search

SelfExplainML / PiML-Toolbox

PiML (Python Interpretable Machine Learning) toolbox for model development & diagnostics
https://selfexplainml.github.io/PiML-Toolbox
Apache License 2.0
931 stars 111 forks source link

Colab cannot import piml: initialization of _internal failed #30

Closed faradawn closed 1 year ago

faradawn commented 1 year ago

Hi, I tried "Example_CaliforniaHousing.ipynb" for a long time but still couldn't get the initial importing of PiML working. Tried on 2023-03-18 using Google Colab py39 runtime without a hardware accelerator.

Running the first cell !pip install piml, I got most all dependencies installed, but an error was thrown:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.

I ignored the error, restarted the runtime, and moved to the next cell from piml import Experiment. I got an error (trimmed to the end):

File /usr/local/lib/python3.9/dist-packages/numba/np/ufunc/decorators.py:3
      1 import inspect
----> 3 from numba.np.ufunc import _internal
      4 from numba.np.ufunc.parallel import ParallelUFuncBuilder, ParallelGUFuncBuilder
      6 from numba.core.registry import TargetRegistry

SystemError: initialization of _internal failed without raising an exception

Is there a way to resolve this? Thanks!

Extra:

Full error of the first cell:

!pip install piml

Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Collecting piml
  Downloading PiML-0.4.3-cp39-none-manylinux_2_5_x86_64.whl (9.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.8/9.8 MB 40.6 MB/s eta 0:00:00
Collecting natsort>=8.2.0
  Downloading natsort-8.3.1-py3-none-any.whl (38 kB)
Collecting shap>=0.39.0
  Downloading shap-0.41.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (572 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 572.4/572.4 KB 19.8 MB/s eta 0:00:00
Collecting pygam>=0.8.0
  Downloading pygam-0.9.0-py3-none-any.whl (522 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 522.2/522.2 KB 25.7 MB/s eta 0:00:00
Requirement already satisfied: torch>=1.11.0 in /usr/local/lib/python3.9/dist-packages (from piml) (1.13.1+cu116)
Requirement already satisfied: numpy>=1.21.4 in /usr/local/lib/python3.9/dist-packages (from piml) (1.22.4)
Requirement already satisfied: pandas>=1.3.5 in /usr/local/lib/python3.9/dist-packages (from piml) (1.4.4)
Requirement already satisfied: scikit-learn>=0.24.2 in /usr/local/lib/python3.9/dist-packages (from piml) (1.2.2)
Requirement already satisfied: statsmodels>=0.12.2 in /usr/local/lib/python3.9/dist-packages (from piml) (0.13.5)
Requirement already satisfied: matplotlib>=3.1.2 in /usr/local/lib/python3.9/dist-packages (from piml) (3.7.1)
Requirement already satisfied: lightgbm>=3.1.1 in /usr/local/lib/python3.9/dist-packages (from piml) (3.3.5)
Requirement already satisfied: scipy>=1.5.3 in /usr/local/lib/python3.9/dist-packages (from piml) (1.10.1)
Collecting dcor>=0.5.3
  Downloading dcor-0.6-py3-none-any.whl (55 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.5/55.5 KB 1.2 MB/s eta 0:00:00
Requirement already satisfied: xlrd>=1.2.0 in /usr/local/lib/python3.9/dist-packages (from piml) (2.0.1)
Requirement already satisfied: xgboost>=1.4.2 in /usr/local/lib/python3.9/dist-packages (from piml) (1.7.4)
Collecting ipython>=7.12.0
  Downloading ipython-8.11.0-py3-none-any.whl (793 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 793.3/793.3 KB 29.6 MB/s eta 0:00:00
Requirement already satisfied: joblib>=1.1.0 in /usr/local/lib/python3.9/dist-packages (from piml) (1.1.1)
Requirement already satisfied: psutil>=5.9.0 in /usr/local/lib/python3.9/dist-packages (from piml) (5.9.4)
Collecting lime>=0.2.0.1
  Downloading lime-0.2.0.1.tar.gz (275 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 275.7/275.7 KB 14.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: seaborn>=0.11.2 in /usr/local/lib/python3.9/dist-packages (from piml) (0.12.2)
Collecting momentchi2
  Downloading momentchi2-0.1.8-py3-none-any.whl (11 kB)
Collecting dill>=0.3.6
  Downloading dill-0.3.6-py3-none-any.whl (110 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 110.5/110.5 KB 6.2 MB/s eta 0:00:00
Requirement already satisfied: packaging>=20.5 in /usr/local/lib/python3.9/dist-packages (from piml) (23.0)
Requirement already satisfied: ipywidgets>=7.7.0 in /usr/local/lib/python3.9/dist-packages (from piml) (7.7.1)
Requirement already satisfied: numba>=0.51 in /usr/local/lib/python3.9/dist-packages (from dcor>=0.5.3->piml) (0.56.4)
