ImportError: cannot import name 'false_discovery_control' from 'scipy.stats'

[zhangrengang]

Hi, I get an ImportError as follows:

$ phykit -h
Traceback (most recent call last):
  File "/bin/phykit", line 6, in <module>
    from phykit.phykit import main
  File "/bin/miniconda3/envs/phytop/lib/python3.10/site-packages/phykit/phykit.py", line 15,
in <module>
    from .services.alignment import (
  File "/bin/miniconda3/envs/phytop/lib/python3.10/site-packages/phykit/services/alignment/__init__.py", line 5, in <module>
    from .compositional_bias_per_site import CompositionalBiasPerSite
  File "/bin/miniconda3/envs/phytop/lib/python3.10/site-packages/phykit/services/alignment/compositional_bias_per_site.py", line 1, in <module>
    from scipy.stats import chisquare, false_discovery_control
ImportError: cannot import name 'false_discovery_control' from 'scipy.stats' (/bin/miniconda3/envs/phytop/lib/python3.10/site-packages/scipy/stats/__init__.py)

$ python -c "import scipy; print(scipy.__version__)"
1.9.3

$ python -V
Python 3.10.8

phykit is installed via conda.

[JLSteenwyk]

Hi @zhangrengang,

Thank you so much for your interest in PhyKIT. I apologize for the trouble with installing via Conda.

The PhyKIT team has decided to let bioconda manage conda installation — see here https://anaconda.org/bioconda/phykit — because more downloads were coming from them than us.

Nonetheless, I would be happy to help you troubleshoot.

Here are two options for a path forward:

1. Try installing via PyPi. This is my personal preference. To do so, you can install PhyKIT in a virtual environment as follows:

# create virtual environment
python -m venv venv
# activate virtual environment
source venv/bin/activate
# install phykit
pip install phykit

2. Please provide all commands that you used to install PhyKIT and we can try and diagnose from there.

Thank you again!

Best,

Jacob

[zhangrengang]

Hi @JLSteenwyk ,

Thank you.

The conda command that I used to install PhyKIT is mamba install phykit -n phytop. The channel bioconda is in the conda config file, so is not specified. In the installation process, scipy was not upgraded.

I have installed phykit via pip, but another error raises:

$ miniconda3/envs/rates/bin/pip install phykit
Looking in indexes: http://mirrors.aliyun.com/pypi/simple/
Collecting phykit
  Downloading http://mirrors.aliyun.com/pypi/packages/8b/c4/f77024e49d8dbed1d87ff7fa01c74357ece085685ce95aeb65b18fb11c21/phykit-2.0.1-py2.py3-none-any.whl (69 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 69.7/69.7 kB 1.9 MB/s eta 0:00:00
Collecting numpy>=1.24.0
  Downloading http://mirrors.aliyun.com/pypi/packages/b9/14/78635daab4b07c0930c919d451b8bf8c164774e6a3413aed04a6d95758ce/numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.5/19.5 MB 9.3 MB/s eta 0:00:00
Collecting scikit-learn>=1.4.2
  Downloading http://mirrors.aliyun.com/pypi/packages/2a/9d/d332ec76e2cc442fce98bc43a44e69d3c281e6b4ede6b6db2616dc6fbec6/scikit_learn-1.5.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
(13.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.4/13.4 MB 9.3 MB/s eta 0:00:00
Collecting cython
  Downloading http://mirrors.aliyun.com/pypi/packages/64/42/73859619d9261c2de163f293144064f6df613b0f4e3fcf5cfd0543804f98/Cython-3.0.11-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6
MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 8.9 MB/s eta 0:00:00
Collecting scipy>=1.11.3
  Downloading http://mirrors.aliyun.com/pypi/packages/35/f5/d0ad1a96f80962ba65e2ce1de6a1e59edecd1f0a7b55990ed208848012e0/scipy-1.13.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.6
MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.6/38.6 MB 8.7 MB/s eta 0:00:00
Requirement already satisfied: biopython>=1.82 in ./miniconda3/envs/rates/lib/python3.9/site-packages (from phykit) (1.84)
Collecting joblib>=1.2.0
  Downloading http://mirrors.aliyun.com/pypi/packages/91/29/df4b9b42f2be0b623cbd5e2140cafcaa2bef0759a00b7b70104dcfe2fb51/joblib-1.4.2-py3-none-any.whl (301 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 301.8/301.8 kB 11.8 MB/s eta 0:00:00
Collecting threadpoolctl>=3.1.0
  Downloading http://mirrors.aliyun.com/pypi/packages/4b/2c/ffbf7a134b9ab11a67b0cf0726453cedd9c5043a4fe7a35d1cefa9a1bcfb/threadpoolctl-3.5.0-py3-none-any.whl (18 kB)
Installing collected packages: threadpoolctl, numpy, joblib, cython, scipy, scikit-learn, phykit
  Attempting uninstall: numpy
    Found existing installation: numpy 1.23.3
    Uninstalling numpy-1.23.3:
      Successfully uninstalled numpy-1.23.3
  Attempting uninstall: scipy
    Found existing installation: scipy 1.9.1
    Uninstalling scipy-1.9.1:
      Successfully uninstalled scipy-1.9.1
Successfully installed cython-3.0.11 joblib-1.4.2 numpy-2.0.2 phykit-2.0.1 scikit-learn-1.5.2 scipy-1.13.1 threadpoolctl-3.5.0


