Installation Problem

[iacopogentile]

Hi,

I am trying to install IBSpy on my institute HPC cluster, on a local conda env, however it failed during the test run, reporting this error:

======================================================================
ERROR: test_run_affinity_propagation (test_result_set.TestResultSet)
----------------------------------------------------------------------
multiprocess.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/multiprocess/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 156, in <lambda>
    wrapped_function = lambda x: self._function_window_wrapper_tabix(x, function, chromosome, assembly = assembly)
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 116, in _function_window_wrapper_tabix
    return function(m), chromosome, start, end
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 195, in run_single_run
    raise ex
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 189, in run_single_run
    runs = cluster_by_haplotype(gr, seed=seed, iterations=iterations, dampings=dampings, max_missing=max_missing)
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/window_affinity_propagation.py", line 163, in cluster_by_haplotype
    desc_stats = descriptive_stats(gr)
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/window_affinity_propagation.py", line 116, in descriptive_stats
    ret['skew'] = skew(melted['value'])
  File "/usr/local/lib/python3.9/site-packages/scipy/stats/_axis_nan_policy.py", line 523, in axis_nan_policy_wrapper
    res = hypotest_fun_out(*samples, **kwds)
  File "/usr/local/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 1194, in skew
    m2 = _moment(a, 2, axis, mean=mean)
  File "/usr/local/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 1072, in _moment
    eps = np.finfo(a_zero_mean.dtype).resolution * 10
  File "/usr/local/lib/python3.9/site-packages/numpy/core/getlimits.py", line 516, in __new__
    raise ValueError("data type %r not inexact" % (dtype))
ValueError: data type <class 'numpy.object_'> not inexact
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/src/IBSpy-0.4.4/tests/test_result_set.py", line 165, in test_run_affinity_propagation
    ret = ibspy_results.run_affinity_propagation()
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 213, in run_affinity_propagation
    for best, chromosome, start, end in self.map_window_iterator_tabix(function= run_single_run, chromosome=chr):
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 160, in map_window_iterator_tabix
    newlist = [x for x in res]
  File "/usr/local/src/IBSpy-0.4.4/IBSpy/IBSpy_result_set.py", line 160, in <listcomp>
    newlist = [x for x in res]
  File "/usr/local/lib/python3.9/site-packages/multiprocess/pool.py", line 870, in next
    raise value
ValueError: data type <class 'numpy.object_'> not inexact

======================================================================
FAIL: test_cluster_by_haplotype_long (test_affinity_propagation.TestAffinityPropagation)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/src/IBSpy-0.4.4/tests/test_affinity_propagation.py", line 90, in test_cluster_by_haplotype_long
    self.assertAlmostEqual(best.random_state, 2906402158)
AssertionError: 3181143732 != 2906402158 within 7 places (274741574 difference).

I also tried to use singularity with the def file available (I added a line that allowed to install sklearn via scikit-learn) but outputed the same error.

Best,

Iacopo