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report.txt
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TensorFlow 2.0 Upgrade Script
-----------------------------
Converted 14 files
Detected 9 issues that require attention
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
File: ../../../../../../../DeepTCR/DeepTCR.py
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../../../../../../../DeepTCR/DeepTCR.py:2259:26: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
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File: ../../../../../../../DeepTCR/functions/data_processing.py
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../../../../../../../DeepTCR/functions/data_processing.py:181:4: WARNING: *.save requires manual check. (This warning is only applicable if the code saves a tf.Keras model) Keras model.save now saves to the Tensorflow SavedModel format by default, instead of HDF5. To continue saving to HDF5, add the argument save_format='h5' to the save() function.
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File: ../../../../../../../DeepTCR/functions/Layers.py
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../../../../../../../DeepTCR/functions/Layers.py:12:33: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
../../../../../../../DeepTCR/functions/Layers.py:24:33: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
../../../../../../../DeepTCR/functions/Layers.py:36:33: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
../../../../../../../DeepTCR/functions/Layers.py:48:34: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
../../../../../../../DeepTCR/functions/Layers.py:60:34: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
../../../../../../../DeepTCR/functions/Layers.py:81:29: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
../../../../../../../DeepTCR/functions/Layers.py:154:37: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
================================================================================
Detailed log follows:
================================================================================
================================================================================
Input tree: '../../../../../../../DeepTCR/'
================================================================================
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Processing file '../../../../../../../DeepTCR/DeepTCR.py'
outputting to '../../../../../../../DeepTCR2/DeepTCR.py'
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2251:24: INFO: Renamed 'tf.set_random_seed' to 'tf.compat.v1.set_random_seed'
2255:31: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
2257:25: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
2258:25: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
2259:26: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
2259:26: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
2262:32: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
2265:57: INFO: Renamed 'tf.random_normal' to 'tf.random.normal'
2265:74: INFO: Added keywords to args of function 'tf.shape'
2268:28: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
2269:28: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
2276:41: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2277:41: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2282:45: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2285:55: INFO: Added keywords to args of function 'tf.transpose'
2288:45: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2294:52: INFO: Added keywords to args of function 'tf.argmax'
2297:42: INFO: Added keywords to args of function 'tf.reduce_sum'
2297:132: INFO: Added keywords to args of function 'tf.reduce_sum'
2299:40: INFO: Added keywords to args of function 'tf.reduce_mean'
2303:42: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2304:42: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2309:46: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2312:55: INFO: Added keywords to args of function 'tf.transpose'
2315:46: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
2321:53: INFO: Added keywords to args of function 'tf.argmax'
2324:43: INFO: Added keywords to args of function 'tf.reduce_sum'
2324:136: INFO: Added keywords to args of function 'tf.reduce_sum'
2325:41: INFO: Added keywords to args of function 'tf.reduce_mean'
2384:33: INFO: Added keywords to args of function 'tf.reduce_sum'
2385:33: INFO: Added keywords to args of function 'tf.reduce_mean'
2392:33: INFO: Added keywords to args of function 'tf.reduce_sum'
2393:33: INFO: Added keywords to args of function 'tf.reduce_mean'
2400:34: INFO: Added keywords to args of function 'tf.reduce_mean'
2402:29: INFO: Renamed 'tf.train.AdamOptimizer' to 'tf.compat.v1.train.AdamOptimizer'
2407:37: INFO: Renamed 'tf.train.AdamOptimizer' to 'tf.compat.v1.train.AdamOptimizer'
2413:31: INFO: Renamed 'tf.train.Saver' to 'tf.compat.v1.train.Saver'
2416:12: INFO: Renamed 'tf.reset_default_graph' to 'tf.compat.v1.reset_default_graph'
2417:21: INFO: Renamed 'tf.ConfigProto' to 'tf.compat.v1.ConfigProto'
2420:17: INFO: Renamed 'tf.Session' to 'tf.compat.v1.Session'
2421:25: INFO: Renamed 'tf.global_variables_initializer' to 'tf.compat.v1.global_variables_initializer'
3700:20: INFO: Renamed 'tf.set_random_seed' to 'tf.compat.v1.set_random_seed'
3706:27: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
3708:27: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
3718:36: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
3720:38: INFO: Renamed 'tf.nn.softmax_cross_entropy_with_logits_v2' to 'tf.nn.softmax_cross_entropy_with_logits'
3726:34: INFO: Added keywords to args of function 'tf.reduce_mean'
3733:34: INFO: Added keywords to args of function 'tf.reduce_mean'
3735:34: INFO: Added keywords to args of function 'tf.reduce_mean'
3745:36: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
3747:30: INFO: Added keywords to args of function 'tf.reduce_mean'
3749:25: INFO: Renamed 'tf.train.AdamOptimizer' to 'tf.compat.v1.train.AdamOptimizer'
3752:25: INFO: `name` passed to `name_scope`. Because you may be re-entering an existing scope, it is not safe to convert automatically, the v2 name_scope does not support re-entering scopes by name.
