biolm-sdk 0.0.1__tar.gz

biolm_sdk-0.0.1/AUTHORS.rst

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+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Nikhil Haas <nikhil@nikhilhaas.com>
+
+Contributors
+------------
+
+None yet. Why not be the first?

biolm_sdk-0.0.1/CONTRIBUTING.rst

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+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/BioLM/py-biolm/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+BioLM AI could always use more documentation, whether as part of the
+official BioLM AI docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/BioLM/py-biolm/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `biolmai` for local development.
+
+1. Fork the `biolmai` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/biolmai.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv biolmai
+    $ cd biolmai/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 biolmai tests
+    $ python setup.py test or pytest
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
+   https://travis-ci.com/BioLM/py-biolm/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ pytest tests.test_biolmai
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

biolm_sdk-0.0.1/HISTORY.rst

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+=======
+History
+=======
+
+0.1.0 (2023-09-04)
+------------------
+
+* First release on PyPI.

biolm_sdk-0.0.1/LICENSE

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+Apache Software License 2.0
+
+Copyright (c) 2023, Nikhil Haas
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+

biolm_sdk-0.0.1/MANIFEST.in

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+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

biolm_sdk-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: biolm-sdk
+Version: 0.0.1
+Summary: BioLM Python client for the hosted platform and biolm-hub
+Home-page: https://github.com/BioLM/py-biolm
+Author: BioLM
+Author-email: BioLM <support@biolm.ai>
+License: Apache Software License 2.0
+Keywords: biolm,biolmai,bioai
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: httpx>=0.23.0
+Requires-Dist: httpcore
+Requires-Dist: Click>=6.0
+Requires-Dist: requests
+Requires-Dist: aiodns
+Requires-Dist: synchronicity>=0.5.0; python_version >= "3.9"
+Requires-Dist: synchronicity<0.5.0; python_version < "3.9"
+Requires-Dist: typing_extensions; python_version < "3.9"
+Requires-Dist: aiohttp<=3.8.6; python_version < "3.12"
+Requires-Dist: aiohttp>=3.9.0; python_version >= "3.12"
+Requires-Dist: async-lru
+Requires-Dist: aiofiles
+Requires-Dist: cryptography
+Requires-Dist: h2
+Requires-Dist: nest_asyncio
+Requires-Dist: rich>=13.0.0
+Requires-Dist: pyyaml>=5.0
+Requires-Dist: jsonschema<5,>=4.0
+Provides-Extra: pipeline
+Requires-Dist: pandas<3,>=1.3.0; extra == "pipeline"
+Requires-Dist: numpy<3,>=1.20; extra == "pipeline"
+Requires-Dist: tqdm>=4.60.0; extra == "pipeline"
+Requires-Dist: matplotlib>=3.3.0; extra == "pipeline"
+Requires-Dist: seaborn>=0.11.0; extra == "pipeline"
+Requires-Dist: scikit-learn>=1.0; extra == "pipeline"
+Requires-Dist: umap-learn>=0.5.0; extra == "pipeline"
+Requires-Dist: biotite>=0.34.0; extra == "pipeline"
+Requires-Dist: biopython>=1.78; extra == "pipeline"
+Requires-Dist: scipy>=1.7.0; extra == "pipeline"
+Requires-Dist: duckdb<2,>=0.9.0; extra == "pipeline"
+Requires-Dist: pyarrow>=10.0.0; extra == "pipeline"
