project structure changed for packaging 🔥

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)
 

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 *

helen.py → 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):

helen_train.py → 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):

modules/python/CallConsensusInterface.py → 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
 """

modules/python/DownloadModel.py → 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):

modules/python/PairwiseAlignment.py → 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
 
 

modules/python/PolishInterface.py → 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

modules/python/Stitch.py → 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
 

modules/python/StitchInterface.py → 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.
 

modules/python/TestInterface.py → 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.

modules/python/TrainInterface.py → 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

modules/python/helper/test_pairwisealigner.py → 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"

modules/python/hyperbandInterface.py → 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:

modules/python/models/ModelHander.py → 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:

modules/python/models/dataloader.py → 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):

modules/python/models/dataloader_debug.py → 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.
 """

modules/python/models/dataloader_predict.py → 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):

modules/python/models/hyperband.py → 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
 """

modules/python/models/predict.py → 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.
 

modules/python/models/predict_cpu.py → 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.
 

modules/python/models/predict_gpu.py → 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.
 

modules/python/models/test.py → 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.

modules/python/models/test_debug.py → 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.
 """

modules/python/models/train.py → 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.

modules/python/models/train_distributed.py → 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'
 

helen/version.py

@@ -0,0 +1 @@
+__version__ = "0.0.15"