3752:25: INFO: Renamed 'tf.name_scope' to 'tf.compat.v1.name_scope'
3754:48: INFO: Added keywords to args of function 'tf.argmax'
3754:76: INFO: Added keywords to args of function 'tf.argmax'
3755:38: INFO: Added keywords to args of function 'tf.reduce_mean'
3760:27: INFO: Renamed 'tf.train.Saver' to 'tf.compat.v1.train.Saver'
3786:8: INFO: Renamed 'tf.reset_default_graph' to 'tf.compat.v1.reset_default_graph'
3787:17: INFO: Renamed 'tf.ConfigProto' to 'tf.compat.v1.ConfigProto'
3789:13: INFO: Renamed 'tf.Session' to 'tf.compat.v1.Session'
3790:21: INFO: Renamed 'tf.global_variables_initializer' to 'tf.compat.v1.global_variables_initializer'
4622:20: INFO: Renamed 'tf.set_random_seed' to 'tf.compat.v1.set_random_seed'
4629:27: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
4631:27: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
4633:27: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
4638:38: INFO: Renamed 'tf.sparse.matmul' to 'tf.sparse.sparse_dense_matmul'
4644:45: INFO: Renamed 'tf.sparse.matmul' to 'tf.sparse.sparse_dense_matmul'
4651:42: INFO: Renamed 'tf.layers.dropout' to 'tf.compat.v1.layers.dropout'
4652:42: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
4662:36: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
4664:38: INFO: Renamed 'tf.nn.softmax_cross_entropy_with_logits_v2' to 'tf.nn.softmax_cross_entropy_with_logits'
4696:36: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
4698:30: INFO: Added keywords to args of function 'tf.reduce_mean'
4700:28: INFO: Renamed 'tf.trainable_variables' to 'tf.compat.v1.trainable_variables'
4702:29: INFO: Renamed 'tf.train.AdamOptimizer' to 'tf.compat.v1.train.AdamOptimizer'
4704:29: INFO: Renamed 'tf.train.AdamOptimizer' to 'tf.compat.v1.train.AdamOptimizer'
4706:35: INFO: Added keywords to args of function 'tf.gradients'
4717:44: INFO: Added keywords to args of function 'tf.argmax'
4717:72: INFO: Added keywords to args of function 'tf.argmax'
4718:34: INFO: Added keywords to args of function 'tf.reduce_mean'
4723:27: INFO: Renamed 'tf.train.Saver' to 'tf.compat.v1.train.Saver'
4746:8: INFO: Renamed 'tf.reset_default_graph' to 'tf.compat.v1.reset_default_graph'
4747:17: INFO: Renamed 'tf.ConfigProto' to 'tf.compat.v1.ConfigProto'
4749:13: INFO: Renamed 'tf.Session' to 'tf.compat.v1.Session'
4750:21: INFO: Renamed 'tf.global_variables_initializer' to 'tf.compat.v1.global_variables_initializer'
5619:8: INFO: Renamed 'tf.reset_default_graph' to 'tf.compat.v1.reset_default_graph'
5620:17: INFO: Renamed 'tf.ConfigProto' to 'tf.compat.v1.ConfigProto'
5623:20: INFO: Renamed 'tf.train.import_meta_graph' to 'tf.compat.v1.train.import_meta_graph'
5624:16: INFO: Renamed 'tf.get_default_graph' to 'tf.compat.v1.get_default_graph'
5625:13: INFO: Renamed 'tf.Session' to 'tf.compat.v1.Session'
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Processing file '../../../../../../../DeepTCR/__init__.py'
outputting to '../../../../../../../DeepTCR2/__init__.py'
