update dependencies and package up

README.md

@@ -9,14 +9,15 @@ Based this local-search mechanism, a model architecture called Mutation Factoriz
 The dependencies can be set up using the following commands:
 
 ```bash
-conda create -n pex python=3.8 -y
+conda create -n pex python=3.10 -y
 conda activate pex
-conda install pytorch=1.10.2 cudatoolkit=11.3 -c pytorch -y
-conda install numpy=1.19 pandas=1.3 -y
+conda install pytorch pytorch-cuda -c pytorch -c nvidia -y
 conda install -c conda-forge tape_proteins=0.5 -y
-pip install sequence-models==1.2.0
+pip install -e .
 ```
 
+If you run into dependency version issues, try `pip install -r requirements.txt` before running `pip install -e .`.
+
 Clone this repository and download the oracle landscape models by the following commands:
 
 ```bash

algorithm/__init__.py → pex/algorithm/__init__.py

@@ -14,4 +14,4 @@ def get_algorithm(args, model, alphabet, starting_sequence):
 
 for file_name in os.listdir(os.path.dirname(__file__)):
     if file_name.endswith('.py') and not file_name.startswith('_'):
-        importlib.import_module('algorithm.' + file_name[:-3])
+        importlib.import_module('pex.algorithm.' + file_name[:-3])

algorithm/pex.py → pex/algorithm/pex.py

@@ -1,7 +1,7 @@
 import random
 import numpy as np
 from . import register_algorithm
-from utils.seq_utils import hamming_distance, random_mutation
+from pex.utils.seq_utils import hamming_distance, random_mutation
 
 @register_algorithm("pex")
 class ProximalExploration:

landscape/__init__.py → pex/landscape/__init__.py

@@ -28,4 +28,4 @@ def get_landscape(args):
 
 for file_name in os.listdir(os.path.dirname(__file__)):
     if file_name.endswith('.py') and not file_name.startswith('_'):
-        importlib.import_module('landscape.' + file_name[:-3])
+        importlib.import_module('pex.landscape.' + file_name[:-3])

model/__init__.py → pex/model/__init__.py

@@ -18,4 +18,4 @@ def get_model(args, **kwargs):
 
 for file_name in os.listdir(os.path.dirname(__file__)):
     if file_name.endswith('.py') and not file_name.startswith('_'):
-        importlib.import_module('model.' + file_name[:-3])
+        importlib.import_module('pex.model.' + file_name[:-3])

model/mufacnet.py → pex/model/mufacnet.py

@@ -2,7 +2,7 @@
 import torch.nn as nn
 import numpy as np
 from . import torch_model, register_model
-from utils.seq_utils import sequences_to_mutation_sets
+from pex.utils.seq_utils import sequences_to_mutation_sets
 
 class MuFacNet(nn.Module):
     """

model/torch_model.py → pex/model/torch_model.py

@@ -1,6 +1,6 @@
 import torch
 import numpy as np
-from utils.seq_utils import sequences_to_tensor
+from pex.utils.seq_utils import sequences_to_tensor
 
 class TorchModel:
     def __init__(self, args, alphabet, net, **kwargs):

pyproject.toml

@@ -0,0 +1,28 @@
+[project]
+name = "pex"
+dynamic = ["version", "readme", "dependencies", "optional-dependencies"]
+description = "Proximal Exploration for Model-guided Protein Sequence Design"
+authors = [{name = "Zhizhou Ren", email = "[email protected]"}]
+classifiers=[
+    "Development Status :: 3",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+]
+
+[build-system]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.in"]}
+optional-dependencies = {dev = {file = ["requirements-dev.in"]}}
+readme = {file = "README.md"}
+
+[tool.setuptools.packages.find]
+include = ["pex*"]
+
+[tool.setuptools_scm]
+search_parent_directories = true
+version_scheme = "no-guess-dev"
+local_scheme = "node-and-date"
+fallback_version = "0.0.0"

requirements.in

@@ -0,0 +1,3 @@
+numpy
+pandas<=1.5
+sequence-models

requirements.txt

@@ -0,0 +1,20 @@
+#
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
+#
+#    pip-compile requirements.in
+#
+numpy==1.25.2
+    # via
+    #   -r requirements.in
+    #   pandas
+pandas==1.5.0
+    # via -r requirements.in
+python-dateutil==2.8.2
+    # via pandas
+pytz==2023.3
+    # via pandas
+sequence-models==1.6.0
+    # via -r requirements.in
+six==1.16.0
+    # via python-dateutil

run.py

@@ -1,10 +1,10 @@
 import numpy as np
-from landscape import get_landscape, task_collection, landscape_collection
-from algorithm import get_algorithm, algorithm_collection
-from model import get_model, model_collection
-from model.ensemble import ensemble_rules
-from utils.os_utils import get_arg_parser
-from utils.eval_utils import Runner
+from pex.landscape import get_landscape, task_collection, landscape_collection
+from pex.algorithm import get_algorithm, algorithm_collection
+from pex.model import get_model, model_collection
+from pex.model.ensemble import ensemble_rules
+from pex.utils.os_utils import get_arg_parser
+from pex.utils.eval_utils import Runner
 
 def get_args():
     parser = get_arg_parser()