upgrading requirements to tensorflow2 and adding tf.compat.v1 code so the tf1 code still runs against the tf2 binary

Author: danieldritter

cellbox/cellbox/dataset.py

@@ -7,8 +7,9 @@
 import os
 import numpy as np
 import pandas as pd
-import tensorflow as tf
+import tensorflow.compat.v1 as tf
 from scipy import sparse
+tf.disable_v2_behavior()
 
 
 def factory(cfg):

cellbox/cellbox/kernel.py

@@ -3,7 +3,8 @@
 degree of ODEs, and the envelope forms
 """
 
-import tensorflow as tf
+import tensorflow.compat.v1 as tf
+tf.disable_v2_behavior()
 
 
 def get_envelope(args):

cellbox/cellbox/model.py

@@ -4,10 +4,11 @@
 """
 
 import numpy as np
-import tensorflow as tf
+import tensorflow.compat.v1 as tf
 import cellbox.kernel
 from cellbox.utils import loss, optimize
 # import tensorflow_probability as tfp
+tf.disable_v2_behavior()
 
 
 def factory(args):

cellbox/cellbox/train.py

@@ -7,10 +7,11 @@
 import time
 import numpy as np
 import pandas as pd
-import tensorflow as tf
+import tensorflow.compat.v1 as tf
 from tensorflow.compat.v1.errors import OutOfRangeError
 import cellbox
 from cellbox.utils import TimeLogger
+tf.disable_v2_behavior()
 
 
 def train_substage(model, sess, lr_val, l1_lambda, l2_lambda, n_epoch, n_iter, n_iter_buffer, n_iter_patience, args):

cellbox/cellbox/utils.py

@@ -5,9 +5,9 @@
 
 import time
 import hashlib
-import tensorflow as tf
+import tensorflow.compat.v1 as tf
 import json
-
+tf.disable_v2_behavior()
 
 def loss(x_gold, x_hat, W, l1=0, l2=0, weight=1.):
     """evaluate loss"""

cellbox/setup.py

@@ -17,7 +17,7 @@
     url="https://github.com/dfci/CellBox",
     packages=['cellbox'],
     python_requires='>=3.6',
-    install_requires=['tensorflow==1.15.0', 'numpy==1.16.0', 'pandas==0.24.2', 'scipy==1.3.0'],
+    install_requires=['tensorflow==2.6.2', 'numpy==1.19.5', 'pandas==0.24.2', 'scipy==1.3.0'],
     tests_require=['pytest', 'pandas', 'numpy', 'scipy'],
     setup_requires=['pytest-runner', "pytest"],
     zip_safe=True,

requirements.txt

@@ -8,16 +8,16 @@ importlib-metadata==1.7.0
 Keras-Applications==1.0.8
 Keras-Preprocessing==1.1.2
 Markdown==3.2.2
-numpy==1.16.0
+numpy==1.19.5
 opt-einsum==3.2.1
 pandas==0.24.2
 protobuf==3.12.2
 python-dateutil==2.8.1
 pytz==2020.1
 six==1.15.0
-tensorboard==1.15.0
-tensorflow==1.15.0
-tensorflow-estimator==1.15.1
+tensorboard==2.6.0
+tensorflow==2.6.2
+tensorflow-estimator==2.6.0
 termcolor==1.1.0
 Werkzeug==1.0.1
 wrapt==1.12.1

scripts/main.py

@@ -5,11 +5,11 @@
 import os
 import numpy as np
 import pandas as pd
-import tensorflow as tf
+import tensorflow.compat.v1 as tf
 import shutil
 import argparse
 import json
-
+tf.disable_v2_behavior()
 parser = argparse.ArgumentParser(description='CellBox main script')
 parser.add_argument('-config', '--experiment_config_path', required=True, type=str, help="Path of experiment config")
 parser.add_argument('-i', '--working_index', default=0, type=int)