autoclass:: openprotein.umap.UMAPModel
+   :members:
+   :undoc-members: