diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1f30bdb..54f7b74 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,9 +22,9 @@ option(INSTALL_DEPENDENCIES
         "Install project dependencies"
         ON)
 
-INCLUDE(modules/pybind11.cmake)
-INCLUDE(modules/marginpolish.cmake)
+INCLUDE(helen/modules/pybind11.cmake)
+INCLUDE(helen/modules/marginpolish.cmake)
 
 # pybind11 to interface
-pybind11_add_module(HELEN ${CMAKE_CURRENT_SOURCE_DIR}/modules/src/pybind_api.cpp)
+pybind11_add_module(HELEN helen/modules/src/pybind_api.cpp)
 
diff --git a/MANIFEST.in b/MANIFEST.in
index 8bf3df5..4e10ee1 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,6 @@
 include CMakeLists.txt build.sh LICENSE MANIFEST.in
-include README.md requirements.txt modules/htslib.cmake modules/pybind11.cmake modules/marginpolish.cmake
+include README.md requirements.txt
+recursive-include helen/*
 recursive-include img/ *
 recursive-include docker/ *
 recursive-include modules/headers *
diff --git a/__init__.py b/helen/__init__.py
similarity index 100%
rename from __init__.py
rename to helen/__init__.py
diff --git a/helen.py b/helen/helen.py
similarity index 97%
rename from helen.py
rename to helen/helen.py
index 44a5217..3a0342a 100644
--- a/helen.py
+++ b/helen/helen.py
@@ -1,12 +1,12 @@
 import argparse
 import sys
 import torch
-from version import __version__
-from modules.python.TextColor import TextColor
-from modules.python.PolishInterface import polish_genome
-from modules.python.CallConsensusInterface import call_consensus
-from modules.python.StitchInterface import perform_stitch
-from modules.python.DownloadModel import download_models
+from helen.version import __version__
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.PolishInterface import polish_genome
+from helen.modules.python.CallConsensusInterface import call_consensus
+from helen.modules.python.StitchInterface import perform_stitch
+from helen.modules.python.DownloadModel import download_models
 
 
 def add_polish_arguments(parser):
diff --git a/helen_train.py b/helen/helen_train.py
similarity index 97%
rename from helen_train.py
rename to helen/helen_train.py
index 33a7b56..19f3a30 100644
--- a/helen_train.py
+++ b/helen/helen_train.py
@@ -1,10 +1,10 @@
 import argparse
 import sys
 import torch
-from version import __version__
-from modules.python.TextColor import TextColor
-from modules.python.TrainInterface import train_interface
-from modules.python.TestInterface import test_interface
+from helen.version import __version__
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.TrainInterface import train_interface
+from helen.modules.python.TestInterface import test_interface
 
