Python package

.gitignore

@@ -4,3 +4,5 @@ dev_iDeLUCS/*
 .DS_Store
 Results/
 */__pycache__/*
+build/*
+dist/*

GUI_iDeLUCS.py

@@ -16,17 +16,18 @@
 sys.stdout.write("\r... loading libraries [20%]..........")
 sys.stdout.flush()
 
-from src import models
-from src.utils import SummaryFasta, PlotPolygon, plot_confusion_matrix, \
+from idelucs import LossFunctions, kmers_non_cython, PytorchUtils, ResNet, utils
+from idelucs import models
+from idelucs.utils import SummaryFasta, PlotPolygon, plot_confusion_matrix, \
                       compute_results
-from src.utils_GUI import define_ToolTips
+from idelucs.utils_GUI import define_ToolTips
 import numpy as np
 import torch
 import random
 import pandas as pd
 import os
 import csv
-from src.utils import label_features
+from idelucs.utils import label_features
 sys.stdout.write("\r... loading libraries [50%]..........")
 sys.stdout.flush()
 import umap

README.md

@@ -32,6 +32,18 @@ $ pip install -r requirements.txt
 $ python iDeLUCS.py -h 	
 ```
 
+### (Optional) Using the GUI on Apple Silicon-based Macs
+The current `pip` distribution of `PyQt5` does not support Apple Silicon. However, to make it work we can use the `brew` distribution of `PyQt5` and then point to that distribution from within the `virtualenv`.
+1. Ensure that `homebrew` is installed correctly.
+2. `brew install PyQt5`
+3. Run `brew --prefix PyQt5` to see where `PyQt5` is installed.
+4. Append `/lib/python3.9/site-packages/PyQt5` to the end of the string returned from the previous command.
+5. Navigate to the root `iDeLUCS` folder.
+6. Establish a symbolic link between the `brew` installed `PyQt5` package and the virtual environment's `site-packages` folder.
+    - Example: `ln -s /opt/homebrew/opt/pyqt@5/lib/python3.9/site-packages/PyQt5 /Users/shaneding/Desktop/iDeLUCS/dev_iDeLUCS/lib/python3.10/site-packages`
+
+If the above does not work, try seeing what different versions of python are inside `/opt/homebrew/opt/pyqt@5/lib` and try linking to a different version.
+
 ### Clustering parameters
 
 iDeLUCS assigns a cluster identifier to all the DNA sequences present in a sigle FASTA file. The path to this file must be provided as input in both the CLI and the GUI versions of iDeLUCS. There are several hyperparameters that are required to perform the clustering. The user may use the default values or select a specific one depending on the amount of information that is available about the dataset. 

Unsupervised.py

@@ -8,7 +8,7 @@
 from sklearn import mixture
 from sklearn.cluster import KMeans
 
-from src.utils import SummaryFasta, compute_results, kmersFasta
+from idelucs.utils import SummaryFasta, compute_results, kmersFasta
 import argparse
 import time