biolmai 0.2.3__py2.py3-none-any.whl → 0.2.4__py2.py3-none-any.whl
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- biolmai/__init__.py +17 -3
- biolmai-0.2.4.dist-info/METADATA +134 -0
- {biolmai-0.2.3.dist-info → biolmai-0.2.4.dist-info}/RECORD +8 -8
- {biolmai-0.2.3.dist-info → biolmai-0.2.4.dist-info}/WHEEL +1 -1
- biolmai-0.2.3.dist-info/METADATA +0 -76
- {biolmai-0.2.3.dist-info → biolmai-0.2.4.dist-info}/entry_points.txt +0 -0
- {biolmai-0.2.3.dist-info → biolmai-0.2.4.dist-info}/licenses/AUTHORS.rst +0 -0
- {biolmai-0.2.3.dist-info → biolmai-0.2.4.dist-info}/licenses/LICENSE +0 -0
- {biolmai-0.2.3.dist-info → biolmai-0.2.4.dist-info}/top_level.txt +0 -0
biolmai/__init__.py
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"""Top-level package for BioLM AI."""
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__author__ = """Nikhil Haas"""
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__email__ = "nikhil@biolm.ai"
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__version__ = '0.2.
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__version__ = '0.2.4'
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from biolmai.cls import *
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from biolmai.client import BioLMApi, BioLMApiClient
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from biolmai.biolmai import BioLM
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from typing import Optional, Union, List, Any
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__all__ = []
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__all__ = ['biolm']
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def biolm(
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*,
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entity: str,
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action: str,
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type: Optional[str] = None,
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items: Union[Any, List[Any]],
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params: Optional[dict] = None,
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api_key: Optional[str] = None,
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**kwargs
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) -> Any:
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"""Top-level convenience function that wraps the BioLM class and returns the result."""
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return BioLM(entity=entity, action=action, type=type, items=items, params=params, api_key=api_key, **kwargs)
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Metadata-Version: 2.4
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Name: biolmai
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Version: 0.2.4
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Summary: BioLM Python client
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Home-page: https://github.com/BioLM/py-biolm
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Author: BioLM
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Author-email: BioLM <support@biolm.ai>
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License: Apache Software License 2.0
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Keywords: biolmai
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Intended Audience :: Developers
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Classifier: License :: OSI Approved :: Apache Software License
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Classifier: Natural Language :: English
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Requires-Python: >=3.7
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Description-Content-Type: text/x-rst
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License-File: LICENSE
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License-File: AUTHORS.rst
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Requires-Dist: httpx>=0.23.0
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Requires-Dist: httpcore
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Requires-Dist: Click>=6.0
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Requires-Dist: requests
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Requires-Dist: aiodns
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Requires-Dist: synchronicity>=0.5.0
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Requires-Dist: aiohttp<=3.8.6; python_version < "3.12"
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Requires-Dist: aiohttp>=3.9.0; python_version >= "3.12"
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Requires-Dist: async-lru
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Requires-Dist: aiofiles
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Dynamic: author
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========
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BioLM AI
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========
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.. image:: https://img.shields.io/pypi/v/biolmai.svg
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:target: https://pypi.python.org/pypi/biolmai
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.. image:: https://api.travis-ci.com/BioLM/py-biolm.svg?branch=production
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:target: https://travis-ci.org/github/BioLM/py-biolm
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.. image:: https://readthedocs.org/projects/biolm-ai/badge/?version=latest
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:target: https://biolm-ai.readthedocs.io/en/latest/?version=latest
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:alt: Documentation Status
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Python client and SDK for `BioLM <https://biolm.ai>`_
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Install the package:
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.. code-block:: bash
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pip install biolmai
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Basic usage:
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.. code-block:: python
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from biolmai import biolm
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# Encode a single sequence
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result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
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# Predict a batch of sequences
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result = biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"])
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# Write results to disk
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biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"], output='disk', file_path="results.jsonl")
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Asynchronous usage:
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.. code-block:: python
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from biolmai.client import BioLMApiClient
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import asyncio
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async def main():
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model = BioLMApiClient("esmfold")
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result = await model.predict(items=[{"sequence": "MDNELE"}])
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print(result)
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asyncio.run(main())
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Overview
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========
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The BioLM Python client provides a high-level, user-friendly interface for interacting with the BioLM API. It supports both synchronous and asynchronous usage, automatic batching, flexible error handling, and efficient processing of biological data.