 
 def add_train_arguments(parser):
diff --git a/marginpolish.py b/helen/marginpolish.py
similarity index 100%
rename from marginpolish.py
rename to helen/marginpolish.py
diff --git a/modules/__init__.py b/helen/modules/__init__.py
similarity index 100%
rename from modules/__init__.py
rename to helen/modules/__init__.py
diff --git a/modules/headers/local_reassembly/ssw.h b/helen/modules/headers/local_reassembly/ssw.h
similarity index 100%
rename from modules/headers/local_reassembly/ssw.h
rename to helen/modules/headers/local_reassembly/ssw.h
diff --git a/modules/headers/local_reassembly/ssw_cpp.h b/helen/modules/headers/local_reassembly/ssw_cpp.h
similarity index 100%
rename from modules/headers/local_reassembly/ssw_cpp.h
rename to helen/modules/headers/local_reassembly/ssw_cpp.h
diff --git a/modules/headers/pybind_api.h b/helen/modules/headers/pybind_api.h
similarity index 100%
rename from modules/headers/pybind_api.h
rename to helen/modules/headers/pybind_api.h
diff --git a/modules/marginpolish.cmake b/helen/modules/marginpolish.cmake
similarity index 100%
rename from modules/marginpolish.cmake
rename to helen/modules/marginpolish.cmake
diff --git a/modules/pybind11.cmake b/helen/modules/pybind11.cmake
similarity index 100%
rename from modules/pybind11.cmake
rename to helen/modules/pybind11.cmake
diff --git a/modules/python/CallConsensusInterface.py b/helen/modules/python/CallConsensusInterface.py
similarity index 96%
rename from modules/python/CallConsensusInterface.py
rename to helen/modules/python/CallConsensusInterface.py
index 97778b3..ac0db6c 100644
--- a/modules/python/CallConsensusInterface.py
+++ b/helen/modules/python/CallConsensusInterface.py
@@ -1,10 +1,10 @@
 import sys
 import os
 import torch
-from modules.python.TextColor import TextColor
-from modules.python.models.predict_cpu import predict_cpu
-from modules.python.models.predict_gpu import predict_gpu
-from modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.models.predict_cpu import predict_cpu
+from helen.modules.python.models.predict_gpu import predict_gpu
+from helen.modules.python.FileManager import FileManager
 from os.path import isfile, join
 from os import listdir
 """
diff --git a/modules/python/DataStore.py b/helen/modules/python/DataStore.py
similarity index 100%
rename from modules/python/DataStore.py
rename to helen/modules/python/DataStore.py
diff --git a/modules/python/DownloadModel.py b/helen/modules/python/DownloadModel.py
similarity index 89%
rename from modules/python/DownloadModel.py
rename to helen/modules/python/DownloadModel.py
index 2ac955d..71ac367 100644
--- a/modules/python/DownloadModel.py
+++ b/helen/modules/python/DownloadModel.py
@@ -1,8 +1,8 @@
 import wget
 import sys
 import os
-from modules.python.FileManager import FileManager
-from modules.python.TextColor import TextColor
+from helen.modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
 
 
 def download_models(output_dir):
diff --git a/modules/python/FileManager.py b/helen/modules/python/FileManager.py
similarity index 100%
rename from modules/python/FileManager.py
rename to helen/modules/python/FileManager.py
diff --git a/modules/python/Options.py b/helen/modules/python/Options.py
similarity index 100%
rename from modules/python/Options.py
rename to helen/modules/python/Options.py
diff --git a/modules/python/PairwiseAlignment.py b/helen/modules/python/PairwiseAlignment.py
similarity index 95%
rename from modules/python/PairwiseAlignment.py
rename to helen/modules/python/PairwiseAlignment.py
index 3a2893b..c9b1a14 100644
--- a/modules/python/PairwiseAlignment.py
+++ b/helen/modules/python/PairwiseAlignment.py
@@ -1,6 +1,5 @@
 from build import HELEN
-from modules.python.TextColor import TextColor
-from modules.python.Options import StitchOptions
+from helen.modules.python.Options import StitchOptions
 from collections import defaultdict
 
 
diff --git a/modules/python/PolishInterface.py b/helen/modules/python/PolishInterface.py
similarity index 95%
rename from modules/python/PolishInterface.py
rename to helen/modules/python/PolishInterface.py
index fb18e3d..1bbfb30 100644
--- a/modules/python/PolishInterface.py
+++ b/helen/modules/python/PolishInterface.py
@@ -1,9 +1,9 @@
 import sys
 import time
-from modules.python.TextColor import TextColor
-from modules.python.CallConsensusInterface import call_consensus
-from modules.python.StitchInterface import perform_stitch
-from modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.CallConsensusInterface import call_consensus
+from helen.modules.python.StitchInterface import perform_stitch
+from helen.modules.python.FileManager import FileManager
 """
 The Call Consensus method generates base predictions for images generated through MarginPolish. This script reads
 hdf5 files generated by MarginPolish and produces another Hdf5 file that holds all predictions. The generated hdf5 file
diff --git a/modules/python/Stitch.py b/helen/modules/python/Stitch.py
similarity index 98%
rename from modules/python/Stitch.py
rename to helen/modules/python/Stitch.py
index a3e04d7..bd9b4f6 100644
--- a/modules/python/Stitch.py
+++ b/helen/modules/python/Stitch.py
@@ -4,9 +4,9 @@
 import numpy as np
 from collections import defaultdict
 import operator
-from modules.python.TextColor import TextColor
-from modules.python.Options import StitchOptions
-from modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.Options import StitchOptions
+from helen.modules.python.FileManager import FileManager
 from build import HELEN
 import re
 
