diploSHIC 1.0.4__tar.gz → 1.0.6__tar.gz

{diploSHIC-1.0.4/diploSHIC.egg-info → diploshic-1.0.6}/PKG-INFO

@@ -1,14 +1,22 @@
 Metadata-Version: 2.1
 Name: diploSHIC
-Version: 1.0.4
+Version: 1.0.6
 Summary: diploSHIC
 Home-page: https://github.com/kr-colab/diploSHIC
 Author: Andrew Kern
 Author-email: adkern@uoregon.edu
 License: MIT
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Requires-Dist: scikit-allel
+Requires-Dist: scikit-learn
+Requires-Dist: tensorflow==2.15.0
+Requires-Dist: keras
+Provides-Extra: dev
 
 # diploS/HIC
 This repo contains the implementation for `diploS/HIC` as described in Kern and Schrider (2018; https://doi.org/10.1534/g3.118.200262), along 

{diploSHIC-1.0.4 → diploshic-1.0.6/diploSHIC.egg-info}/PKG-INFO

@@ -1,14 +1,22 @@
 Metadata-Version: 2.1
 Name: diploSHIC
-Version: 1.0.4
+Version: 1.0.6
 Summary: diploSHIC
 Home-page: https://github.com/kr-colab/diploSHIC
 Author: Andrew Kern
 Author-email: adkern@uoregon.edu
 License: MIT
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Requires-Dist: scikit-allel
+Requires-Dist: scikit-learn
+Requires-Dist: tensorflow==2.15.0
+Requires-Dist: keras
+Provides-Extra: dev
 
 # diploS/HIC
 This repo contains the implementation for `diploS/HIC` as described in Kern and Schrider (2018; https://doi.org/10.1534/g3.118.200262), along 

{diploSHIC-1.0.4 → diploshic-1.0.6}/diploSHIC.egg-info/requires.txt

@@ -4,7 +4,7 @@ matplotlib
 pandas
 scikit-allel
 scikit-learn
-tensorflow
+tensorflow==2.15.0
 keras
 
 [dev]

{diploSHIC-1.0.4 → diploshic-1.0.6}/diploshic/diploSHIC

@@ -321,7 +321,7 @@ if argsDict["mode"] in ["train", "predict"]:
     from keras.layers import Dense, Dropout, Activation, Flatten, Input
     from keras.layers import Conv2D, MaxPooling2D, concatenate
     from sklearn.model_selection import train_test_split
-    from keras.preprocessing.image import ImageDataGenerator
+    from tensorflow.keras.preprocessing.image import ImageDataGenerator
     from keras.callbacks import EarlyStopping, ModelCheckpoint
     import keras.backend as K
     import fnmatch
@@ -495,7 +495,7 @@ if argsDict["mode"] == "train":
     model_json = model.to_json()
     with open(outputModel + ".json", "w") as json_file:
         json_file.write(model_json)
-    modWeightsFilepath = outputModel + ".weights.hdf5"
+    modWeightsFilepath = outputModel + ".weights.h5"
     checkpoint = ModelCheckpoint(
         modWeightsFilepath,
         monitor="val_accuracy",
@@ -514,16 +514,16 @@ if argsDict["mode"] == "train":
     start = time.time()
     model.fit(
         datagen.flow(X_train, Y_train, batch_size=32),
-        steps_per_epoch=len(X_train) / 32,
+        steps_per_epoch=int(len(X_train) / 32),
         epochs=epochOption,
         verbose=1,
         callbacks=callbacks_list,
         validation_data=validation_gen.flow(X_valid, Y_valid, batch_size=32),
-        validation_steps=len(X_test) / 32,
+        validation_steps=int(len(X_test) / 32),
     )
     # model.fit(X_train, Y_train, batch_size=32, epochs=100,validation_data=(X_test,Y_test),callbacks=callbacks_list, verbose=1)
     score = model.evaluate(
-        test_gen.flow(X_test, Y_test, batch_size=32), steps=len(Y_test) / 32
+        test_gen.flow(X_test, Y_test, batch_size=32), steps=int(len(Y_test) / 32)
     )
     sys.stderr.write(
         "total time spent fitting and evaluating: %f secs\n"
@@ -534,7 +534,7 @@ if argsDict["mode"] == "train":
     print("diploSHIC loss: %f" % score[0])
     print("diploSHIC accuracy: %f" % score[1])
     if confusionFile:
-        from misc import plot_confusion_matrix
+        from diploshic.misc import plot_confusion_matrix
         import matplotlib.pyplot as plt
 
         plot_confusion_matrix(

{diploSHIC-1.0.4 → diploshic-1.0.6}/setup.py

@@ -9,7 +9,7 @@ shic_stats = Extension("diploshic.shicstats",
                                 "diploshic/utils.c"],
                       )
 setup(name='diploSHIC',
-      version='1.0.4',
+      version='1.0.6',
       description='diploSHIC',
       long_description=long_description,
       long_description_content_type="text/markdown",
@@ -24,7 +24,7 @@ setup(name='diploSHIC',
                         'pandas',
                         'scikit-allel',
                         'scikit-learn',
-                        'tensorflow',
+                        'tensorflow==2.15.0',
                         'keras'],
       scripts=['diploshic/diploSHIC',
               'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py',