Collecting stack-data
  Downloading stack_data-0.6.2-py3-none-any.whl (24 kB)
Requirement already satisfied: pickleshare in /usr/local/lib/python3.9/dist-packages (from ipython>=7.12.0->piml) (0.7.5)
Requirement already satisfied: pexpect>4.3 in /usr/local/lib/python3.9/dist-packages (from ipython>=7.12.0->piml) (4.8.0)
Requirement already satisfied: pygments>=2.4.0 in /usr/local/lib/python3.9/dist-packages (from ipython>=7.12.0->piml) (2.6.1)
Collecting matplotlib-inline
  Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
Collecting prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30
  Downloading prompt_toolkit-3.0.38-py3-none-any.whl (385 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 385.8/385.8 KB 20.2 MB/s eta 0:00:00
Requirement already satisfied: backcall in /usr/local/lib/python3.9/dist-packages (from ipython>=7.12.0->piml) (0.2.0)
Requirement already satisfied: decorator in /usr/local/lib/python3.9/dist-packages (from ipython>=7.12.0->piml) (4.4.2)
Requirement already satisfied: traitlets>=5 in /usr/local/lib/python3.9/dist-packages (from ipython>=7.12.0->piml) (5.7.1)
Collecting jedi>=0.16
  Downloading jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 53.3 MB/s eta 0:00:00
Requirement already satisfied: ipython-genutils~=0.2.0 in /usr/local/lib/python3.9/dist-packages (from ipywidgets>=7.7.0->piml) (0.2.0)
Requirement already satisfied: jupyterlab-widgets>=1.0.0 in /usr/local/lib/python3.9/dist-packages (from ipywidgets>=7.7.0->piml) (3.0.5)
Requirement already satisfied: widgetsnbextension~=3.6.0 in /usr/local/lib/python3.9/dist-packages (from ipywidgets>=7.7.0->piml) (3.6.2)
Requirement already satisfied: ipykernel>=4.5.1 in /usr/local/lib/python3.9/dist-packages (from ipywidgets>=7.7.0->piml) (5.3.4)
Requirement already satisfied: wheel in /usr/local/lib/python3.9/dist-packages (from lightgbm>=3.1.1->piml) (0.40.0)
Requirement already satisfied: tqdm in /usr/local/lib/python3.9/dist-packages (from lime>=0.2.0.1->piml) (4.65.0)
Requirement already satisfied: scikit-image>=0.12 in /usr/local/lib/python3.9/dist-packages (from lime>=0.2.0.1->piml) (0.19.3)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (1.4.4)
Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (1.0.7)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (0.11.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (3.0.9)
Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (8.4.0)
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (2.8.2)
Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (4.39.0)
Requirement already satisfied: importlib-resources>=3.2.0 in /usr/local/lib/python3.9/dist-packages (from matplotlib>=3.1.2->piml) (5.12.0)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.9/dist-packages (from pandas>=1.3.5->piml) (2022.7.1)
Collecting progressbar2<5.0.0,>=4.2.0
  Downloading progressbar2-4.2.0-py2.py3-none-any.whl (27 kB)
Collecting numpy>=1.21.4
  Downloading numpy-1.24.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 38.2 MB/s eta 0:00:00
Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.9/dist-packages (from scikit-learn>=0.24.2->piml) (3.1.0)
Collecting slicer==0.0.7
  Downloading slicer-0.0.7-py3-none-any.whl (14 kB)
Requirement already satisfied: cloudpickle in /usr/local/lib/python3.9/dist-packages (from shap>=0.39.0->piml) (2.2.1)
Requirement already satisfied: patsy>=0.5.2 in /usr/local/lib/python3.9/dist-packages (from statsmodels>=0.12.2->piml) (0.5.3)
Requirement already satisfied: typing-extensions in /usr/local/lib/python3.9/dist-packages (from torch>=1.11.0->piml) (4.5.0)
Requirement already satisfied: zipp>=3.1.0 in /usr/local/lib/python3.9/dist-packages (from importlib-resources>=3.2.0->matplotlib>=3.1.2->piml) (3.15.0)
Requirement already satisfied: tornado>=4.2 in /usr/local/lib/python3.9/dist-packages (from ipykernel>=4.5.1->ipywidgets>=7.7.0->piml) (6.2)
Requirement already satisfied: jupyter-client in /usr/local/lib/python3.9/dist-packages (from ipykernel>=4.5.1->ipywidgets>=7.7.0->piml) (6.1.12)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /usr/local/lib/python3.9/dist-packages (from jedi>=0.16->ipython>=7.12.0->piml) (0.8.3)
Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in /usr/local/lib/python3.9/dist-packages (from numba>=0.51->dcor>=0.5.3->piml) (0.39.1)
Collecting numba>=0.51
  Downloading numba-0.56.3-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 66.3 MB/s eta 0:00:00