diff --git a/modules/python/StitchInterface.py b/helen/modules/python/StitchInterface.py
similarity index 96%
rename from modules/python/StitchInterface.py
rename to helen/modules/python/StitchInterface.py
index 4c02b13..ed49eb7 100644
--- a/modules/python/StitchInterface.py
+++ b/helen/modules/python/StitchInterface.py
@@ -3,9 +3,9 @@
 import os
 from os.path import isfile, join
 from os import listdir
-from modules.python.Stitch import Stitch
-from modules.python.TextColor import TextColor
-from modules.python.FileManager import FileManager
+from helen.modules.python.Stitch import Stitch
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.FileManager import FileManager
 """
 The stitch module generates a consensus sequence from all the predictions we generated from call_consensus.py.
 
diff --git a/modules/python/TestInterface.py b/helen/modules/python/TestInterface.py
similarity index 94%
rename from modules/python/TestInterface.py
rename to helen/modules/python/TestInterface.py
index aa6dd2d..0f2880f 100644
--- a/modules/python/TestInterface.py
+++ b/helen/modules/python/TestInterface.py
@@ -3,13 +3,11 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-import torch
-import torch.nn.parallel
-from modules.python.models.test_debug import test
-from modules.python.models.ModelHander import ModelHandler
-from modules.python.TextColor import TextColor
-from modules.python.FileManager import FileManager
-from modules.python.Options import ImageSizeOptions
+from helen.modules.python.models.test_debug import test
+from helen.modules.python.models.ModelHander import ModelHandler
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.FileManager import FileManager
+from helen.modules.python.Options import ImageSizeOptions
 """
 FREEZE THIS BRANCH TO HAVE 1 WINDOW!!
 Train a model and save the model that performs best.
diff --git a/modules/python/TextColor.py b/helen/modules/python/TextColor.py
similarity index 100%
rename from modules/python/TextColor.py
rename to helen/modules/python/TextColor.py
diff --git a/modules/python/TrainInterface.py b/helen/modules/python/TrainInterface.py
similarity index 95%
rename from modules/python/TrainInterface.py
rename to helen/modules/python/TrainInterface.py
index e4dbd84..66cf427 100644
--- a/modules/python/TrainInterface.py
+++ b/helen/modules/python/TrainInterface.py
@@ -2,11 +2,11 @@
 import torch
 
 # Custom generator for our dataset
-from modules.python.models.train import train
-from modules.python.models.train_distributed import train_distributed
-from modules.python.Options import TrainOptions
-from modules.python.FileManager import FileManager
-from modules.python.TextColor import TextColor
+from helen.modules.python.models.train import train
+from helen.modules.python.models.train_distributed import train_distributed
+from helen.modules.python.Options import TrainOptions
+from helen.modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
 
