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heche-psb / wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
https://wgdv2.readthedocs.io/en/latest/
GNU General Public License v3.0
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Error with numpy==1.24.4 #10

Closed taprs closed 10 months ago

taprs commented 1 year ago

Hi Hengchi and thank you for improving the tool!

I installed wgd v2.0.22 into a brand new venv and got an error upon running wgd viz:


Traceback (most recent call last):
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/bin/wgd", line 11, in 
    load_entry_point('wgd', 'console_scripts', 'wgd')()
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/cli.py", line 557, in viz
    _viz(**kwargs)
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/cli.py", line 560, in _viz
    from wgd.viz import elmm_plot, apply_filters, multi_sp_plot, default_plot,all_dotplots,filter_by_minlength,dotplotunitgene,dotplotingene,filter_mingenumber,dotplotingeneoverall
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd/viz.py", line 20, in 
    from sklearn import mixture
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/mixture/__init__.py", line 5, in 
    from ._gaussian_mixture import GaussianMixture
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/mixture/_gaussian_mixture.py", line 11, in 
    from ._base import BaseMixture, _check_shape
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/mixture/_base.py", line 14, in 
    from .. import cluster
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/cluster/__init__.py", line 6, in 
    from ._spectral import spectral_clustering, SpectralClustering
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/cluster/_spectral.py", line 16, in 
    from ..neighbors import kneighbors_graph, NearestNeighbors
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/neighbors/__init__.py", line 17, in 
    from ._nca import NeighborhoodComponentsAnalysis
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/neighbors/_nca.py", line 22, in 
    from ..decomposition import PCA
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/decomposition/__init__.py", line 17, in 
    from .dict_learning import dict_learning
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/decomposition/dict_learning.py", line 5, in 
    from . import _dict_learning  # type: ignore
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/decomposition/_dict_learning.py", line 21, in 
    from ..linear_model import Lasso, orthogonal_mp_gram, LassoLars, Lars
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/linear_model/__init__.py", line 11, in 
    from ._least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV,
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 34, in 
    method='lar', copy_X=True, eps=np.finfo(np.float).eps,
  File "/netscratch/dep_mercier/grp_novikova/software/wgd/wgd_2.0.22/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

So it seems that the installation instructions include the newest version of numpy:

$ pip freeze | grep numpy
numpy==1.24.4

Installing numpy==1.22 into the venv fixed the issue for me. Maybe it's worth adding numpy version limitation into the installation files?

Best, Nikita

heche-psb commented 1 year ago

Hi, Thanks for pointing it out! I didn't change the requirements.txt pertaining to numpy because the pytest behaved weird if I fixed the version of numpy that it couldn't be compatible with multiple versions of python anymore. I will do some extra test to ensure the compatibility properly. Thanks again for your suggestions!