$ miniconda3/envs/rates/bin/phykit -h
Traceback (most recent call last):
  File "/media/40T/wlx/zrg/bin/phykit", line 5, in <module>
    from phykit.phykit import main
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/phykit/phykit.py", line 35, in <module>
    from .services.tree import (
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/phykit/services/tree/__init__.py", line 20, in <module>
    from .saturation import Saturation
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/phykit/services/tree/saturation.py", line 9, in <module>
    from sklearn.linear_model import LinearRegression
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/__init__.py", line 84, in <module>
    from .base import clone
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/base.py", line 19, in <module>
    from .utils._estimator_html_repr import _HTMLDocumentationLinkMixin, estimator_html_repr
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/utils/__init__.py", line 11, in <module>
    from ._chunking import gen_batches, gen_even_slices
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/utils/_chunking.py", line 8, in <module>
    from ._param_validation import Interval, validate_params
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/utils/_param_validation.py", line 14, in <module>
    from .validation import _is_arraylike_not_scalar
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/utils/validation.py", line 26, in <module>
    from ..utils._array_api import _asarray_with_order, _is_numpy_namespace, get_namespace
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/utils/_array_api.py", line 11, in <module>
    from .fixes import parse_version
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/sklearn/utils/fixes.py", line 24, in <module>
    import pandas as pd
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/pandas/__init__.py", line 22, in <module>
    from pandas.compat import is_numpy_dev as _is_numpy_dev  # pyright: ignore # noqa:F401
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/pandas/compat/__init__.py", line 18, in <module>
    from pandas.compat.numpy import (
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py", line 4, in <module>
    from pandas.util.version import Version
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/pandas/util/__init__.py", line 2, in <module>
    from pandas.util._decorators import (  # noqa:F401
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/pandas/util/_decorators.py", line 14, in <module>
    from pandas._libs.properties import cache_readonly
  File "/bin/miniconda3/envs/rates/lib/python3.9/site-packages/pandas/_libs/__init__.py", line 13, in <module>
    from pandas._libs.interval import Interval
  File "pandas/_libs/interval.pyx", line 1, in init pandas._libs.interval
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

[JLSteenwyk]

Hi @zhangrengang,

Would it be possible to try installing PhyKIT via PyPi in a python environment outside of the conda environment?

best,

Jacob

[JLSteenwyk]

Hi @zhangrengang,

I am following up about the previous message. Any chance you were able to try and install PhyKIT via PyPi outside of the conda environment?

best,

Jacob

[JLSteenwyk]

Hi @zhangrengang,

I am following up again. If I don't hear back, I will assume the issue has been resolved and close the ticket.

Thank you again for using PhyKIT!

Best,

Jacob

[zhangrengang]

Hi @JLSteenwyk , I did not resolve issuse, but have no time to try. You can close the ticket.