 """
 The train module of HELEN trains a deep neural network to perform a multi-task classification. It takes a set of
diff --git a/modules/python/__init__.py b/helen/modules/python/__init__.py
similarity index 100%
rename from modules/python/__init__.py
rename to helen/modules/python/__init__.py
diff --git a/modules/python/helper/VCF_remove_phase.py b/helen/modules/python/helper/VCF_remove_phase.py
similarity index 100%
rename from modules/python/helper/VCF_remove_phase.py
rename to helen/modules/python/helper/VCF_remove_phase.py
diff --git a/modules/python/models/__init__.py b/helen/modules/python/helper/__init__.py
similarity index 100%
rename from modules/python/models/__init__.py
rename to helen/modules/python/helper/__init__.py
diff --git a/modules/python/helper/assess_summary_analyzer.py b/helen/modules/python/helper/assess_summary_analyzer.py
similarity index 100%
rename from modules/python/helper/assess_summary_analyzer.py
rename to helen/modules/python/helper/assess_summary_analyzer.py
diff --git a/modules/python/helper/csv_analyzer.py b/helen/modules/python/helper/csv_analyzer.py
similarity index 100%
rename from modules/python/helper/csv_analyzer.py
rename to helen/modules/python/helper/csv_analyzer.py
diff --git a/modules/python/helper/hdf5_reader.py b/helen/modules/python/helper/hdf5_reader.py
similarity index 100%
rename from modules/python/helper/hdf5_reader.py
rename to helen/modules/python/helper/hdf5_reader.py
diff --git a/modules/python/helper/quast_sv_extractor.py b/helen/modules/python/helper/quast_sv_extractor.py
similarity index 100%
rename from modules/python/helper/quast_sv_extractor.py
rename to helen/modules/python/helper/quast_sv_extractor.py
diff --git a/modules/python/helper/tensor_analyzer.py b/helen/modules/python/helper/tensor_analyzer.py
similarity index 100%
rename from modules/python/helper/tensor_analyzer.py
rename to helen/modules/python/helper/tensor_analyzer.py
diff --git a/modules/python/helper/test_pairwisealigner.py b/helen/modules/python/helper/test_pairwisealigner.py
similarity index 83%
rename from modules/python/helper/test_pairwisealigner.py
rename to helen/modules/python/helper/test_pairwisealigner.py
index a5721f2..47e1b86 100644
--- a/modules/python/helper/test_pairwisealigner.py
+++ b/helen/modules/python/helper/test_pairwisealigner.py
@@ -1,4 +1,4 @@
-from modules.python.PairwiseAlignment import PairWiseAlignment
+from helen.modules import PairWiseAlignment
 
 a = PairWiseAlignment()
 ref = "TAGTATATACACTATACTATATACTAGTGTATTATACTAGTATATACACTATACTATATACTAGTGTATTATACTAGTATATACACTATACTATATACTAGTGTATATACTAGTATATAC"
diff --git a/modules/python/hyperbandInterface.py b/helen/modules/python/hyperbandInterface.py
similarity index 95%
rename from modules/python/hyperbandInterface.py
rename to helen/modules/python/hyperbandInterface.py
index 246ab8f..0fa8b0f 100644
--- a/modules/python/hyperbandInterface.py
+++ b/helen/modules/python/hyperbandInterface.py
@@ -1,17 +1,14 @@
 from __future__ import print_function
-import argparse
 from hyperopt import hp
 from hyperopt.pyll.stochastic import sample
 import pickle
 import sys
-import os
-import time
 
 # Custom generator for our dataset
-from modules.python.models.hyperband import Hyperband
-from modules.python.TextColor import TextColor
-from modules.python.models.train import train
-from modules.python.Options import TrainOptions
+from helen.modules.python.models.hyperband import Hyperband
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.models.train import train
+from helen.modules.python.Options import TrainOptions
 """
 Tune hyper-parameters of a model using hyperband.
 Input:
diff --git a/modules/python/models/ModelHander.py b/helen/modules/python/models/ModelHander.py
similarity index 98%
rename from modules/python/models/ModelHander.py
rename to helen/modules/python/models/ModelHander.py
index 794c5c3..25e64d5 100644
--- a/modules/python/models/ModelHander.py
+++ b/helen/modules/python/models/ModelHander.py
@@ -1,6 +1,6 @@
 import torch
 import os
-from modules.python.models.TransducerModel import TransducerGRU
+from helen.modules.python.models.TransducerModel import TransducerGRU
 
 
 class ModelHandler:
diff --git a/modules/python/models/TransducerModel.py b/helen/modules/python/models/TransducerModel.py
similarity index 100%
rename from modules/python/models/TransducerModel.py
rename to helen/modules/python/models/TransducerModel.py
diff --git a/helen/modules/python/models/__init__.py b/helen/modules/python/models/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/modules/python/models/dataloader.py b/helen/modules/python/models/dataloader.py
similarity index 96%
rename from modules/python/models/dataloader.py
rename to helen/modules/python/models/dataloader.py
index 2221ebb..4764eeb 100644
--- a/modules/python/models/dataloader.py
+++ b/helen/modules/python/models/dataloader.py
@@ -2,8 +2,8 @@
 import torchvision.transforms as transforms
 import h5py
 import sys
-from modules.python.TextColor import TextColor
-from modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.FileManager import FileManager
 
