computeMatrix results in AttributeError: module 'numpy' has no attribute 'NAN'

[yonniejon]

Welcome to deepTools GitHub repository! Before opening the issue please check
that the following requirements are met :

• Search whether this issue (or a similar issue) has been solved before
  using the search tab above. Link the previous issue if appropriate below.

• Paste your deepTools version (deeptools --version) and your python
  version (python --version) below.
  deeptools 3.5.5
  computeMatrix 3.5.5
  Python 3.11.2 (main, May 2 2024, 11:59:08) [GCC 12.2.0] on linux

import numpy as np
np.version
'2.1.0'

• Paste the full deepTools command that produces the issue below
  (ignore if you simply spotted the issue in the code/documentation).
  computeMatrix reference-point -S origins_hg19.Q1_or_Q2.bw -R check.bed -o check.bin_size_10000.11000000_before_after.matrix --referencePoint center --binSize 10000 --beforeRegionStartLength 1000000 --afterRegionStartLength 1000000 --missingDataAsZero -p 16

• Paste the output printed on screen from the command that produces the issue
  below (ignore if you simply spotted the issue in the code/documentation).

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/heatmapper.py", line 174, in compute_sub_matrix_wrapper
return heatmapper.compute_sub_matrix_worker(*args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/heatmapper.py", line 379, in compute_sub_matrix_worker
sub_matrix[:] = np.NAN
^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/numpy/init.py", line 414, in getattr
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'NAN'
"""

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

Traceback (most recent call last):
File "/cs/usr/jrosensk/.local/bin/computeMatrix", line 8, in
sys.exit(main())
^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/computeMatrix.py", line 398, in main
hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/heatmapper.py", line 252, in computeMatrix
res, labels = mapReduce.mapReduce([score_file_list, parameters],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/mapReduce.py", line 142, in mapReduce
res = pool.map_async(func, TASKS).get(9999999)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/multiprocessing/pool.py", line 774, in get
raise self._value
AttributeError: module 'numpy' has no attribute 'NAN'

[yonniejon]

This is a duplicate of #1322