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Illumina / interop

C++ Library to parse Illumina InterOp files
http://illumina.github.io/interop/index.html
GNU General Public License v3.0
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Interop is not compatible with Numpy 2.0.0 #348

Closed Aratz closed 2 months ago

Aratz commented 3 months ago

Numpy 2.0.0 was released a few weeks ago and it breaks interop.

Steps to reproduce

  1. With python 3.10, run pip install interop
  2. Test the installation: python -m interop --test

Expected results

the tests pass

Actual results

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/usr/lib/python3.10/runpy.py", line 187, in _run_module_as_main
    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
  File "/usr/lib/python3.10/runpy.py", line 146, in _get_module_details
    return _get_module_details(pkg_main_name, error)
  File "/usr/lib/python3.10/runpy.py", line 110, in _get_module_details
    __import__(pkg_name)
  File "/tmp/.venv/lib/python3.10/site-packages/interop/__init__.py", line 11, in <module>
    from interop.core import *
  File "/tmp/.venv/lib/python3.10/site-packages/interop/core.py", line 55, in <module>
    import interop.py_interop_run_metrics as interop_metrics
  File "/tmp/.venv/lib/python3.10/site-packages/interop/py_interop_run_metrics.py", line 13, in <module>
    from . import _py_interop_run_metrics
AttributeError: _ARRAY_API not found
Traceback (most recent call last):
  File "/usr/lib/python3.10/runpy.py", line 187, in _run_module_as_main
    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
  File "/usr/lib/python3.10/runpy.py", line 146, in _get_module_details
    return _get_module_details(pkg_main_name, error)
  File "/usr/lib/python3.10/runpy.py", line 110, in _get_module_details
    __import__(pkg_name)
  File "/tmp/.venv/lib/python3.10/site-packages/interop/__init__.py", line 11, in <module>
    from interop.core import *
  File "/tmp/.venv/lib/python3.10/site-packages/interop/core.py", line 55, in <module>
    import interop.py_interop_run_metrics as interop_metrics
  File "/tmp/.venv/lib/python3.10/site-packages/interop/py_interop_run_metrics.py", line 13, in <module>
    from . import _py_interop_run_metrics
ImportError: numpy.core.multiarray failed to import

Proposed solution

As suggested in the error message, numpy should be pinned in the installation script, or interop should be made compatible with numpy 2.0