 
 class SequenceDataset(Dataset):
diff --git a/modules/python/models/dataloader_debug.py b/helen/modules/python/models/dataloader_debug.py
similarity index 97%
rename from modules/python/models/dataloader_debug.py
rename to helen/modules/python/models/dataloader_debug.py
index 2dda85e..04eb613 100644
--- a/modules/python/models/dataloader_debug.py
+++ b/helen/modules/python/models/dataloader_debug.py
@@ -3,8 +3,8 @@
 import h5py
 import sys
 import numpy as np
-from modules.python.TextColor import TextColor
-from modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.FileManager import FileManager
 """
 WARNING: THIS IS A DEBUGGING TOOL INTENDED TO BE USED BY THE DEVELOPERS ONLY.
 """
diff --git a/modules/python/models/dataloader_predict.py b/helen/modules/python/models/dataloader_predict.py
similarity index 96%
rename from modules/python/models/dataloader_predict.py
rename to helen/modules/python/models/dataloader_predict.py
index 83c5ca5..8e25000 100644
--- a/modules/python/models/dataloader_predict.py
+++ b/helen/modules/python/models/dataloader_predict.py
@@ -3,9 +3,9 @@
 import torchvision.transforms as transforms
 import h5py
 import sys
-from modules.python.TextColor import TextColor
-from modules.python.Options import ImageSizeOptions
-from modules.python.FileManager import FileManager
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.Options import ImageSizeOptions
+from helen.modules.python.FileManager import FileManager
 
 
 class SequenceDataset(Dataset):
diff --git a/modules/python/models/hyperband.py b/helen/modules/python/models/hyperband.py
similarity index 99%
rename from modules/python/models/hyperband.py
rename to helen/modules/python/models/hyperband.py
index 9f42d53..926581e 100644
--- a/modules/python/models/hyperband.py
+++ b/helen/modules/python/models/hyperband.py
@@ -3,7 +3,7 @@
 from math import log, ceil
 from time import time, ctime
 import sys
-from modules.python.TextColor import TextColor
+from helen.modules.python.TextColor import TextColor
 import logging
 from datetime import datetime
 """
diff --git a/modules/python/models/predict.py b/helen/modules/python/models/predict.py
similarity index 96%
rename from modules/python/models/predict.py
rename to helen/modules/python/models/predict.py
index 39f8536..255284e 100644
--- a/modules/python/models/predict.py
+++ b/helen/modules/python/models/predict.py
@@ -2,13 +2,12 @@
 import torch
 import torch.nn as nn
 from torch.utils.data import DataLoader
-from modules.python.models.dataloader_predict import SequenceDataset
-from modules.python.TextColor import TextColor
+from helen.modules.python.models.dataloader_predict import SequenceDataset
+from helen.modules.python.TextColor import TextColor
 from tqdm import tqdm
-import numpy as np
-from modules.python.models.ModelHander import ModelHandler
-from modules.python.Options import ImageSizeOptions, TrainOptions
-from modules.python.DataStore import DataStore
+from helen.modules.python.models.ModelHander import ModelHandler
+from helen.modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.DataStore import DataStore
 """
 This script implements the predict method that is used by the call consensus method.
 
diff --git a/modules/python/models/predict_cpu.py b/helen/modules/python/models/predict_cpu.py
similarity index 97%
rename from modules/python/models/predict_cpu.py
rename to helen/modules/python/models/predict_cpu.py
index 45b0821..01067a4 100644
--- a/modules/python/models/predict_cpu.py
+++ b/helen/modules/python/models/predict_cpu.py
@@ -8,11 +8,11 @@
 import torch.nn as nn
 import time
 from torch.utils.data import DataLoader
-from modules.python.models.dataloader_predict import SequenceDataset
-from modules.python.TextColor import TextColor
-from modules.python.models.ModelHander import ModelHandler
-from modules.python.Options import ImageSizeOptions, TrainOptions
-from modules.python.DataStore import DataStore
+from helen.modules.python.models.dataloader_predict import SequenceDataset
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.models.ModelHander import ModelHandler
+from helen.modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.DataStore import DataStore
 """
 This script implements the predict method that is used by the call consensus method.
 