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+========
+BioLM AI
+========
+
+
+.. image:: https://img.shields.io/pypi/v/biolm.svg
+        :target: https://pypi.python.org/pypi/biolm
+
+.. image:: https://api.travis-ci.com/BioLM/py-biolm.svg?branch=production
+        :target: https://travis-ci.org/github/BioLM/py-biolm
+
+.. image:: https://readthedocs.org/projects/biolm-ai/badge/?version=latest
+        :target: https://biolm-ai.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+Python client and SDK for `BioLM <https://biolm.ai>`_
+
+Install the package:
+
+.. code-block:: bash
+
+    pip install biolm
+
+Open-source models (biolm-hub):
+
+.. code-block:: bash
+
+    # In biolm-hub: bh serve
+    biolm hub set
+    biolm model list
+    biolm model run esm2-8m encode -i seq.json
+
+See ``docs/cli/hub.rst``.
+
+Basic usage:
+
+.. code-block:: python
+
+    from biolm import biolm
+
+    # Encode a single sequence
+    result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
+
+    # Predict a batch of sequences
+    result = biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"])
+
+    # Write results to disk
+    biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"], output='disk', file_path="results.jsonl")
+
+Asynchronous usage:
+
+.. code-block:: python
+
+    from biolm.core.http import BioLMApiClient
+    import asyncio
+
+    async def main():
+        model = BioLMApiClient("esmfold")
+        result = await model.predict(items=[{"sequence": "MDNELE"}])
+        print(result)
+
+    asyncio.run(main())
+
+Overview
+========
+
+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.
+
+Main features:
+
+- High-level BioLM constructor for quick requests
+- Sync and async interfaces
+- Automatic or custom rate limiting/throttling
+- Schema-based batch size detection
+- Flexible input formats (single key + list, or list of dicts)
+- Low memory usage via generators
+- Flexible error handling (raise, continue, or stop on error)
+- Universal HTTP client for both sync and async
+
+Features
+========
+
+- **High-level constructor**: Instantly run an API call with a single line.
+- **Sync and async**: Use `BioLM` for sync, or `BioLMApiClient` for async.
+- **Flexible rate limiting**: Use API throttle, disable, or set your own (e.g., '1000/second').
+- **Schema-based batching**: Automatically queries API for max batch size.
+- **Flexible input**: Accepts a single key and list, or list of dicts, or list of lists for advanced batching.
+- **Low memory**: Uses generators for validation and batching.
+- **Error handling**: Raise HTTPX errors, continue on error, or stop on first error.
+- **Disk output**: Write results as JSONL to disk.
+- **Universal HTTP client**: Efficient for both sync and async.
+- **Direct access to schema and batching**: Use `BioLMApi` for advanced workflows, including `.schema()`, `.call()`, and `._batch_call_autoschema_or_manual()`.
+
+**Example endpoints and actions:**
+
+- `esm2-8m/encode`: Embedding for protein sequences.
+- `esmfold/predict`: Structure prediction for protein sequences.
+- `progen2-oas/generate`: Sequence generation from a context string.
+- `dnabert2/predict`: Masked prediction for protein sequences.
+- `ablang2/encode`: Embeddings for paired-chain antibodies.
+
+* Free software: Apache Software License 2.0
+* Documentation: https://docs.biolm.ai

