biolmai 0.1.10__tar.gz → 0.2.3__tar.gz

{biolmai-0.1.10 → biolmai-0.2.3}/PKG-INFO

@@ -1,10 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: biolmai
-Version: 0.1.10
-Summary: Python client and SDK for https://biolm.ai
+Version: 0.2.3
+Summary: BioLM Python client
 Home-page: https://github.com/BioLM/py-biolm
-Author: Nikhil Haas
-Author-email: nhaas@biolm.ai
+Author: BioLM
+Author-email: BioLM <support@biolm.ai>
 License: Apache Software License 2.0
 Keywords: biolmai
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -12,15 +12,30 @@ Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.6
-Provides-Extra: aiodns
+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
@@ -59,13 +74,3 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
-
-
-=======
-History
-=======
-
-0.1.0 (2023-09-04)
-------------------
-
-* First release on PyPI.

{biolmai-0.1.10 → biolmai-0.2.3}/biolmai/__init__.py

@@ -1,8 +1,10 @@
 """Top-level package for BioLM AI."""
 __author__ = """Nikhil Haas"""
 __email__ = "nikhil@biolm.ai"
-__version__ = '0.1.10'
+__version__ = '0.2.3'
 
 from biolmai.cls import *
+from biolmai.client import BioLMApi, BioLMApiClient
+from biolmai.biolmai import BioLM
 
 __all__ = []

{biolmai-0.1.10 → biolmai-0.2.3}/biolmai/api.py

@@ -4,8 +4,12 @@ import inspect
 import time
 from functools import lru_cache
 
-import numpy as np
-import pandas as pd
+try:
+    import numpy as np
+    import pandas as pd
+except ImportError:
+    pass
+
 import requests
 from requests.adapters import HTTPAdapter
 from requests.packages.urllib3.util.retry import Retry

biolmai-0.2.3/biolmai/biolmai.py

@@ -0,0 +1,121 @@
+"""Main module."""
+import logging
+
+log = logging.getLogger("biolm_util")
+
+from typing import Optional, Union, List, Any
+from biolmai.client import BioLMApi, is_list_of_lists
+
+
+class BioLM:
+    """
+    Universal client for BioLM API.
+
+    Args:
+        entity (str): The entity name (model, database, calculation, etc).
+        action (str): The action to perform (e.g., 'generate', 'encode', 'predict', 'search', 'finetune').
+        type (str): The type of item (e.g., 'sequence', 'pdb', 'fasta_str').
+        item (Union[Any, List[Any]]): The item(s) to process.
+        params (Optional[dict]): Optional parameters for the action.
+        raise_httpx (bool): Whether to raise HTTPX errors.
+        stop_on_error (bool): Stop on first error if True.
+        output (str): 'memory' or 'disk'.
+        file_path (Optional[str]): Output file path if output='disk'.
+        api_key (Optional[str]): API key for authentication.
+    """
+    def __new__(
+        cls,
+        *,
+        entity: str,
+        action: str,
+        type: Optional[str] = None,
+        items: Union[Any, List[Any]],
+        params: Optional[dict] = None,
+        api_key: Optional[str] = None,
+        **kwargs
+    ):
+        self = super().__new__(cls)
+        self.entity = entity
+        self.action = action
+        self.type = type
+        self.items = items
+        self.params = params
+        self.api_key = api_key
+        self._class_kwargs = kwargs
+        return self.run()
+
+    def run(self) -> Any:
+        """
+        Run the specified action on the entity with the given item(s).
+        Returns the result(s), unpacked if a single item was provided.
+        """
+        # if not self.items:
+            # return self.items
+
+        # Always pass a list of items to BioLMModel
+        if isinstance(self.items, list):
+            items = self.items
+        else:
+            items = [self.items]
+
+        is_lol, first_n, rest_iter = is_list_of_lists(items, check_n=10)
+        if is_lol:
+            for batch in first_n:
+                if not all(isinstance(x, dict) for x in batch):
+                    raise ValueError("All items in each batch must be dicts when passing a list of lists.")
+            if self.type is not None:
+                raise ValueError("Do not specify `type` when passing a list of lists of dicts for `items`.")
+            items_dicts = list(first_n) + list(rest_iter)
+        elif all(isinstance(v, dict) for v in items):
+            items_dicts = items
+        else:
+            if self.type is None:
+                raise ValueError("If `items` are not dicts, `type` must be specified.")
+            items_dicts = [{self.type: v} for v in items]
+
+        unwrap_single = self._class_kwargs.pop('unwrap_single', True)
+
+        # Instantiate BioLMModel with correct settings
+        # Need these for the `action` method on BioLMApi; other kwargs to BioLMApi init
+        action_kwargs = {k: v for k, v in dict(
+            stop_on_error=self._class_kwargs.pop('stop_on_error', None),
+            output=self._class_kwargs.pop('output', None),
+            file_path=self._class_kwargs.pop('file_path', None),
+        ).items() if v is not None}
+
+        model = BioLMApi(
+            self.entity,
+            api_key=self.api_key,
+            unwrap_single=unwrap_single,
+            **self._class_kwargs,
+        )
+
+        # Map action to method
+        action_map = {
+            'generate': model.generate,
+            'predict': model.predict,
+            'encode': model.encode,
+            'search': getattr(model, 'search', None),
+            'finetune': getattr(model, 'finetune', None),
+            'lookup': model.lookup,
+        }
+        if self.action not in action_map or action_map[self.action] is None:
+            raise ValueError(f"Action '{self.action}' is not amongst the available actions {', '.join(action_map.keys())}.")
+
+        # Prepare kwargs for the method
+        method = action_map[self.action]
+        kwargs = {
+            'items': items_dicts,
+            'params': self.params,
+        }
+        kwargs.update(action_kwargs)
+        # Remove None values
+        kwargs = {k: v for k, v in kwargs.items() if v is not None}
+
+        # Call the method
+        result = method(**kwargs)
+
+        return result
+
+# Example usage:
+# result = BioLM(entity="esmfold", action="predict", type="sequence", item="MKT...").run()