Problem with importing the predict module

[fenghua0811]

Dear MHCnuggets maintainers,

When I install mhcnuggets,I use command
"from mhcnuggets.src.predict import predict"
show "bash: from: Command not found..."
then I use command
"which mhcnuggets.src.predict"
show "/usr/bin/which: no mhcnuggets.src.predict in ..."
What is the reason for this, is there a problem with which part of me?

Thanks
Faustina

[XiaoshanShao]

All the example code we have are supposed to be operated in python not bash. Looks like you are trying to use python code in bash

[fenghua0811]

Thanks for your help, looking at your other answers, I found that mhcnuggets needs to run when python=2, but when I install with pip in the environment of python=2.7 in conda, I will have the problem of low version：

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-wli8dl/biopython/
You are using pip version 9.0.1, however version 23.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Then I tried to download mhcnuggets at python=3 and copy it to python=2.7, and this problem occurred：

Python 2.7.18 |Anaconda, Inc.| (default, Jun  4 2021, 14:47:46) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from mhcnuggets.src.predict import predict
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "mhcnuggets/src/predict.py", line 10, in <module>
    import numpy as np
ImportError: No module named numpy

When I installed numpy, I found that I already had this module：

$ python2.7 -m pip install numpy
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Requirement already satisfied: numpy in /home/fenghua/software/envs/mhcnuggets/lib/python2.7/site-packages (1.24.3)
ERROR: Package 'numpy' requires a different Python: 2.7.18 not in '>=3.8'

Do you know what the reason is?

[XiaoshanShao]

We have already updated all the codes to be used in python 3 environment, so you do not need to install it in the python 2.7 environment. If you want to run it in python 2.7, you will need use older versions of all dependencies, including numpy and tensorflow. And not sure what you mean by copying mhcnuggets to python 2.7, did you do a github download or pip install? I would strongly suggest you do a pip install.

[fenghua0811]

When I

 from mhcnuggets.src.predict import predict

This situation has occurred

2023-07-17 11:04:20.390134: I tensorflow/core/util/port.cc:110] 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`.
2023-07-17 11:04:20.392739: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-07-17 11:04:20.445762: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-07-17 11:04:20.446367: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-07-17 11:04:21.066302: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT

After searching for tensort, I found that NVIDIA drivers are required, if I don't have an NVIDIA graphics card, is there any other way to use this software?