biolmai 0.2.3__py2.py3-none-any.whl → 0.2.5__py2.py3-none-any.whl

biolmai/__init__.py

@@ -1,10 +1,24 @@
 """Top-level package for BioLM AI."""
 __author__ = """Nikhil Haas"""
 __email__ = "nikhil@biolm.ai"
-__version__ = '0.2.3'
+__version__ = '0.2.5'
 
-from biolmai.cls import *
 from biolmai.client import BioLMApi, BioLMApiClient
 from biolmai.biolmai import BioLM
+from typing import Optional, Union, List, Any
 
-__all__ = []
+__all__ = ['biolm']
+
+
+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)

biolmai/auth.py

@@ -1,3 +1,4 @@
+import ast
 import json
 import os
 import pprint
@@ -9,6 +10,47 @@ import requests
 from biolmai.const import ACCESS_TOK_PATH, BASE_DOMAIN, GEN_TOKEN_URL, USER_BIOLM_DIR
 
 
+def parse_credentials_file(file_path):
+    """Parse credentials file, handling JSON, Python dict syntax, and mixed types.
+    
+    Returns a dict with 'access' and 'refresh' keys as strings, or None if parsing fails.
+    Uses ast.literal_eval() which is safe and only evaluates Python literals.
+    """
+    try:
+        with open(file_path, 'r') as f:
+            content = f.read().strip()
+        
+        # Try JSON first
+        try:
+            data = json.loads(content)
+        except json.JSONDecodeError:
+            # Fall back to safe Python literal evaluation for dict syntax like {access: 123, refresh: 456}
+            # ast.literal_eval() is safe - it only evaluates literals, no code execution
+            try:
+                data = ast.literal_eval(content)
+            except (ValueError, SyntaxError):
+                return None
+        
+        # Ensure we have a dictionary
+        if not isinstance(data, dict):
+            return None
+            
+        # Extract access and refresh, converting to strings
+        access = data.get("access")
+        refresh = data.get("refresh")
+        
+        # Convert to strings if they exist
+        if access is not None:
+            access = str(access)
+        if refresh is not None:
+            refresh = str(refresh)
+            
+        return {"access": access, "refresh": refresh}
+        
+    except Exception:
+        return None
+
+
 def validate_user_auth(api_token=None, access=None, refresh=None):
     """Validates an API token, to be used as 'Authorization: Token 1235abc'
     authentication method."""
@@ -61,8 +103,12 @@ def get_auth_status():
     elif os.path.exists(ACCESS_TOK_PATH):
         msg = f"Credentials file found {ACCESS_TOK_PATH}. Validating token..."
         click.echo(msg)
-        with open(ACCESS_TOK_PATH) as f:
-            access_refresh_dict = json.load(f)
+        access_refresh_dict = parse_credentials_file(ACCESS_TOK_PATH)
+        if access_refresh_dict is None:
+            click.echo(f"Error reading credentials file {ACCESS_TOK_PATH}.")
+            click.echo("The file may be corrupted or contain invalid data.")
+            click.echo("Please login again by running `biolmai login`.")
+            return
         access = access_refresh_dict.get("access")
         refresh = access_refresh_dict.get("refresh")
         resp = validate_user_auth(access=access, refresh=refresh)
@@ -156,8 +202,14 @@ def get_user_auth_header():
     if api_token:
         headers = {"Authorization": f"Token {api_token}"}
     elif os.path.exists(ACCESS_TOK_PATH):
-        with open(ACCESS_TOK_PATH) as f:
-            access_refresh_dict = json.load(f)
+        access_refresh_dict = parse_credentials_file(ACCESS_TOK_PATH)
+        if access_refresh_dict is None:
+            err = (
+                f"Error reading credentials file {ACCESS_TOK_PATH}. "
+                "The file may be corrupted or contain invalid data. "
+                "Please run `biolmai login` to re-authenticate."
+            )
+            raise AssertionError(err)
         access = access_refresh_dict.get("access")
         refresh = access_refresh_dict.get("refresh")
         headers = {

biolmai-0.2.5.dist-info/METADATA

@@ -0,0 +1,134 @@
+Metadata-Version: 2.4
+Name: biolmai
+Version: 0.2.5
+Summary: BioLM Python client
+Home-page: https://github.com/BioLM/py-biolm
+Author: BioLM
+Author-email: BioLM <support@biolm.ai>
+License: Apache Software License 2.0
+Keywords: biolmai
+Classifier: Development Status :: 2 - Pre-Alpha
+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: >=3.7
+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
+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
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+========
+BioLM AI
+========
+
+
+.. image:: https://img.shields.io/pypi/v/biolmai.svg
+        :target: https://pypi.python.org/pypi/biolmai
+
+.. 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 biolmai
+
+Basic usage:
+
+.. code-block:: python
+
+    from biolmai 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 biolmai.client 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

