ModuleNotFoundError: No module named 'tensorflow.keras'

[xiekunwhy]

Hi,

I install helixer following https://github.com/weberlab-hhu/Helixer/blob/72bcb2331525f9e951a6d155b7ce67c07f8e4ca0/docs/dev_install.md, after everything was done, I got following error when I trying to run Helixer.py. Do you known how to fixed this error?

Helixer.py -h
/public2/home/sl_qybio/sl_qybio/miniforge3/envs/helixer/bin/Helixer.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('helixer==0.3.1')
2024-06-07 16:47:36.280351: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2024-06-07 16:47:36.321215: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Traceback (most recent call last):
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/helixer/bin/Helixer.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/Helixer/Helixer.py", line 14, in <module>
    from helixer.prediction.HybridModel import HybridModel
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/Helixer/helixer/prediction/HybridModel.py", line 4, in <module>
    from tensorflow.keras.models import Model
ModuleNotFoundError: No module named 'tensorflow.keras'

Best,
Kun

[xiekunwhy]

down tensorflow to 2.15.0 solved this problem.

[alisandra]

glad to here it.

That said, I can only recommend the simplicity of running via apptainer (providing Helixer and HelixerPost both; and already available on most hpc systems).

Nevertheless if install is necessary:
https://apptainer.org/docs/admin/main/installation.html

Then run as follows (except replacing 'singularity' with 'apptainer'): https://github.com/gglyptodon/helixer-docker?tab=readme-ov-file#running-via-singularity