upgrading python packages to more recent versions. Tensorflow version is now 2.11.0

Author: danieldritter

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/train.py

@@ -60,7 +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'])
@@ -79,7 +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:
@@ -90,18 +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/setup.py

@@ -17,7 +17,7 @@
     url="https://github.com/dfci/CellBox",
     packages=['cellbox'],
     python_requires='>=3.6',
-    install_requires=['tensorflow==2.6.2', 'numpy==1.19.5', '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,

requirements.txt

@@ -1,25 +1,48 @@
-absl-py==0.9.0
+absl-py==1.4.0
 astor==0.8.1
-gast==0.2.2
+astunparse==1.6.3
+cachetools==5.3.0
+cellbox==0.3.1
+charset-normalizer==3.0.1
+flatbuffers==23.1.21
+gast==0.4.0
+google-auth==2.16.0
+google-auth-oauthlib==0.4.6
 google-pasta==0.2.0
-grpcio==1.30.0
-h5py==2.10.0
-importlib-metadata==1.7.0
+grpcio==1.51.1
+h5py==3.8.0
+idna==3.4
+importlib-metadata==6.0.0
+keras==2.11.0
 Keras-Applications==1.0.8
 Keras-Preprocessing==1.1.2
-Markdown==3.2.2
-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==2.6.0
-tensorflow==2.6.2
-tensorflow-estimator==2.6.0
-termcolor==1.1.0
-Werkzeug==1.0.1
-wrapt==1.12.1
-zipp==3.1.0
-scipy==1.3.0
+libclang==15.0.6.1
+Markdown==3.4.1
+MarkupSafe==2.1.2
+numpy==1.24.1
+oauthlib==3.2.2
+opt-einsum==3.3.0
+packaging==23.0
+pandas==1.5.3
+protobuf==3.19.6
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+python-dateutil==2.8.2
+pytz==2022.7.1
+requests==2.28.2
+requests-oauthlib==1.3.1
+rsa==4.9
+scipy==1.10.0
+six==1.16.0
+tensorboard==2.11.2
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.11.0
+tensorflow-estimator==2.11.0
+tensorflow-io-gcs-filesystem==0.30.0
+termcolor==2.2.0
+typing_extensions==4.4.0
+urllib3==1.26.14
+Werkzeug==2.2.2
+wrapt==1.14.1
+zipp==3.12.0

requirements_old.txt

@@ -0,0 +1,25 @@
+absl-py==0.9.0
+astor==0.8.1
+gast==0.2.2
+google-pasta==0.2.0
+grpcio==1.30.0
+h5py==2.10.0
+importlib-metadata==1.7.0
+Keras-Applications==1.0.8
+Keras-Preprocessing==1.1.2
+Markdown==3.2.2
+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==2.6.0
+tensorflow==2.6.2
+tensorflow-estimator==2.6.0
+termcolor==1.1.0
+Werkzeug==1.0.1
+wrapt==1.12.1
+zipp==3.1.0
+scipy==1.3.0