From ea97c21ef788e57f0856f214db083de777c451b5 Mon Sep 17 00:00:00 2001
From: Vasudha Jha <reachvasudha27@gmail.com>
Date: Mon, 24 Jul 2023 13:32:07 -0700
Subject: [PATCH] fix umap imports

---
 README.md                          | 6 +++---
 genomap/genoDR/genoDimReduction.py | 2 +-
 genomap/genoMOI/genoMOI.py         | 2 +-
 genomap/genoVis/genoVis.py         | 2 +-
 requirements.txt                   | 2 +-
 setup.py                           | 2 +-
 6 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index d1ab89a..b993f9c 100644
--- a/README.md
+++ b/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
diff --git a/genomap/genoDR/genoDimReduction.py b/genomap/genoDR/genoDimReduction.py
index 1ba3e74..52b1255 100644
--- a/genomap/genoDR/genoDimReduction.py
+++ b/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
diff --git a/genomap/genoMOI/genoMOI.py b/genomap/genoMOI/genoMOI.py
index 691168d..31859e6 100644
--- a/genomap/genoMOI/genoMOI.py
+++ b/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
diff --git a/genomap/genoVis/genoVis.py b/genomap/genoVis/genoVis.py
index f53ebf9..25278dc 100644
--- a/genomap/genoVis/genoVis.py
+++ b/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
diff --git a/requirements.txt b/requirements.txt
index 550191a..9bb771a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,5 +18,5 @@ scikit-learn
 tensorflow
 torch
 tqdm
-umap
+umap-learn
 
diff --git a/setup.py b/setup.py
index ad9566b..5f65a8c 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setup(
     name="genomap",
-    version="1.3.3",
+    version="1.3.4",
     author="Md Tauhidul Islam",
     author_email="tauhid@stanford.edu",
     description="Genomap converts tabular gene expression data into spatially meaningful images.",