Bringing up to date

ejohnson643 · May 3, 2022 · 0e98903 · 0e98903
1 parent 20d3a6e
commit 0e98903
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Showing 3 changed files with 15 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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},