Merge pull request #41 from sanderlab/tf2_refactor

TF2 Refactor

binder/requirements.txt

@@ -10,16 +10,16 @@ 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

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):
@@ -59,7 +60,7 @@ def train_substage(model, sess, lr_val, l1_lambda, l2_lambda, n_epoch, n_iter, n
         while True:
             if idx_iter > n_iter or n_unchanged > n_iter_patience:
                 break
-            t0 = time.clock()
+            t0 = time.perf_counter()
             try:
                 _, loss_train_i, loss_train_mse_i = sess.run(
                     (model.op_optimize, model.train_loss, model.train_mse_loss), feed_dict=args.feed_dicts['train_set'])
@@ -78,7 +79,7 @@ def train_substage(model, sess, lr_val, l1_lambda, l2_lambda, n_epoch, n_iter, n
                                                                               n_iter_patience))
             append_record("record_eval.csv",
                           [idx_epoch, idx_iter, loss_train_i, loss_valid_i, loss_train_mse_i,
-                           loss_valid_mse_i, None, time.clock() - t0])
+                           loss_valid_mse_i, None, time.perf_counter() - t0])
             # early stopping
             idx_iter += 1
             if new_loss < best_params.loss_min:
@@ -89,18 +90,18 @@ def train_substage(model, sess, lr_val, l1_lambda, l2_lambda, n_epoch, n_iter, n
                 n_unchanged += 1
 
     # Evaluation on valid set
-    t0 = time.clock()
+    t0 = time.perf_counter()
     sess.run(model.iter_eval.initializer, feed_dict=args.feed_dicts['valid_set'])
     loss_valid_i, loss_valid_mse_i = eval_model(sess, model.iter_eval, (model.eval_loss, model.eval_mse_loss),
                                                 args.feed_dicts['valid_set'], n_batches_eval=args.n_batches_eval)
-    append_record("record_eval.csv", [-1, None, None, loss_valid_i, None, loss_valid_mse_i, None, time.clock() - t0])
+    append_record("record_eval.csv", [-1, None, None, loss_valid_i, None, loss_valid_mse_i, None, time.perf_counter() - t0])
 
     # Evaluation on test set
-    t0 = time.clock()
+    t0 = time.perf_counter()
     sess.run(model.iter_eval.initializer, feed_dict=args.feed_dicts['test_set'])
     loss_test_mse = eval_model(sess, model.iter_eval, model.eval_mse_loss,
                                args.feed_dicts['test_set'], n_batches_eval=args.n_batches_eval)
-    append_record("record_eval.csv", [-1, None, None, None, None, None, loss_test_mse, time.clock() - t0])
+    append_record("record_eval.csv", [-1, None, None, None, None, None, loss_test_mse, time.perf_counter() - t0])
 
     best_params.save()
     args.logger.log("------------------ Substage {} finished!-------------------".format(substage_i))

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/cellbox/version.py

@@ -2,7 +2,7 @@
 This module defines the version of the package
 """
 
-__version__ = '0.3.1'
+__version__ = '0.3.2'
 VERSION = __version__
 
 
@@ -104,14 +104,14 @@ def get_msg():
 
         """        
         version 0.2.3
-        -- June 8, 2020 --
+        -- Jun 8, 2020 --
         * Add support to L2 loss (alone or together with L1, i.e. elastic net)
         * Clean the example configs folder
         """,
 
         """
         version 0.3.0
-        -- June 8, 2020 --
+        -- Jun 8, 2020 --
         Add support for alternative form of perturbation
         * Previous: add u on activity nodes
         * New: fix activity nodes directly
@@ -123,10 +123,16 @@ def get_msg():
 
         """
         version 0.3.1
-        -- Sept 25, 2020 --
+        -- Sep 25, 2020 --
         * Release version for publication
         * Add documentation        
         * Rename package to 'cellbox'        
+        """,
+
+        """
+        version 0.3.2
+        -- Feb 10, 2023 --
+        * Modify CellBox to support TF2     
         """
     ]
     print(
@@ -138,12 +144,12 @@ def get_msg():
         " | |___|  __/ | | |_) | (_) >  <   \n"
         "  \_____\___|_|_|____/ \___/_/\_\  \n"
         "Running CellBox scripts developed in Sander lab\n"
-        "Maintained by Bo Yuan, Judy Shen, and Augustin Luna"
+        "Maintained by Bo Yuan, Judy Shen, and Augustin Luna; contributions by Daniel Ritter"
     )
 
     print(changelog[-1])
     print(
-        "Tutorials and documentations are available at https://github.com/dfci/CellBox\n"
+        "Tutorials and documentations are available at https://github.com/sanderlab/CellBox\n"
         "If you want to discuss the usage or to report a bug, please use the 'Issues' function at GitHub.\n"
         "If you find CellBox useful for your research, please consider citing the corresponding publication.\n"
         "For more information, please email us at [email protected] and [email protected], "

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==2.11.0', 'numpy==1.24.1', 'pandas==1.5.3', 'scipy==1.10.0'],
     tests_require=['pytest', 'pandas', 'numpy', 'scipy'],
     setup_requires=['pytest-runner', "pytest"],
     zip_safe=True,