Hi,

I'm trying to install the python package using a Python 3 environment on the cluster. Since I wasn't able to install tensorflow-io-nightly , I changed it to tensorflow-io in the requirements.txt file. When I run pytest to test the installation, there are some errors:

ERROR bear_model/tests/test_core.py - ValueError: numpy.ndarray size changed, may indicate binary incompati...
ERROR bear_model/tests/test_dataloader.py - ValueError: numpy.ndarray size changed, may indicate binary inc...
ERROR bear_model/tests/test_run.py
ERROR bear_model/tests/test_summarize.py

How can I solve it? Thank you in advance

Hi! This error occurs when following the tutorial step by step (after downloading BEAR and installing the required packages).

Start: Stage 1... 2021-09-11 11:12:47.502770
Stage 2... 2021-09-11 11:12:49.422647
Traceback (most recent call last):
  File "summarize.py", line 607, in <module>
    main(args)
  File "summarize.py", line 570, in main
    n_bins = run(args)
  File "summarize.py", line 553, in run
    total_size = stage2(unit2is, args)
  File "summarize.py", line 304, in stage2
    out_size += unit2i.get_size()
  File "summarize.py", line 289, in get_size
    out_size = os.path.getsize(self.out_file)
  File "/home/remita/pyenvs/bear/lib/python3.7/genericpath.py", line 50, in getsize
    return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: 'data/ysd1_kmc_out_0_full_6.tsv'

After investigation, it appears that KMC cannot find the default tmp folder tests/exdata/tmp/ and throws an error in the stderr data/ysd1_kmc_stderr_0_full_6.txt

--- kmc ---
Error: Cannot create file in specified working directory: tests/exdata/tmp/
--- kmc dump ---
Error: Cannot open file data/ysd1_kmc_inter_0_full_6.res.kmc_pre

So in the tutorial, it is better to add that the user must create the default tmp folder tests/exdata/tmp/ or specify an existing folder with the option -t of the script summarize.py.

Thank you.

I see that this uses Python 3, but it might be nice to specify the specific version that will work - especially for when making conda environments compatible.

I also noticed this comment in the setup.py:

NOTE: This file must remain Python 2 compatible for the foreseeable future,

to ensure that we error out properly for people with outdated setuptools

and/or pip.

Not sure if this has any affect on users python version.