ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

[shappiron]

Describe the bug I created new conda environment and installed only scikit-fda (with all needed requirements). When I try to import skfda I got:

ValueError                                Traceback (most recent call last)
<ipython-input-1-7e246c0798e0> in <module>
      4 #import matplotlib.pyplot as plt
      5 
----> 6 import skfda
      7 from skfda.datasets import fetch_growth
      8 from skfda.exploratory.visualization import FPCAPlot

~/anaconda3/lib/python3.7/site-packages/skfda/__init__.py in <module>
     35 from .representation._functional_data import concatenate
     36 
---> 37 from . import representation, datasets, preprocessing, exploratory, misc, ml, \
     38     inference
     39 

~/anaconda3/lib/python3.7/site-packages/skfda/datasets/__init__.py in <module>
     13     fetch_weather,
     14 )
---> 15 from ._samples_generators import (
     16     make_gaussian,
     17     make_gaussian_process,

~/anaconda3/lib/python3.7/site-packages/skfda/datasets/_samples_generators.py in <module>
     10 from .. import FDataGrid
     11 from .._utils import RandomStateLike, _cartesian_product, _to_grid_points
---> 12 from ..misc import covariances
     13 from ..preprocessing.registration import normalize_warping
     14 from ..representation._typing import DomainRangeLike, GridPointsLike

~/anaconda3/lib/python3.7/site-packages/skfda/misc/__init__.py in <module>
----> 1 from . import covariances, kernels, lstsq, metrics, operators, regularization
      2 from ._math import (
      3     cumsum,
      4     exp,
      5     inner_product,

~/anaconda3/lib/python3.7/site-packages/skfda/misc/covariances.py in <module>
      7 import sklearn.gaussian_process.kernels as sklearn_kern
      8 
----> 9 from ..exploratory.visualization._utils import _create_figure, _figure_to_svg
     10 
     11 

~/anaconda3/lib/python3.7/site-packages/skfda/exploratory/__init__.py in <module>
      1 from . import depth
----> 2 from . import outliers
      3 from . import stats
      4 from . import visualization

~/anaconda3/lib/python3.7/site-packages/skfda/exploratory/outliers/__init__.py in <module>
      4 )
      5 from ._iqr import IQROutlierDetector
----> 6 from ._outliergram import OutliergramOutlierDetector
      7 from .neighbors_outlier import LocalOutlierFactor

~/anaconda3/lib/python3.7/site-packages/skfda/exploratory/outliers/_outliergram.py in <module>
      6 from ...representation import FDataGrid
      7 from ..depth._depth import ModifiedBandDepth
----> 8 from ..stats import modified_epigraph_index
      9 
     10 

~/anaconda3/lib/python3.7/site-packages/skfda/exploratory/stats/__init__.py in <module>
----> 1 from ._stats import (
      2     cov,
      3     depth_based_median,
      4     geometric_median,
      5     gmean,

~/anaconda3/lib/python3.7/site-packages/skfda/exploratory/stats/_stats.py in <module>
      8 from scipy.stats import rankdata
      9 
---> 10 from ...misc.metrics import Metric, l2_distance, l2_norm
     11 from ...representation import FData, FDataGrid
     12 from ..depth import Depth, ModifiedBandDepth

~/anaconda3/lib/python3.7/site-packages/skfda/misc/metrics/__init__.py in <module>
      1 """Metrics, norms and related utilities."""
      2 
----> 3 from ._elastic_metrics import (
      4     amplitude_distance,
      5     fisher_rao_distance,

~/anaconda3/lib/python3.7/site-packages/skfda/misc/metrics/_elastic_metrics.py in <module>
      6 import scipy.integrate
      7 
----> 8 from ...preprocessing.registration import (
      9     ElasticRegistration,
     10     normalize_warping,

~/anaconda3/lib/python3.7/site-packages/skfda/preprocessing/__init__.py in <module>
----> 1 from . import registration
      2 from . import smoothing
      3 from . import dim_reduction

~/anaconda3/lib/python3.7/site-packages/skfda/preprocessing/registration/__init__.py in <module>
      5 """
      6 
----> 7 from . import elastic, validation
      8 from ._landmark_registration import (
      9     landmark_registration,

~/anaconda3/lib/python3.7/site-packages/skfda/preprocessing/registration/elastic.py in <module>
      9 
     10 import scipy.integrate
---> 11 from fdasrsf.utility_functions import optimum_reparam
     12 
     13 from ... import FDataGrid

~/anaconda3/lib/python3.7/site-packages/fdasrsf/__init__.py in <module>
     20 del sys
     21 
---> 22 from .time_warping import fdawarp, align_fPCA, align_fPLS, pairwise_align_bayes, pairwise_align_functions
     23 from .time_warping import pairwise_align_bayes_infHMC
     24 from .plot_style import f_plot, rstyle, plot_curve, plot_reg_open_curve, plot_geod_open_curve, plot_geod_close_curve

~/anaconda3/lib/python3.7/site-packages/fdasrsf/time_warping.py in <module>
      7 import numpy as np
      8 import matplotlib.pyplot as plt
----> 9 import fdasrsf.utility_functions as uf
     10 import fdasrsf.bayesian_functions as bf
     11 import fdasrsf.fPCA as fpca

~/anaconda3/lib/python3.7/site-packages/fdasrsf/utility_functions.py in <module>
     19 from joblib import Parallel, delayed
     20 import numpy.random as rn
---> 21 import optimum_reparamN2 as orN2
     22 import optimum_reparam_N as orN
     23 import cbayesian as bay

src/optimum_reparamN2.pyx in init optimum_reparamN2()

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

To Reproduce import skfda

import skfda
...

Version information

• OS: Linux
• Python version: 3.8
• scikit-fda version: 0.7.1

[vnmabus]

I think this is the same as https://github.com/jdtuck/fdasrsf_python/issues/20

Please, check if the workaround suggested in that issue works for you.

[shappiron]

Thank you for the answer. I handle the problem by downgrading python to version 3.7. The other required packages are following versions: numpy==1.21.5 numba==0.55.1 matplotlib==3.5.1 scipy==1.7.3 setuptools==50.3.0.post20201006 Cython==0.29.27 scikit-learn==1.0.2 multimethod==1.7 findiff==0.8.9 fdasrsf==2.3.7