Numpy2 ci #429
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Numpy2 ci #429
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This patch fixes the following symptom when running gubbins with Numpy
version 2 and more:
Running joint ancestral reconstruction with pyjar
Traceback (most recent call last):
File "/usr/bin/run_gubbins", line 33, in <module>
sys.exit(load_entry_point('gubbins==3.4', 'console_scripts', 'run_gubbins.py')())
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/share/gubbins/gubbins/run_gubbins.py", line 166, in main
gubbins.common.parse_and_run(parser.parse_args(), parser.description)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/share/gubbins/gubbins/common.py", line 373, in parse_and_run
jar(sequence_names = ordered_sequence_names, # complete polymorphism alignment
~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
base_patterns = base_pattern_bases_array, # array of unique base patterns in alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
...<8 lines>...
verbose = input_args.verbose,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
max_pos = max_pos)
^^^^^^^^^^^^^^^^^^
File "/usr/share/gubbins/gubbins/pyjar.py", line 646, in jar
node_pij = numpy.full((num_nodes,16), numpy.NINF, dtype=numpy.float32)
^^^^^^^^^^
File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__
raise AttributeError(
...<3 lines>...
)
AttributeError: `np.NINF` was removed in the NumPy 2.0 release. Use `-np.inf` instead.
Signed-Off-By: Étienne Mollier <[email protected]>
Fix runtime failures with Numpy ≥ 2
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Adds patch from @emollier (#426) via a branch to run CI checks.