add setup.py

setup.py

@@ -7,8 +7,20 @@
  url='https://github.com/YangLabHKUST/SpatialScope',
  author='Xiaomeng Wan ([email protected]), Jiashun Xiao ([email protected])',
  license='GPLv3',
- packages=find_packages(['src','SCGrad']),
- scripts=['src/Cell_Type_Identification.py'],#'src/Nuclei_Segmentation.py', 'Singlet_Doublet_Classification.py', 'Decomposition.py'],
+ packages=find_packages(),
+ scripts=['src/Cell_Type_Identification.py','src/Nuclei_Segmentation.py', 'src/Singlet_Doublet_Classification.py', 'src/Decomposition.py','src/Train_scRef.py'],
  include_package_data=True, # 启用清单文件MANIFEST.in
- exclude_package_date={'':['.gitignore']}
-)
+ exclude_package_date={'':['.gitignore']},
+ install_requires = ['scanpy',
+ 'squidpy',
+ 'stardist',
+ 'tensorflow',
+ 'qpsolvers',
+ 'torch',
+ 'scikit-learn',
+ 'pandas',
+ 'matplotlib',
+ 'scipy',
+ 'ray']
+)
+

src/Cell_Type_Identification.py

@@ -23,9 +23,10 @@
 import warnings
 warnings.filterwarnings('ignore')
 
-# from WaveGrad.utils import configure_logging
-from src.utils import *
-from src.utils_CTI import *
+import sys
+sys.path.append(os.path.dirname(os.path.realpath(__file__)))
+from utils import *
+from utils_CTI import *
 num_cpus = psutil.cpu_count(logical=False) 
 os.environ["PYTHONPATH"] = os.getcwd()+ ":" + os.environ.get("PYTHONPATH", "")
 ray.shutdown()
@@ -277,16 +278,7 @@ def CellTypeIdentification(self, nu = 10, n_neighbo = 10, hs_ST = False, VisiumC
  --SC_Data ./Ckpts_scRefs/Heart_D2/Ref_Heart_sanger_D2.h5ad 
  <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 
  """ 
- def str2bool(v):
- if isinstance(v, bool):
- return v
- if v.lower() in ("yes", "true", "t", "y", "1"):
- return True
- elif v.lower() in ("no", "false", "f", "n", "0"):
- return False
- else:
- raise argparse.ArgumentTypeError("Boolean value expected.")
-
+
  parser = argparse.ArgumentParser(description='simulation sour_sep')
  parser.add_argument('--tissue', type=str, help='tissue name', default=None)
  parser.add_argument('--out_dir', type=str, help='output path', default=None)
@@ -296,7 +288,7 @@ def str2bool(v):
  parser.add_argument('--SC_Data', type=str, help='single cell reference data path', default=None)
  parser.add_argument('--cell_class_column', type=str, help='input cell class label column in scRef file', default = 'cell_type') 
  parser.add_argument('--hs_ST', action="store_true", help='high resolution ST data such as Slideseq, DBiT-seq, and HDST, MERFISH etc.')
- parser.add_argument("--VisiumCellsPlot", type=str2bool, const=True, default=True, nargs="?", help="whether to plot in VisiumCells mode or just scatter plot")
+ parser.add_argument("--VisiumCellsPlot", action="store_true", help="whether to plot in VisiumCells mode or just scatter plot")
  parser.add_argument('--UMI_min_sigma', type=int, help='WarmStart parameter', default=300)
  parser.add_argument('--InitProp', type=str, help='whether to run warmstart', default = None) 
  args = parser.parse_args()

src/Decomposition.py

@@ -9,10 +9,11 @@
 import logging
 import scipy
 import json
+import sys
+sys.path.append(os.path.dirname(os.path.realpath(__file__)))
 
 from SCGrad import SCGradNN, EMAHelper
 
-
 import warnings
 warnings.filterwarnings('ignore')
 

src/Nuclei_Segmentation.py

@@ -8,6 +8,9 @@
 import pandas as pd
 from PIL import Image 
 Image.MAX_IMAGE_PIXELS = 1000000000 
+import sys
+import os
+sys.path.append(os.path.dirname(os.path.realpath(__file__)))
 from utils import *
 
 

src/Singlet_Doublet_Classification.py

@@ -22,7 +22,8 @@
 
 import warnings
 warnings.filterwarnings('ignore')
-
+import sys
+sys.path.append(os.path.dirname(os.path.realpath(__file__)))
 from utils import *
 from utils_CTI import *
 num_cpus = psutil.cpu_count(logical=False) 

src/Train_scRef.py

@@ -12,7 +12,8 @@
 from torch import nn
 from torch.utils.data import DataLoader
 
-
+import sys
+sys.path.append(os.path.dirname(os.path.realpath(__file__)))
 from SCGrad import SCGradNN, EMAHelper
 from utils import configure_logging,ConfigWrapper
 import tqdm

src/utils_CTI.py

@@ -23,7 +23,8 @@
 import seaborn as sns
 import warnings
 warnings.filterwarnings('ignore')
-from src.utils_pyRCTD import *
+sys.path.append(os.path.dirname(os.path.realpath(__file__)))
+from utils_pyRCTD import *
 
 
 def find_neighbors(position, q=0.004, p=1):