biolm_sdk-0.0.1/README.rst

@@ -0,0 +1,106 @@
+========
+BioLM AI
+========
+
+
+.. image:: https://img.shields.io/pypi/v/biolm.svg
+        :target: https://pypi.python.org/pypi/biolm
+
+.. image:: https://api.travis-ci.com/BioLM/py-biolm.svg?branch=production
+        :target: https://travis-ci.org/github/BioLM/py-biolm
+
+.. image:: https://readthedocs.org/projects/biolm-ai/badge/?version=latest
+        :target: https://biolm-ai.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+Python client and SDK for `BioLM <https://biolm.ai>`_
+
+Install the package:
+
+.. code-block:: bash
+
+    pip install biolm
+
+Open-source models (biolm-hub):
+
+.. code-block:: bash
+
+    # In biolm-hub: bh serve
+    biolm hub set
+    biolm model list
+    biolm model run esm2-8m encode -i seq.json
+
+See ``docs/cli/hub.rst``.
+
+Basic usage:
+
+.. code-block:: python
+
+    from biolm import biolm
+
+    # Encode a single sequence
+    result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
+
+    # Predict a batch of sequences
+    result = biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"])
+
+    # Write results to disk
+    biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"], output='disk', file_path="results.jsonl")
+
+Asynchronous usage:
+
+.. code-block:: python
+
+    from biolm.core.http import BioLMApiClient
+    import asyncio
+
+    async def main():
+        model = BioLMApiClient("esmfold")
+        result = await model.predict(items=[{"sequence": "MDNELE"}])
+        print(result)
+
+    asyncio.run(main())
+
+Overview
+========
+
+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.
+
+Main features:
+
+- High-level BioLM constructor for quick requests
+- Sync and async interfaces
+- Automatic or custom rate limiting/throttling
+- Schema-based batch size detection
+- Flexible input formats (single key + list, or list of dicts)
+- Low memory usage via generators
+- Flexible error handling (raise, continue, or stop on error)
+- Universal HTTP client for both sync and async
+
+Features
+========
+
+- **High-level constructor**: Instantly run an API call with a single line.
+- **Sync and async**: Use `BioLM` for sync, or `BioLMApiClient` for async.
+- **Flexible rate limiting**: Use API throttle, disable, or set your own (e.g., '1000/second').
+- **Schema-based batching**: Automatically queries API for max batch size.
+- **Flexible input**: Accepts a single key and list, or list of dicts, or list of lists for advanced batching.
+- **Low memory**: Uses generators for validation and batching.
+- **Error handling**: Raise HTTPX errors, continue on error, or stop on first error.
+- **Disk output**: Write results as JSONL to disk.
+- **Universal HTTP client**: Efficient for both sync and async.
+- **Direct access to schema and batching**: Use `BioLMApi` for advanced workflows, including `.schema()`, `.call()`, and `._batch_call_autoschema_or_manual()`.
+
+**Example endpoints and actions:**
+
+- `esm2-8m/encode`: Embedding for protein sequences.
+- `esmfold/predict`: Structure prediction for protein sequences.
+- `progen2-oas/generate`: Sequence generation from a context string.
+- `dnabert2/predict`: Masked prediction for protein sequences.
+- `ablang2/encode`: Embeddings for paired-chain antibodies.
+
+* Free software: Apache Software License 2.0
+* Documentation: https://docs.biolm.ai

biolm_sdk-0.0.1/biolm/__init__.py

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+"""Top-level package for BioLM."""
+__author__ = """Nikhil Haas"""
+__email__ = "nikhil@biolm.ai"
+__version__ = '0.0.1'
+
+from biolm.core.http import BioLMApi, BioLMApiClient
+from biolm.client import BioLM
+from biolm.models import Model, predict, encode, generate
+from biolm.protocols import Protocol
+from biolm.workspaces import Workspace
+from biolm.volumes import Volume
+from biolm.examples import get_example, list_models
+from biolm.io import (
+    load_fasta,
+    to_fasta,
+    load_csv,
+    to_csv,
+    load_pdb,
+    to_pdb,
+    load_json,
+    to_json,
+)
+
+try:
+    from biolm import pipeline
+    _HAS_PIPELINE = True
+except ImportError:
+    _HAS_PIPELINE = False
+
+from typing import Optional, Union, List, Any
+
+__all__ = [
+    'BioLM',
+    'biolm',
+    'BioLMApi',
+    'BioLMApiClient',
+    'Model',
+    'Protocol',
+    'Workspace',
+    'Volume',
+    'predict',
+    'encode',
+    'generate',
+    'get_example',
+    'list_models',
+    'load_fasta',
+    'to_fasta',
+    'load_csv',
+    'to_csv',
+    'load_pdb',
+    'to_pdb',
+    'load_json',
+    'to_json',
+]
+if _HAS_PIPELINE:
+    __all__.append('pipeline')
+
+
+def biolm(
+    *,
+    entity: str,
+    action: str,
+    type: Optional[str] = None,
+    items: Union[Any, List[Any]],
+    params: Optional[dict] = None,
+    api_key: Optional[str] = None,
+    **kwargs
+) -> Any:
+    """Top-level convenience function that wraps the BioLM class and returns the result."""
+    return BioLM(
+        entity=entity,
+        action=action,
+        type=type,
+        items=items,
+        params=params,
+        api_key=api_key,
+        **kwargs
+    )