first commit for the open-sourced version

.bumpversion.cfg

@@ -0,0 +1,12 @@
+[bumpversion]
+current_version = 0.0.3
+tag = True
+commit = True
+
+[bumpversion:file:pyproject.toml]
+
+[bumpversion:file:ginkgo_ai_client/__init__.py]
+
+[bumpversion:file:CHANGES.md]
+search = Unreleased
+replace = {new_version} ({utcnow.year}-{utcnow.month:0>2}-{utcnow.day:0>2})

.github/workflows/test.yml

@@ -0,0 +1,29 @@
+name: Test
+
+on: [push, pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: Install dependencies
+        run: |
+          pip install '.[test]'
+      - name: Run tests
+        env:
+          GINKGOAI_API_KEY: ${{ secrets.GINKGOAI_API_KEY }}
+        run: |
+          pytest

.gitignore

@@ -0,0 +1,34 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# Virtual environment directories
+env/
+venv/
+ENV/
+.venv/
+.ENV/
+
+# Distribution / packaging
+build/
+dist/
+*.egg-info/
+*.egg
+
+# Log files
+*.log
+
+# Unit test / coverage reports
+*.coverage
+.coverage.*
+.cache
+
+# Jupyter Notebook checkpoints
+.ipynb_checkpoints/
+
+# IDE specific files
+.vscode/
+.idea/
+
+# NOTE(vz): Personal pattern for keeping a non-shared sandbox directory in projects
+_sandbox/

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: |
+            (?x)^(
+                .bumpversion.cfg
+            )$
+
+  # Fast Python linter and formatter - replaces flake8, isort, and black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.9
+    hooks:
+      # Run the Ruff linter
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      # Run the Ruff formatter
+      - id: ruff-format

CHANGES.md

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+# Changelog
+
+Major changes to `profound` are documented here.
+Version numbers for the project follow the conventions described in :pep:`440`
+and `Semantic versioning 2.0.0 <http://semver.org/>`\_, with the exceptions that:
+
+- versions below `1.0.0` will be numbered as `0.major.minor-or-patch`
+
+- versions above `1.0.0` will be numbered as `major.minor.patch`, as is
+  typical
+
+## 0.0.3 (2024-10-28)
+
+- Added UTR model and ESM
+- Added batch inference
+
+## 0.0.2 (2024-10-18)
+
+- First version, AAO only

LICENCE

@@ -0,0 +1,7 @@
+Copyright 2024 Ginkgo Bioworks
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+# ginkgo-ai-client
+
+**Work in progress: this repo was just made public and we are still working on integration**
+
+A python client for [Ginkgo's AI model API](https://models.ginkgobioworks.ai/), to run inference on public and Ginkgo-proprietary models.
+Learn more in the [Model API announcement](https://www.ginkgobioworks.com/2024/09/17/ginkgo-model-api-ai-research/).
+
+## Prerequisites
+
+Register at https://models.ginkgobioworks.ai/ to get credits and an API KEY (of the form `b396553a-326a-4478-22eb-223e6ef9ee49`).
+Store the API KEY in the `GINKGOAI_API_KEY` environment variable.
+
+## Installation
+
+Install the python client with pip:
+
+```bash
+pip install ginkgo-ai-client
+```
+
+## Usage:
+
+**Note: This is an alpha version of the client and its interface may vary in the future.**
+
+The client requires an API key (and defaults to `os.environ.get("GINKGOAI_API_KEY")` if none is explicitly provided)
+
+```python
+from ginkgo_ai_client import GinkgoAIClient, aa0_masked_inference_params
+
+client = GinkgoAIClient()
+prediction = client.query(aa0_masked_inference_params("MPK<mask><mask>RRL"))
+# prediction["sequence"] == "MPKYLRRL"
+
+predictions = client.batch_query([
+    aa0_masked_inference_params("MPK<mask><mask>RRL"),
+    aa0_masked_inference_params("M<mask>RL"),
+    aa0_masked_inference_params("MLLM<mask><mask>R"),
+])
+# predictions[0]["result"]["sequence"] == "MPKYLRRL"
+```
+
+## Available models
+
+See the reference docs for more details on usage and parameters
+
+| Model | Description                                 | Reference                                                                                    | Supported queries            | Versions |
+| ----- | ------------------------------------------- | -------------------------------------------------------------------------------------------- | ---------------------------- | -------- |
+| ESM2  | Large Protein language model from Meta      | [Github](https://github.com/facebookresearch/esm?tab=readme-ov-file#esmfold)                 | Embeddings, masked inference | 3B, 650M |
+| AA0   | Ginkgo's proprietary protein language model | [Announcement](https://www.ginkgobioworks.com/2024/09/17/aa-0-protein-llm-technical-review/) | Embeddings, masked inference | 650M     |
+| 3UTR  | Ginkgo's proprietary 3'UTR language model   | [Preprint](https://www.biorxiv.org/content/10.1101/2024.10.07.616676v1)                      | Embeddings, masked inference | 650M     |
+
+## License
+
+This project is licensed under the MIT License. See the `LICENSE` file for details.

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+livehtml:
+	sphinx-autobuild -n "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

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+# Docs
+
+Note: you can get live docs running with `make livehtml`.

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_static/custom.css

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+.w-64 {
+    width: 26rem;
+}

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+project = "ginkgo_ai_client"
+copyright = "2024, Ginkgo Bioworks"
+author = "Ginkgo Bioworks"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "myst_parser",  # for markdown support
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "shibuya"
+html_static_path = ["_static"]
+html_css_files = ["custom.css"]

docs/source/index.rst

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+.. ginkgo_ai_client documentation master file, created by
+   sphinx-quickstart on Wed Oct 30 17:29:16 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+
+----
+
+API Documentation
+-----------------
+
+GinkgoAIClient
+~~~~~~~~~~~~~~
+
+.. automodule:: ginkgo_ai_client.client
+   :members:
+
+Query Parameters
+~~~~~~~~~~~~~~~~
+
+.. automodule:: ginkgo_ai_client.query_parameters
+   :members:
+
+.. .. toctree::
+..    :maxdepth: 2
+..    :caption: Contents:

ginkgo_ai_client/__init__.py

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+__version__ = "0.0.3"
+
+from .client import GinkgoAIClient
+
+from .query_parameters import (
+    aa0_masked_inference_params,
+    aa0_mean_embedding_params,
+    esm_mean_embedding_params,
+    esm_masked_inference_params,
+    three_utr_masked_inference_params,
+    three_utr_mean_embedding_params,
+)
+
+__all__ = [
+    "GinkgoAIClient",
+    "aa0_masked_inference_params",
+    "aa0_mean_embedding_params",
+    "esm_mean_embedding_params",
+    "esm_masked_inference_params",
+    "three_utr_masked_inference_params",
+    "three_utr_mean_embedding_params",
+]