diff --git a/modules/python/models/predict_gpu.py b/helen/modules/python/models/predict_gpu.py
similarity index 97%
rename from modules/python/models/predict_gpu.py
rename to helen/modules/python/models/predict_gpu.py
index dd84bad..4f8c254 100644
--- a/modules/python/models/predict_gpu.py
+++ b/helen/modules/python/models/predict_gpu.py
@@ -7,11 +7,11 @@
 import torch.nn as nn
 import time
 from torch.utils.data import DataLoader
-from modules.python.models.dataloader_predict import SequenceDataset
-from modules.python.TextColor import TextColor
-from modules.python.models.ModelHander import ModelHandler
-from modules.python.Options import ImageSizeOptions, TrainOptions
-from modules.python.DataStore import DataStore
+from helen.modules.python.models.dataloader_predict import SequenceDataset
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.models.ModelHander import ModelHandler
+from helen.modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.DataStore import DataStore
 """
 This script implements the predict method that is used by the call consensus method.
 
diff --git a/modules/python/models/test.py b/helen/modules/python/models/test.py
similarity index 97%
rename from modules/python/models/test.py
rename to helen/modules/python/models/test.py
index b9a6179..990e967 100644
--- a/modules/python/models/test.py
+++ b/helen/modules/python/models/test.py
@@ -5,9 +5,9 @@
 import torch.nn as nn
 from torch.utils.data import DataLoader
 import numpy as np
-from modules.python.models.dataloader import SequenceDataset
-from modules.python.TextColor import TextColor
-from modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.models.dataloader import SequenceDataset
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.Options import ImageSizeOptions, TrainOptions
 """
 This script implements the test method.
 The test method evaluates a trained model on a given test dataset and report various accuracy matrices.
diff --git a/modules/python/models/test_debug.py b/helen/modules/python/models/test_debug.py
similarity index 98%
rename from modules/python/models/test_debug.py
rename to helen/modules/python/models/test_debug.py
index f5c9294..3720977 100644
--- a/modules/python/models/test_debug.py
+++ b/helen/modules/python/models/test_debug.py
@@ -5,9 +5,9 @@
 from torch.utils.data import DataLoader
 import numpy as np
 from tqdm import tqdm
-from modules.python.models.dataloader_debug import SequenceDataset
-from modules.python.TextColor import TextColor
-from modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.models.dataloader_debug import SequenceDataset
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.Options import ImageSizeOptions,
 """
 WARNING: THIS IS A DEBUGGING TOOL INTENDED TO BE USED BY THE DEVELOPERS ONLY.
 """
diff --git a/modules/python/models/train.py b/helen/modules/python/models/train.py
similarity index 97%
rename from modules/python/models/train.py
rename to helen/modules/python/models/train.py
index 5465b73..ed15720 100644
--- a/modules/python/models/train.py
+++ b/helen/modules/python/models/train.py
@@ -5,11 +5,11 @@
 from tqdm import tqdm
 
 from torch.utils.data import DataLoader
-from modules.python.models.dataloader import SequenceDataset
-from modules.python.TextColor import TextColor
-from modules.python.models.test import test
-from modules.python.Options import ImageSizeOptions, TrainOptions
-from modules.python.models.ModelHander import ModelHandler
+from helen.modules.python.models.dataloader import SequenceDataset
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.models.test import test
+from helen.modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.models.ModelHander import ModelHandler
 """
 This script implements the train method of HELEN.
 The train method trains a model on a given set of images and saves model files after each epoch.
diff --git a/modules/python/models/train_distributed.py b/helen/modules/python/models/train_distributed.py
similarity index 97%
rename from modules/python/models/train_distributed.py
rename to helen/modules/python/models/train_distributed.py
index 07b54e7..855416f 100644
--- a/modules/python/models/train_distributed.py
+++ b/helen/modules/python/models/train_distributed.py
@@ -7,11 +7,11 @@
 import torch.multiprocessing as mp
 
