Merge pull request #43 from VasudhaJha/feature/export-all-files

fix umap imports

README.md

@@ -56,7 +56,7 @@ import matplotlib.pyplot as plt
 from sklearn.cluster import KMeans
 from sklearn.decomposition import PCA
 import phate
-import umap
+import umap.umap_ as umap
 
 data = pd.read_csv('TM_data.csv', header=None,
                    delim_whitespace=False)
@@ -93,7 +93,7 @@ import scipy.io as sio
 import numpy as np
 import genomap.genoDR as gp
 import matplotlib.pyplot as plt
-import umap
+import umap.umap_ as umap
 
 dx = sio.loadmat('reducedData_divseq.mat')
 data=dx['X']
@@ -127,7 +127,7 @@ import matplotlib.pyplot as plt
 from sklearn.cluster import KMeans
 from sklearn.decomposition import PCA
 import phate
-import umap
+import umap.umap_ as umap
 import genomap.genoTraj as gp
 
 # Load data

genomap/genoDR/genoDimReduction.py

@@ -9,7 +9,7 @@
 import scanpy as sc
 from sklearn.feature_selection import VarianceThreshold
 from tensorflow.keras.optimizers import Adam
-import umap
+import umap.umap_ as umap
 
 from genomap.genomap import construct_genomap
 from genomap.utils.ConvIDEC import ConvIDEC

genomap/genoMOI/genoMOI.py

@@ -6,7 +6,7 @@
 """
 
 from tensorflow.keras.optimizers import Adam
-import umap
+import umap.umap_ as umap
 import numpy as np
 import scanorama
 import phate

genomap/genoVis/genoVis.py

@@ -9,7 +9,7 @@
 from genomap.utils.ConvIDEC import ConvIDEC
 from sklearn.feature_selection import VarianceThreshold
 from genomap.genomap import construct_genomap
-import umap
+import umap.umap_ as umap
 from genomap.utils.gTraj_utils import nearest_divisible_by_four
 import scanpy as sc
 import numpy as np

requirements.txt

@@ -18,5 +18,5 @@ scikit-learn
 tensorflow
 torch
 tqdm
-umap
+umap-learn
 

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="genomap",
-    version="1.3.3",
+    version="1.3.4",
     author="Md Tauhidul Islam",
     author_email="[email protected]",
     description="Genomap converts tabular gene expression data into spatially meaningful images.",