matchms scores formatter numpy import issues

[hechth]

Link to history: https://umsa.cerit-sc.cz/u/hechth/h/hbm-aplcms-qcs-lc-pos-ramclustr

Seems like some internal issues - maybe the bioconda recipe needs some pins and some newer version of numpy causes problems? Probably applying the same pins as in the poetry file of matchms in the bioconda recipe would make sense.

OpenBLAS blas_thread_init: pthread_create failed for thread 1 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 2 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 3 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 4 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 5 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 6 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 7 of 8: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
  File "/mnt/volume/shared/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/1e58bf51a0e5/matchms_formatter/formatter.py", line 2, in <module>
    from matchms.importing import scores_from_json
  File "/usr/local/lib/python3.9/site-packages/matchms/__init__.py", line 1, in <module>
    from matchms.filtering.SpectrumProcessor import SpectrumProcessor
  File "/usr/local/lib/python3.9/site-packages/matchms/filtering/__init__.py", line 75, in <module>
    from .default_filters import default_filters
  File "/usr/local/lib/python3.9/site-packages/matchms/filtering/default_filters.py", line 1, in <module>
    from matchms.typing import SpectrumType
  File "/usr/local/lib/python3.9/site-packages/matchms/typing.py", line 2, in <module>
    import numpy as np
  File "/usr/local/lib/python3.9/site-packages/numpy/__init__.py", line 141, in <module>
    from . import core
  File "/usr/local/lib/python3.9/site-packages/numpy/core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/usr/local/lib/python3.9/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/usr/local/lib/python3.9/site-packages/numpy/core/overrides.py", line 6, in <module>
    from numpy.core._multiarray_umath import (
KeyboardInterrupt

[hechth]

@zargham-ahmad I think this is solved?

[hechth]

this still persists in version 0.24.0 of the matchms galaxy tools - also, this doesn't seem to be happening on usegalaxy.eu

@bgruening maybe you have some idea what could be the reason this fails? Are you aware of some backwards compatibility issues with older Galaxy version?

[hechth]

Our assumption is that this is somehow related to pandas, numpy or scipy, but we have no absolute idea. One way would be to check out a different version of Galaxy, for example the one used at for UMSA.