 from torch.utils.data import DataLoader
-from modules.python.models.dataloader import SequenceDataset
-from modules.python.TextColor import TextColor
-from modules.python.models.ModelHander import ModelHandler
-from modules.python.models.test import test
-from modules.python.Options import ImageSizeOptions, TrainOptions
+from helen.modules.python.models.dataloader import SequenceDataset
+from helen.modules.python.TextColor import TextColor
+from helen.modules.python.models.ModelHander import ModelHandler
+from helen.modules.python.models.test import test
+from helen.modules.python.Options import ImageSizeOptions,
 
 os.environ['PYTHONWARNINGS'] = 'ignore:semaphore_tracker:UserWarning'
 
diff --git a/modules/src/local_reassembly/ssw.c b/helen/modules/src/local_reassembly/ssw.c
similarity index 100%
rename from modules/src/local_reassembly/ssw.c
rename to helen/modules/src/local_reassembly/ssw.c
diff --git a/modules/src/local_reassembly/ssw_cpp.cpp b/helen/modules/src/local_reassembly/ssw_cpp.cpp
similarity index 100%
rename from modules/src/local_reassembly/ssw_cpp.cpp
rename to helen/modules/src/local_reassembly/ssw_cpp.cpp
diff --git a/modules/src/pybind_api.cpp b/helen/modules/src/pybind_api.cpp
similarity index 100%
rename from modules/src/pybind_api.cpp
rename to helen/modules/src/pybind_api.cpp
diff --git a/helen/version.py b/helen/version.py
new file mode 100644
index 0000000..6561790
--- /dev/null
+++ b/helen/version.py
@@ -0,0 +1 @@
+__version__ = "0.0.15"
diff --git a/setup.py b/setup.py
index 89d0a77..d355520 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 import re
 import sys
 
-from setuptools import setup, Extension
+from setuptools import find_packages, setup, Extension
 from setuptools.command.build_ext import build_ext
 from distutils.version import LooseVersion
 import subprocess
@@ -108,7 +108,7 @@ def get_dependencies():
 
 def get_version():
     version = {}
-    with open("version.py") as fp:
+    with open("./helen/version.py") as fp:
         exec(fp.read(), version)
     return version['__version__']
 
@@ -136,13 +136,7 @@ def get_long_description():
     setup(
         name='helen',
         version=get_version(),
-        packages=['', 'modules/python', 'modules/python/models', 'modules/python/helper'],
-        package_dir={'modules/python': 'modules/python',
-                     'modules/python/models': 'modules/python/models',
-                     'modules/python/helper': 'modules/python/helper'},
-        package_data={
-
-        },
+        packages=find_packages(),
         url='https://github.com/kishwarshafin/helen',
         author=__author__,
         author_email="kishwar.shafin@gmail.com",
@@ -153,10 +147,10 @@ def get_long_description():
         install_requires=python_dependencies,
         entry_points={
             'console_scripts': [
-                '{0} = {0}:main'.format(__pkg_name__),
-                '{0}_train = {0}_train:main'.format(__pkg_name__),
-                'marginpolish = marginpolish:main'.format(__pkg_name__),
-                'marginPolish = marginpolish:main'.format(__pkg_name__)
+                '{0} = {0}.{0}:main'.format(__pkg_name__),
+                '{0}_train = {0}.{0}_train:main'.format(__pkg_name__),
+                'marginpolish = {0}.marginpolish:main'.format(__pkg_name__),
+                'marginPolish = {0}.marginpolish:main'.format(__pkg_name__)
             ]
         },
         ext_modules=[CMakeExtension('HELEN')],
diff --git a/version.py b/version.py
deleted file mode 100644
index 4ae81f3..0000000
--- a/version.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = "0.0.13"