diff --git a/EMBEDR/utility.py b/EMBEDR/utility.py index 23a0598..9be1ddf 100644 --- a/EMBEDR/utility.py +++ b/EMBEDR/utility.py @@ -1,7 +1,6 @@ from collections import Counter import numpy as np import os -import pandas as pd from time import time ############################################################################### @@ -40,6 +39,7 @@ def load_data(data_name, load_metadata=True): import scanpy as sc + import pandas as pd metadata = None if data_name.lower() == 'mnist': diff --git a/projects/Figures/Figure_04v1_GlobalParameterSweep.ipynb b/projects/Figures/Figure_04v1_GlobalParameterSweep.ipynb index 930e727..c8c2e43 100644 --- a/projects/Figures/Figure_04v1_GlobalParameterSweep.ipynb +++ b/projects/Figures/Figure_04v1_GlobalParameterSweep.ipynb @@ -59,13 +59,14 @@ "name": "stdout", "output_type": "stream", "text": [ - "(4771, 50)\n" + "(5037, 50)\n" ] } ], "source": [ - "data = sc.read_h5ad(\"../../data/tabula-muris/04_facs_processed_data/FACS/Processed_Marrow.h5ad\")\n", - "sc.tl.leiden(data)\n", + "# data = sc.read_h5ad(\"../../data/tabula-muris/04_facs_processed_data/FACS/Processed_Marrow.h5ad\")\n", + "data = sc.read_h5ad(\"../../data/TabulaMuris/FACS/Processed_Marrow.h5ad\")\n", + "# sc.tl.leiden(data)\n", "\n", "X = data.obsm['X_pca'].astype(float).copy()\n", "print(X.shape)\n", @@ -1338,9 +1339,9 @@ ], "metadata": { "kernelspec": { - "display_name": "EMBEDR_kernel", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "embedr" + "name": "python3" }, "language_info": { "codemirror_mode": { diff --git a/setup.py b/setup.py index 97a53e3..93297dd 100644 --- a/setup.py +++ b/setup.py @@ -263,8 +263,16 @@ def build_extensions(self): "numba", "umap-learn" ], + setup_requires=[ + 'setuptools>=18.0', + 'numpy', + 'cython' + ], extras_require={ "pynndescent": "pynndescent~=0.5.0", + "scanpy": "scanpy>=1.0", + "pandas": "pandas", + "seaborn": "seaborn" }, ext_modules=extensions, cmdclass={"build_ext": MyBuildExt},