dayhoff-tools 1.1.26__tar.gz → 1.1.27__tar.gz

{dayhoff_tools-1.1.26 → dayhoff_tools-1.1.27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.26
+Version: 1.1.27
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -10,22 +10,32 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Provides-Extra: embedders
 Provides-Extra: full
 Requires-Dist: biopython (>=1.84) ; extra == "full"
+Requires-Dist: biopython (>=1.85) ; extra == "embedders"
 Requires-Dist: boto3 (>=1.36.8) ; extra == "full"
 Requires-Dist: docker (>=7.1.0) ; extra == "full"
+Requires-Dist: fair-esm (>=2.0.0) ; extra == "embedders"
 Requires-Dist: fair-esm (>=2.0.0) ; extra == "full"
 Requires-Dist: firebase-admin (>=6.5.0)
 Requires-Dist: h5py (>=3.11.0) ; extra == "full"
+Requires-Dist: h5py (>=3.13.0) ; extra == "embedders"
+Requires-Dist: numpy (>=1.26.4) ; extra == "embedders"
+Requires-Dist: pandas (>=2.2.3) ; extra == "embedders"
 Requires-Dist: pandas (>=2.2.3) ; extra == "full"
 Requires-Dist: pyyaml (>=6.0)
 Requires-Dist: questionary (>=2.0.1)
 Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
 Requires-Dist: requests (>=2.31.0)
+Requires-Dist: sentencepiece (>=0.2.0) ; extra == "embedders"
 Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
 Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
 Requires-Dist: toml (>=0.10)
+Requires-Dist: torch (>=2.4.0) ; extra == "embedders"
+Requires-Dist: tqdm (>=4.67.1) ; extra == "embedders"
 Requires-Dist: transformers (==4.36.2) ; extra == "full"
+Requires-Dist: transformers (>=4.36.2) ; extra == "embedders"
 Requires-Dist: typer (>=0.9.0)
 Description-Content-Type: text/markdown
 

{dayhoff_tools-1.1.26 → dayhoff_tools-1.1.27}/dayhoff_tools/embedders.py

@@ -1,7 +1,6 @@
 import logging
 import os
 import time
-from abc import ABC, abstractmethod
 from typing import Dict, List, Literal, Optional, Tuple, cast
 
 import h5py

{dayhoff_tools-1.1.26 → dayhoff_tools-1.1.27}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.1.26"
+version = "1.1.27"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
@@ -35,6 +35,17 @@ full = [
     "transformers==4.36.2",
     "sentencepiece>=0.2.0",
 ]
+embedders = [
+    "biopython>=1.85",
+    "fair-esm>=2.0.0",
+    "h5py>=3.13.0",
+    "numpy>=1.26.4",
+    "pandas>=2.2.3",
+    "sentencepiece>=0.2.0",
+    "torch>=2.4.0",
+    "tqdm>=4.67.1",
+    "transformers>=4.36.2",
+]
 
 [[tool.uv.index]]
 name = "torch-cuda"