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Processing file '../../../../../../../DeepTCR/phenograph/classify.py'
outputting to '../../../../../../../DeepTCR2/phenograph/classify.py'
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Processing file '../../../../../../../DeepTCR/phenograph/__init__.py'
outputting to '../../../../../../../DeepTCR2/phenograph/__init__.py'
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Processing file '../../../../../../../DeepTCR/phenograph/bruteforce_nn.py'
outputting to '../../../../../../../DeepTCR2/phenograph/bruteforce_nn.py'
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Processing file '../../../../../../../DeepTCR/phenograph/core.py'
outputting to '../../../../../../../DeepTCR2/phenograph/core.py'
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Processing file '../../../../../../../DeepTCR/phenograph/cluster.py'
outputting to '../../../../../../../DeepTCR2/phenograph/cluster.py'
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Processing file '../../../../../../../DeepTCR/functions/plot_func.py'
outputting to '../../../../../../../DeepTCR2/functions/plot_func.py'
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Processing file '../../../../../../../DeepTCR/functions/__init__.py'
outputting to '../../../../../../../DeepTCR2/functions/__init__.py'
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Processing file '../../../../../../../DeepTCR/functions/utils_u.py'
outputting to '../../../../../../../DeepTCR2/functions/utils_u.py'
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Processing file '../../../../../../../DeepTCR/functions/utils_s.py'
outputting to '../../../../../../../DeepTCR2/functions/utils_s.py'
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576:13: INFO: Renamed 'tf.SparseTensorValue' to 'tf.compat.v1.SparseTensorValue'
660:13: INFO: Renamed 'tf.SparseTensorValue' to 'tf.compat.v1.SparseTensorValue'
784:13: INFO: Renamed 'tf.SparseTensorValue' to 'tf.compat.v1.SparseTensorValue'
901:13: INFO: Renamed 'tf.SparseTensorValue' to 'tf.compat.v1.SparseTensorValue'
1001:4: INFO: Renamed 'tf.reset_default_graph' to 'tf.compat.v1.reset_default_graph'
1002:13: INFO: Renamed 'tf.ConfigProto' to 'tf.compat.v1.ConfigProto'
1005:16: INFO: Renamed 'tf.train.import_meta_graph' to 'tf.compat.v1.train.import_meta_graph'
1006:12: INFO: Renamed 'tf.get_default_graph' to 'tf.compat.v1.get_default_graph'
1007:9: INFO: Renamed 'tf.Session' to 'tf.compat.v1.Session'
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Processing file '../../../../../../../DeepTCR/functions/data_processing.py'
outputting to '../../../../../../../DeepTCR2/functions/data_processing.py'
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181:4: WARNING: *.save requires manual check. (This warning is only applicable if the code saves a tf.Keras model) Keras model.save now saves to the Tensorflow SavedModel format by default, instead of HDF5. To continue saving to HDF5, add the argument save_format='h5' to the save() function.
