np.Inf removed in numpy 2.0 #219
Description
Hi,
I get an error related to numpy when running MS2rescore 3.1.4 installed via conda.
This may be related to these old np.Inf values in the deeplc.py script that are not longer supported by NumPy 2.0
https://github.com/compomics/ms2rescore/blob/8d9f0321437d4c0794b8ce919f957b2663ddb111/ms2rescore/feature_generators/deeplc.py#L134-L136
File "/sfs/9/ws/iizle01-reprocess/runs/lumos_2_global_test/work/58/bf0c61c9ca76b3eca1821b7ac3455a/./ms2rescore_cli.py", line 177, in <module>
sys.exit(main())
^^^^^^
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/sfs/9/ws/iizle01-reprocess/runs/lumos_2_global_test/work/58/bf0c61c9ca76b3eca1821b7ac3455a/./ms2rescore_cli.py", line 173, in main
rescore_idxml(kwargs["psm_file"], kwargs["output_path"], config)
File "/sfs/9/ws/iizle01-reprocess/runs/lumos_2_global_test/work/58/bf0c61c9ca76b3eca1821b7ac3455a/./ms2rescore_cli.py", line 82, in rescore_idxml
rescore(config, psm_list)
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/ms2rescore/core.py", line 79, in rescore
fgen.add_features(psm_list)
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/ms2rescore/feature_generators/deeplc.py", line 182, in add_features
if peptide_rt_diff_dict[peptide]["rt_diff_best"] > rt_diffs_run[i]:
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/ms2rescore/feature_generators/deeplc.py", line 131, in <lambda>
"observed_retention_time_best": np.Inf,
^^^^^^
File "/home-link/iizle01/bin/miniconda3/envs/ms2rescore/lib/python3.12/site-packages/numpy/__init__.py", line 400, in __getattr__
raise AttributeError(
AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead.`