Failed import

[oseynnes]

Hello. I am not sure this is a bug related to Pingouin or my environment (this is why I did not start a new issue) but I get a type error when importing:

File "<ipython-input-5-7fb0a28d427d>", line 6, in <module> import pingouin as pg File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/pingouin/__init__.py", line 7, in <module> from .equivalence import * File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/pingouin/equivalence.py", line 5, in <module> from pingouin.parametric import ttest File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/pingouin/parametric.py", line 7, in <module> import pandas_flavor as pf File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/pandas_flavor/__init__.py", line 8, in <module> from .xarray import ( File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/pandas_flavor/xarray.py", line 2, in <module> from xarray import register_dataarray_accessor, register_dataset_accessor File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module> from xarray import testing, tutorial File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/testing/__init__.py", line 2, in <module> from xarray.testing.assertions import ( # noqa: F401 File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/testing/assertions.py", line 11, in <module> from xarray.core import duck_array_ops, formatting, utils File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/core/duck_array_ops.py", line 37, in <module> from xarray.core import dask_array_ops, dtypes, nputils File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/core/dask_array_ops.py", line 3, in <module> from xarray.core import dtypes, nputils File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/core/nputils.py", line 14, in <module> if module_available("numpy", minversion="2.0.0.dev0"): File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/xarray/namedarray/utils.py", line 62, in module_available return Version(version) >= Version(minversion) File "/Users/oliviers/miniforge3/envs/analysis/lib/python3.10/site-packages/packaging/version.py", line 198, in __init__ match = self._regex.search(version) TypeError: expected string or bytes-like object

[remrama]

At a quick glance it doesn't look like this is pingouin's fault. It seems like it relates to an import buried within.

Have you tried creating a new minimal conda environment and re-importing from there?

If you still get the same issue in a new conda environment, maybe export the conda environment details and post them here so someone can try to replicate the issue on a separate system.

[oseynnes]

Thanks! Yes, unfortunately the problem may come from my side. Here are the details of a minimal environment:

name: stats
channels:
  - conda-forge
  - plotly
dependencies:
  - brotli=1.1.0=hb547adb_1
  - brotli-bin=1.1.0=hb547adb_1
  - brotli-python=1.1.0=py311ha891d26_1
  - bzip2=1.0.8=h93a5062_5
  - ca-certificates=2024.2.2=hf0a4a13_0
  - certifi=2024.2.2=pyhd8ed1ab_0
  - charset-normalizer=3.3.2=pyhd8ed1ab_0
  - contourpy=1.2.1=py311hcc98501_0
  - cycler=0.12.1=pyhd8ed1ab_0
  - fonttools=4.51.0=py311h05b510d_0
  - freetype=2.12.1=hadb7bae_2
  - idna=3.7=pyhd8ed1ab_0
  - joblib=1.4.2=pyhd8ed1ab_0
  - kiwisolver=1.4.5=py311he4fd1f5_1
  - lcms2=2.16=ha0e7c42_0
  - lerc=4.0.0=h9a09cb3_0
  - libblas=3.9.0=22_osxarm64_openblas
  - libbrotlicommon=1.1.0=hb547adb_1
  - libbrotlidec=1.1.0=hb547adb_1
  - libbrotlienc=1.1.0=hb547adb_1
  - libcblas=3.9.0=22_osxarm64_openblas
  - libcxx=17.0.6=h5f092b4_0
  - libdeflate=1.20=h93a5062_0
  - libexpat=2.6.2=hebf3989_0
  - libffi=3.4.2=h3422bc3_5
  - libgfortran=5.0.0=13_2_0_hd922786_3
  - libgfortran5=13.2.0=hf226fd6_3
  - libjpeg-turbo=3.0.0=hb547adb_1
  - liblapack=3.9.0=22_osxarm64_openblas
  - libopenblas=0.3.27=openmp_h6c19121_0
  - libpng=1.6.43=h091b4b1_0
  - libsqlite=3.45.3=h091b4b1_0
  - libtiff=4.6.0=h07db509_3
  - libwebp-base=1.4.0=h93a5062_0
  - libxcb=1.15=hf346824_0
  - libzlib=1.2.13=h53f4e23_5
  - littleutils=0.2.2=py_0
  - llvm-openmp=18.1.5=hde57baf_0
  - matplotlib-base=3.8.4=py311h000fb6e_2
  - mpmath=1.3.0=pyhd8ed1ab_0
  - munkres=1.1.4=pyh9f0ad1d_0
  - ncurses=6.5=hb89a1cb_0
  - numpy=1.26.4=py311h7125741_0
  - openjpeg=2.5.2=h9f1df11_0
  - openssl=3.3.0=hfb2fe0b_2
  - outdated=0.2.2=pyhd8ed1ab_0
  - packaging=24.0=pyhd8ed1ab_0
  - pandas=2.2.2=py311h4b4568b_1
  - pandas-flavor=0.6.0=pyhd8ed1ab_1
  - patsy=0.5.6=pyhd8ed1ab_0
  - pillow=10.3.0=py311h0b5d0a1_0
  - pingouin=0.5.4=pyhd8ed1ab_0
  - pip=24.0=pyhd8ed1ab_0
  - pthread-stubs=0.4=h27ca646_1001
  - pyparsing=3.1.2=pyhd8ed1ab_0
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.11.9=h932a869_0_cpython
  - python-dateutil=2.9.0=pyhd8ed1ab_0
  - python-tzdata=2024.1=pyhd8ed1ab_0
  - python_abi=3.11=4_cp311
  - pytz=2024.1=pyhd8ed1ab_0
  - readline=8.2=h92ec313_1
  - requests=2.32.2=pyhd8ed1ab_0
  - scikit-learn=1.5.0=py311hbfb48bc_0
  - scipy=1.13.0=py311hceeca8c_1
  - seaborn=0.13.2=hd8ed1ab_2
  - seaborn-base=0.13.2=pyhd8ed1ab_2
  - setuptools=70.0.0=pyhd8ed1ab_0
  - six=1.16.0=pyh6c4a22f_0
  - statsmodels=0.14.2=py311h5d790af_0
  - tabulate=0.9.0=pyhd8ed1ab_1
  - threadpoolctl=3.5.0=pyhc1e730c_0
  - tk=8.6.13=h5083fa2_1
  - tzdata=2024a=h0c530f3_0
  - urllib3=2.2.1=pyhd8ed1ab_0
  - wheel=0.43.0=pyhd8ed1ab_1
  - xarray=2024.5.0=pyhd8ed1ab_0
  - xorg-libxau=1.0.11=hb547adb_0
  - xorg-libxdmcp=1.1.3=h27ca646_0
  - xz=5.2.6=h57fd34a_0
  - zstd=1.5.6=hb46c0d2_0
prefix: /Users/oliviers/miniforge3/envs/stats

[remrama]

I think it's on your end. I could not get this environment to solve, but after creating a new environment with the minimal file below, I had no issue importing pinguoin:

name: test-stats
dependencies:
  - python=3.12
  - conda-forge::pingouin=0.5

I would suggest building a new environment manually, starting with pinguoin, adding package-by-package, and importing pingouin after each new package to see if there is a specific step where it causes a problem.

I suspect you won't have issues, but if you do, unfortunately the only think of would be to uninstall/reinstall conda. I know that can be a pain if you have lots of environments you use frequently, but in my experience it's good practice to clean house every once in a while anyways.

Btw, I'm using miniconda, which may or may not be making a difference.

[oseynnes]

Hello. I got it to work but can't really explain it: by installing Pingouin before any other package (in particular pandas).
Thanks for the help!