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Processing file '../../../../../../../DeepTCR/functions/Layers.py'
outputting to '../../../../../../../DeepTCR2/functions/Layers.py'
--------------------------------------------------------------------------------
10:19: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
12:33: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
12:33: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
22:19: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
24:33: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
24:33: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
34:19: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
36:33: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
36:33: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
46:20: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
48:34: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
48:34: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
58:20: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
60:34: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
60:34: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
80:15: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
81:29: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
81:29: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
88:9: INFO: Renamed 'tf.variable_scope' to 'tf.compat.v1.variable_scope'
98:15: INFO: Renamed 'tf.layers.conv2d' to 'tf.compat.v1.layers.conv2d'
99:19: INFO: Renamed 'tf.layers.flatten' to 'tf.compat.v1.layers.flatten'
99:37: INFO: Added keywords to args of function 'tf.reduce_max'
100:37: INFO: Added keywords to args of function 'tf.argmax'
102:15: INFO: Renamed 'tf.layers.dropout' to 'tf.compat.v1.layers.dropout'
105:17: INFO: Renamed 'tf.layers.conv2d' to 'tf.compat.v1.layers.conv2d'
107:17: INFO: Renamed 'tf.layers.dropout' to 'tf.compat.v1.layers.dropout'
108:21: INFO: Renamed 'tf.layers.flatten' to 'tf.compat.v1.layers.flatten'
108:39: INFO: Added keywords to args of function 'tf.reduce_max'
110:17: INFO: Renamed 'tf.layers.conv2d' to 'tf.compat.v1.layers.conv2d'
112:17: INFO: Renamed 'tf.layers.dropout' to 'tf.compat.v1.layers.dropout'
113:21: INFO: Renamed 'tf.layers.flatten' to 'tf.compat.v1.layers.flatten'
113:39: INFO: Added keywords to args of function 'tf.reduce_max'
116:19: INFO: Renamed 'tf.layers.flatten' to 'tf.compat.v1.layers.flatten'
124:25: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
130:24: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
135:14: INFO: Renamed 'tf.placeholder_with_default' to 'tf.compat.v1.placeholder_with_default'
136:26: INFO: Renamed 'tf.placeholder_with_default' to 'tf.compat.v1.placeholder_with_default'
137:12: INFO: Renamed 'tf.sparse.placeholder' to 'tf.compat.v1.sparse.placeholder'
138:16: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
139:18: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
140:11: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
141:11: INFO: Renamed 'tf.placeholder' to 'tf.compat.v1.placeholder'
153:13: INFO: Renamed 'tf.variable_scope' to 'tf.compat.v1.variable_scope'
154:37: WARNING: tf.get_variable requires manual check. tf.get_variable returns ResourceVariables by default in 2.0, which have well-defined semantics and are stricter about shapes. You can disable this behavior by passing use_resource=False, or by calling tf.compat.v1.disable_resource_variables().
154:37: INFO: Renamed 'tf.get_variable' to 'tf.compat.v1.get_variable'
229:17: INFO: Renamed 'tf.layers.dropout' to 'tf.compat.v1.layers.dropout'
230:17: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
241:29: INFO: Renamed 'tf.layers.conv2d_transpose' to 'tf.compat.v1.layers.conv2d_transpose'
254:20: INFO: Added keywords to args of function 'tf.shape'
258:17: INFO: Added keywords to args of function 'tf.reduce_mean'
263:26: INFO: Added keywords to args of function 'tf.reduce_sum'
267:16: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
268:16: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
269:16: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
270:34: INFO: Added keywords to args of function 'tf.transpose'
271:11: INFO: Renamed 'tf.nn.softmax_cross_entropy_with_logits_v2' to 'tf.nn.softmax_cross_entropy_with_logits'
273:16: INFO: Added keywords to args of function 'tf.argmax'
274:13: INFO: Added keywords to args of function 'tf.argmax'
275:15: INFO: Added keywords to args of function 'tf.reduce_mean'
280:16: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
281:16: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
282:16: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
283:34: INFO: Added keywords to args of function 'tf.transpose'
284:11: INFO: Added keywords to args of function 'tf.reduce_mean'
287:15: INFO: Added keywords to args of function 'tf.reduce_mean'
292:12: INFO: Added keywords to args of function 'tf.reduce_sum'
292:30: INFO: Renamed 'tf.log' to 'tf.math.log'
295:29: INFO: Renamed 'tf.log' to 'tf.math.log'
295:44: INFO: Added keywords to args of function 'tf.shape'
298:12: INFO: Added keywords to args of function 'tf.linalg.norm'
299:25: INFO: Added keywords to args of function 'tf.reduce_sum'
344:13: INFO: Renamed 'tf.layers.dropout' to 'tf.compat.v1.layers.dropout'
350:13: INFO: Renamed 'tf.variable_scope' to 'tf.compat.v1.variable_scope'
351:23: INFO: Renamed 'tf.layers.dense' to 'tf.compat.v1.layers.dense'
353:11: INFO: Added keywords to args of function 'tf.reduce_mean'
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Processing file '../../../../../../../DeepTCR/functions/act_fun.py'
outputting to '../../../../../../../DeepTCR2/functions/act_fun.py'
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