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Main features:
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- High-level BioLM constructor for quick requests
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- Sync and async interfaces
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- Automatic or custom rate limiting/throttling
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- Schema-based batch size detection
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- Flexible input formats (single key + list, or list of dicts)
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- Low memory usage via generators
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- Flexible error handling (raise, continue, or stop on error)
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- Universal HTTP client for both sync and async
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Features
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========
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- **High-level constructor**: Instantly run an API call with a single line.
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- **Sync and async**: Use `BioLM` for sync, or `BioLMApiClient` for async.
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- **Flexible rate limiting**: Use API throttle, disable, or set your own (e.g., '1000/second').
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- **Schema-based batching**: Automatically queries API for max batch size.
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- **Flexible input**: Accepts a single key and list, or list of dicts, or list of lists for advanced batching.
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- **Low memory**: Uses generators for validation and batching.
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- **Error handling**: Raise HTTPX errors, continue on error, or stop on first error.
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- **Disk output**: Write results as JSONL to disk.
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- **Universal HTTP client**: Efficient for both sync and async.
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- **Direct access to schema and batching**: Use `BioLMApi` for advanced workflows, including `.schema()`, `.call()`, and `._batch_call_autoschema_or_manual()`.
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**Example endpoints and actions:**
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- `esm2-8m/encode`: Embedding for protein sequences.
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- `esmfold/predict`: Structure prediction for protein sequences.
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- `progen2-oas/generate`: Sequence generation from a context string.
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- `dnabert2/predict`: Masked prediction for protein sequences.
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- `ablang2/encode`: Embeddings for paired-chain antibodies.
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* Free software: Apache Software License 2.0
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* Documentation: https://docs.biolm.ai
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biolmai/__init__.py,sha256=
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biolmai/__init__.py,sha256=Rt-5K0TkHdQdPjK_h_plsb8YHSfO6xSkTApCIhY081U,693
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biolmai/api.py,sha256=tqxQ-FoZosE88YmLJPQKskjNQdcb5jzZccywGP73lDc,13002
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biolmai/asynch.py,sha256=BVypJhhEEK2Bek2AhqNGn7FIRJehAbJflUdeeslbXFE,9073
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biolmai/auth.py,sha256=flI9KAD90qdXyLDnpJTrc9voKsiK0uWtD2ehsPBn8r4,6329
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biolmai/ltc.py,sha256=al7HZc5tLyUR5fmpIb95hOz5ctudVsc0xzjd_c2Ew3M,49
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biolmai/payloads.py,sha256=BOhEKl9kWkKMXy1YiNw2_eC6MJ4Dn6vKNvkhEBsM7Lw,1735
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biolmai/validate.py,sha256=58XMWrdWoDRmfiNAayWqrYaH3_bjRmEpG_yx6XSjTrM,4168
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biolmai-0.2.
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biolmai-0.2.4.dist-info/licenses/AUTHORS.rst,sha256=TB_ACuFPgVmxn1NspYwksTdT6jdZeShcxfafmi-XWKQ,158
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biolmai-0.2.4.dist-info/licenses/LICENSE,sha256=8yt0SdP38I7a3g0zWqZjNe0VSDQhJA4bWLQSqqKtAVg,583
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biolmai-0.2.4.dist-info/METADATA,sha256=-m6zspmcBxVhCZxoDHYrIR8o5NH-5wobPl-hlHzj0MI,4619
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biolmai-0.2.4.dist-info/WHEEL,sha256=JNWh1Fm1UdwIQV075glCn4MVuCRs0sotJIq-J6rbxCU,109
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biolmai-0.2.4.dist-info/entry_points.txt,sha256=ylQnDpCYrxF1F9z_T7NRQcYMWYF5ia_KsTUuboxjEAM,44
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biolmai-0.2.4.dist-info/top_level.txt,sha256=jyQO45JN3g_jbdI8WqMnb0aEIzf4h1MrmPAZkKgfnwY,8
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biolmai-0.2.4.dist-info/RECORD,,
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Version: 0.2.3
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Summary: BioLM Python client
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Home-page: https://github.com/BioLM/py-biolm
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Author: BioLM
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Author-email: BioLM <support@biolm.ai>
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License: Apache Software License 2.0
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Keywords: biolmai
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Classifier: Development Status :: 2 - Pre-Alpha
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BioLM AI
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Python client and SDK for https://biolm.ai
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* Free software: Apache Software License 2.0
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This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
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.. _Cookiecutter: https://github.com/audreyr/cookiecutter
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