Double fix install requires

Also:
- bump version number
- sort imports

Author: JonathanShor

docs/conf.py

@@ -23,7 +23,7 @@
 author = "Adam Gayoso and Jonathan Shor"
 
 # The full version, including alpha/beta/rc tags
-release = "2.5.0"
+release = "2.5.2"
 
 
 # -- General configuration ---------------------------------------------------

doubletdetection/doubletdetection.py

@@ -3,18 +3,18 @@
 import collections
 import warnings
 
+import anndata
 import numpy as np
-from sklearn.utils import check_array
-from sklearn.utils.sparsefuncs_fast import inplace_csr_row_normalize_l1
-from scipy.io import mmread
-from scipy.stats import hypergeom
+import phenograph
 import scipy.sparse as sp_sparse
-from scipy.sparse import csr_matrix
 import tables
 import scanpy as sc
-import anndata
+from scipy.io import mmread
+from scipy.sparse import csr_matrix
+from scipy.stats import hypergeom
+from sklearn.utils import check_array
+from sklearn.utils.sparsefuncs_fast import inplace_csr_row_normalize_l1
 from tqdm.auto import tqdm
-import phenograph
 
 
 def load_10x_h5(file, genome):

doubletdetection/plot.py

@@ -1,12 +1,11 @@
-from sklearn.decomposition import PCA
-import umap
-
 import os
 import warnings
-import numpy as np
-from sklearn.utils import check_array
 
 import matplotlib
+import numpy as np
+import umap
+from sklearn.decomposition import PCA
+from sklearn.utils import check_array
 
 try:
     os.environ["DISPLAY"]

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name="doubletdetection",
-    version="2.5.0",
+    version="2.5.2",
     description="Method to detect and enable removal of doublets from single-cell RNA-sequencing "
     "data",
     url="https://github.com/JonathanShor/DoubletDetection",
@@ -25,9 +25,17 @@
     include_package_data=True,
     packages=["doubletdetection"],
     install_requires=[
-        "phenograph @ https://api.github.com/repos/JonathanShor/PhenoGraph/tarball/v1.6",
+        "numpy>=1.14.2",
+        "pandas>=0.22.0",
+        "scipy>=1.0.1",
+        "scikit-learn",
+        "tables>=3.4.2",
+        "umap-learn>=0.3.7",
         "matplotlib>=3.1",
+        "phenograph @ https://api.github.com/repos/JonathanShor/PhenoGraph/tarball/v1.6",
         "scanpy>=1.4.4",
         "louvain",
+        "tqdm",
+        "anndata",
     ],
 )