clean

Author: sarahalamdari

README.md

@@ -32,17 +32,17 @@ If you use the code, data, models, or results. please cite our [preprint](https:
 
 ## Installation
 **Requirements**: 
-* PyTorch: 2.2 and above
+* PyTorch: 2.2 and above (2.7 recommended)
 * CUDA 12.0 and above
 * Optionally install Flash Attention 2 following installation instructions here: https://github.com/Dao-AILab/flash-attention
 
-We recommend creating a clean conda environment with Python 3.10.16
+We recommend creating a clean conda environment with Python 3.10
 
 ```bash
-conda create --name dayhoff python=3.10.16
+conda create --name dayhoff python=3.10
 ```
 
-In that new environment, install PyTorch, mamba-ssm, and causal-conv1d. Then install Dayhoff. Optionally, install Flash Attention 2.
+In that new environment, install PyTorch, mamba-ssm, and causal-conv1d, then install Dayhoff. Optionally, install Flash Attention 2.
 
 ```bash
 pip install dayhoff

img/fig1_schematic.png

@@ -4,12 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dayhoff"
-version = "0.0.5"
+version = "0.1.0"
 description = "Python package for generation of protein sequences and evolutionary alignments via discrete diffusion models"
 readme = "README.md"
 requires-python = ">=3.10.16"
 license = "MIT"
-license-files = ["LICEN[CS]E*"]
+license-files = [
+"LICENSE"
+]
 authors = [
     { name = "Kevin K. Yang", email = "kevyan@microsoft.com"},
     { name = "Sarah A. Alamdari", email = "salamdari@microsoft.com"},
@@ -24,12 +26,10 @@ authors = [
     { name = "Neil Tenenholtz", email = "netenenh@microsoft.com"},    
     { name = "Ava P. Amini", email = "ava.amini@microsoft.com"}
 ]
-
-
 classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
-    # "License :: OSI Approved :: MIT License",
+    #"License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent"
 ]
 
@@ -42,6 +42,7 @@ dependencies = [
   "biopython>=1.85",
   "sequence-models>=1.8",
   "scipy>=1.13",
+  "evodiff>=1.1",
 ]
 
 [project.optional-dependencies]
@@ -74,7 +75,6 @@ Repository = "https://github.com/microsoft/dayhoff"
 Issues = "https://github.com/microsoft/dayhoff/issues"
 HuggingFace = "https://huggingface.co/collections/microsoft/dayhoff-atlas-6866d679465a2685b06ee969"
 
-
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["dayhoff*"]