Tensorflow 2.x Compatibility

[kevin931]

Issue

There appears to be a compatibility issue with tensorflow 2.x because the contrib library has been removed. Here is the error I got:

Traceback (most recent call last):
  File "/home/kevin/anaconda3/envs/cytof/bin/scvis", line 8, in <module>
    from scvis.run import train, map
  File "/home/kevin/anaconda3/envs/cytof/lib/python3.8/site-packages/scvis/run.py", line 9, in <module>
    from scvis.model import SCVIS
  File "/home/kevin/anaconda3/envs/cytof/lib/python3.8/site-packages/scvis/model.py", line 8, in <module>
    from scvis.vae import GaussianVAE
  File "/home/kevin/anaconda3/envs/cytof/lib/python3.8/site-packages/scvis/vae.py", line 2, in <module>
    from scvis.tf_helper import weight_xavier_relu, bias_variable, shape
  File "/home/kevin/anaconda3/envs/cytof/lib/python3.8/site-packages/scvis/tf_helper.py", line 3, in <module>
    X_INIT = tf.contrib.layers.xavier_initializer()
AttributeError: module 'tensorflow' has no attribute 'contrib'

My Setup

• OS: WSL Ubuntu 20.04
• Python version and runtime: 3.8.8 (in a conda envrionment)
• TensorFlow version: 2.4.1
• scvis version: 0.1.0 (bioconda)

Some thoughts on fixes

A trivial, temporary fix will be to change the version requirement in setup.py and the yaml for bioconda distribution. I have not looked into the source code so I cannot comment on how difficult it will be upgrade and maintain compatibility with tensorflow 1.x.