numpy' has no attribute 'float'.

[Rohit-Satyam]

Hi

I am running into an error that says module 'numpy' has no attribute 'float'. How can I fix this?

Versions used

nanopolish version 0.14.0
Python 3.8.18

nanopolish eventalign -t 100 --reads test/RE12_fastq/RE12.fastq --bam results/01_alignment/RE12.filt.sort.bam --genome resources/Sars_cov_2.ASM985889v3.101.transcriptome.fa --samples --print-read-names --scale-events | \
tee eventalign.txt | \
nanocompore eventalign_collapse -t 100 -o results/02_nanopolish/eventalign_collapse --log_level "debug"

lib/python3.8/site-packages/sklearn/utils/multiclass.py:13: DeprecationWarning: Please use `spmatrix` from the `scipy.sparse` namespace, the `scipy.sparse.base` namespace is deprecated.
  from scipy.sparse.base import spmatrix
Traceback (most recent call last):
  File "bin/nanocompore", line 6, in <module>
    from nanocompore.__main__ import main
  File "lib/python3.8/site-packages/nanocompore/__main__.py", line 19, in <module>
    from nanocompore.SampComp import SampComp
  File "lib/python3.8/site-packages/nanocompore/SampComp.py", line 22, in <module>
    from nanocompore.TxComp import txCompare
  File "lib/python3.8/site-packages/nanocompore/TxComp.py", line 16, in <module>
    from sklearn.mixture import GaussianMixture
  File "lib/python3.8/site-packages/sklearn/mixture/__init__.py", line 5, in <module>
    from .gaussian_mixture import GaussianMixture
  File "lib/python3.8/site-packages/sklearn/mixture/gaussian_mixture.py", line 11, in <module>
    from .base import BaseMixture, _check_shape
  File "lib/python3.8/site-packages/sklearn/mixture/base.py", line 13, in <module>
    from .. import cluster
  File "lib/python3.8/site-packages/sklearn/cluster/__init__.py", line 6, in <module>
    from .spectral import spectral_clustering, SpectralClustering
  File "lib/python3.8/site-packages/sklearn/cluster/spectral.py", line 16, in <module>
    from ..neighbors import kneighbors_graph
  File "lib/python3.8/site-packages/sklearn/neighbors/__init__.py", line 16, in <module>
    from .nca import NeighborhoodComponentsAnalysis
  File "lib/python3.8/site-packages/sklearn/neighbors/nca.py", line 21, in <module>
    from ..decomposition import PCA
  File "lib/python3.8/site-packages/sklearn/decomposition/__init__.py", line 11, in <module>
    from .sparse_pca import SparsePCA, MiniBatchSparsePCA
  File "lib/python3.8/site-packages/sklearn/decomposition/sparse_pca.py", line 11, in <module>
    from ..linear_model import ridge_regression
  File "lib/python3.8/site-packages/sklearn/linear_model/__init__.py", line 15, in <module>
    from .least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV,
  File "lib/python3.8/site-packages/sklearn/linear_model/least_angle.py", line 30, in <module>
    method='lar', copy_X=True, eps=np.finfo(np.float).eps,
  File "lib/python3.8/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

[lmulroney]

Hi @Rohit-Satyam,

How did you install nanocompore?

Thanks,
Logan

[Rohit-Satyam]

Hi

I used the following command to install nanocompore

mamba create -n nanocompore -c bioconda -c conda-forge bedparse nextflow nanopolish bedtools samtools minimap2 f5c nanocompore

The error was resolved by downgrading numpy

mamba install -c conda-forge -c bioconda numpy==1.20

[Rohit-Satyam]

But it would be helpful if you could update the code so that users don't have to downgrade it anymore