{biolmai-0.2.3.dist-info → biolmai-0.2.5.dist-info}/RECORD

@@ -1,7 +1,7 @@
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+biolmai/__init__.py,sha256=Gt1leXWNTQMB_CEaZP16IqKYBHVx5Rl8gKFmwS_-uSI,693
 biolmai/api.py,sha256=tqxQ-FoZosE88YmLJPQKskjNQdcb5jzZccywGP73lDc,13002
 biolmai/asynch.py,sha256=BVypJhhEEK2Bek2AhqNGn7FIRJehAbJflUdeeslbXFE,9073
-biolmai/auth.py,sha256=flI9KAD90qdXyLDnpJTrc9voKsiK0uWtD2ehsPBn8r4,6329
+biolmai/auth.py,sha256=cjU0ZTJAWTg8IdOYYQ1d-jLXinkYN1EbAyt12lJohgg,8317
 biolmai/biolmai.py,sha256=_NxDPiwT7cnKgnRCRoGZvzBd4jVHJ8DNCuSu3FTznCs,4373
 biolmai/cli.py,sha256=bdb4q8QlN73A6Ttz0e-dBIwoct7PYqy5WSc52jCMIyU,1967
 biolmai/client.py,sha256=nD6sjjnQGinn0tzDVxaKWhsw2AQ3VNhgbsX-Smm9ghc,28310
@@ -10,10 +10,10 @@ biolmai/const.py,sha256=vCSj-itsusZWoLR27DYQSpuq024GQz3-uKJuDUoPF0Y,1153
 biolmai/ltc.py,sha256=al7HZc5tLyUR5fmpIb95hOz5ctudVsc0xzjd_c2Ew3M,49
 biolmai/payloads.py,sha256=BOhEKl9kWkKMXy1YiNw2_eC6MJ4Dn6vKNvkhEBsM7Lw,1735
 biolmai/validate.py,sha256=58XMWrdWoDRmfiNAayWqrYaH3_bjRmEpG_yx6XSjTrM,4168
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-biolmai-0.2.3.dist-info/RECORD,,
+biolmai-0.2.5.dist-info/licenses/AUTHORS.rst,sha256=TB_ACuFPgVmxn1NspYwksTdT6jdZeShcxfafmi-XWKQ,158
+biolmai-0.2.5.dist-info/licenses/LICENSE,sha256=8yt0SdP38I7a3g0zWqZjNe0VSDQhJA4bWLQSqqKtAVg,583
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+biolmai-0.2.5.dist-info/RECORD,,

{biolmai-0.2.3.dist-info → biolmai-0.2.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (79.0.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

biolmai-0.2.3.dist-info/METADATA

@@ -1,76 +0,0 @@
-Metadata-Version: 2.4
-Name: biolmai
-Version: 0.2.3
-Summary: BioLM Python client
-Home-page: https://github.com/BioLM/py-biolm
-Author: BioLM
-Author-email: BioLM <support@biolm.ai>
-License: Apache Software License 2.0
-Keywords: biolmai
-Classifier: Development Status :: 2 - Pre-Alpha
-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: >=3.7
-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
-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
-Dynamic: author
-Dynamic: home-page
-Dynamic: license-file
-Dynamic: requires-python
-
-========
-BioLM AI
-========
-
-
-.. image:: https://img.shields.io/pypi/v/biolmai.svg
-        :target: https://pypi.python.org/pypi/biolmai
-
-.. 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 https://biolm.ai
-
-
-* Free software: Apache Software License 2.0
-* Documentation: https://biolm-ai.readthedocs.io.
-
-
-Features
---------
-
-* TODO
-
-Credits
--------
-
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
-
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage