Merck / Merck/deepbgc

WARNING: Tensor flow backened message when running deepbgc info into the CLI

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Description

Hi,

I currently have deepbgc installed onto a conda environment. The program works but when I run it, I am getting a warning message that looks like the following:

`Using TensorFlow backend.
WARNING 04/10 11:54:59 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:74: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.

WARNING 04/10 11:54:59 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

WARNING 04/10 11:54:59 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.

WARNING 04/10 11:54:59 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:133: The name tf.placeholder_with_default is deprecated. Please use tf.compat.v1.placeholder_with_default instead.

WARNING 04/10 11:54:59 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3445: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version.
Instructions for updating:
Please use rate instead of keep_prob. Rate should be set to rate = 1 - keep_prob.
WARNING 04/10 11:55:00 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.

WARNING 04/10 11:55:00 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:181: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

WARNING 04/10 11:55:00 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:186: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

WARNING 04/10 11:55:00 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:190: The name tf.global_variables is deprecated. Please use tf.compat.v1.global_variables instead.

WARNING 04/10 11:55:00 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:199: The name tf.is_variable_initialized is deprecated. Please use tf.compat.v1.is_variable_initialized instead.

WARNING 04/10 11:55:00 From /EFS/tools/miniconda/envs/deepbgc2/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:206: The name tf.variables_initializer is deprecated. Please use tf.compat.v1.variables_initializer instead.`

Any way to deal with these message flags? I currently have version 1.15.4 of the tensorflow package installed onto the environment and version 0.1.30 of deepbgc installed

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing deepbgc info in the reported conda environment with TensorFlow 1.15.4 and deepbgc 0.1.30, then inspect how the TensorFlow/Keras dependencies are configured. Done means determining whether the deprecation warnings can be eliminated or documenting the supported dependency combination and expected CLI behavior.

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Assessment

Tech stack
python, tensorflow
Domain
cli, machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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