  Downloading numba-0.56.2-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 83.7 MB/s eta 0:00:00
  Downloading numba-0.56.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 82.7 MB/s eta 0:00:00
  Downloading numba-0.55.2-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 79.0 MB/s eta 0:00:00
Collecting llvmlite<0.39,>=0.38.0rc1
  Downloading llvmlite-0.38.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 15.6 MB/s eta 0:00:00
Collecting numba>=0.51
  Downloading numba-0.55.1-1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 82.6 MB/s eta 0:00:00
  Downloading numba-0.55.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 75.4 MB/s eta 0:00:00
  Downloading numba-0.54.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 84.7 MB/s eta 0:00:00
Collecting llvmlite<0.38,>=0.37.0rc1
  Downloading llvmlite-0.37.0-cp39-cp39-manylinux2014_x86_64.whl (26.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 26.3/26.3 MB 52.4 MB/s eta 0:00:00
Collecting numba>=0.51
  Downloading numba-0.54.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 76.4 MB/s eta 0:00:00
  Downloading numba-0.53.1-cp39-cp39-manylinux2014_x86_64.whl (3.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 77.7 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /usr/local/lib/python3.9/dist-packages (from numba>=0.51->dcor>=0.5.3->piml) (63.4.3)
Collecting llvmlite<0.37,>=0.36.0rc1
  Downloading llvmlite-0.36.0-cp39-cp39-manylinux2010_x86_64.whl (25.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.3/25.3 MB 48.9 MB/s eta 0:00:00
Requirement already satisfied: six in /usr/local/lib/python3.9/dist-packages (from patsy>=0.5.2->statsmodels>=0.12.2->piml) (1.15.0)
Requirement already satisfied: ptyprocess>=0.5 in /usr/local/lib/python3.9/dist-packages (from pexpect>4.3->ipython>=7.12.0->piml) (0.7.0)
Requirement already satisfied: python-utils>=3.0.0 in /usr/local/lib/python3.9/dist-packages (from progressbar2<5.0.0,>=4.2.0->pygam>=0.8.0->piml) (3.5.2)
Requirement already satisfied: wcwidth in /usr/local/lib/python3.9/dist-packages (from prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30->ipython>=7.12.0->piml) (0.2.6)
Requirement already satisfied: imageio>=2.4.1 in /usr/local/lib/python3.9/dist-packages (from scikit-image>=0.12->lime>=0.2.0.1->piml) (2.9.0)
Requirement already satisfied: PyWavelets>=1.1.1 in /usr/local/lib/python3.9/dist-packages (from scikit-image>=0.12->lime>=0.2.0.1->piml) (1.4.1)
Requirement already satisfied: tifffile>=2019.7.26 in /usr/local/lib/python3.9/dist-packages (from scikit-image>=0.12->lime>=0.2.0.1->piml) (2023.3.15)
Requirement already satisfied: networkx>=2.2 in /usr/local/lib/python3.9/dist-packages (from scikit-image>=0.12->lime>=0.2.0.1->piml) (3.0)
Requirement already satisfied: notebook>=4.4.1 in /usr/local/lib/python3.9/dist-packages (from widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (6.3.0)
Collecting asttokens>=2.1.0
  Downloading asttokens-2.2.1-py2.py3-none-any.whl (26 kB)
Collecting pure-eval
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting executing>=1.2.0
  Downloading executing-1.2.0-py2.py3-none-any.whl (24 kB)
Requirement already satisfied: terminado>=0.8.3 in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.17.1)
Requirement already satisfied: argon2-cffi in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (21.3.0)
Requirement already satisfied: jupyter-core>=4.6.1 in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (5.2.0)
Requirement already satisfied: nbconvert in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (6.5.4)
Requirement already satisfied: jinja2 in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (3.1.2)
Requirement already satisfied: pyzmq>=17 in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (23.2.1)
Requirement already satisfied: Send2Trash>=1.5.0 in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (1.8.0)
Requirement already satisfied: prometheus-client in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.16.0)
Requirement already satisfied: nbformat in /usr/local/lib/python3.9/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (5.7.3)
Requirement already satisfied: platformdirs>=2.5 in /usr/local/lib/python3.9/dist-packages (from jupyter-core>=4.6.1->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (3.1.1)
Requirement already satisfied: argon2-cffi-bindings in /usr/local/lib/python3.9/dist-packages (from argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (21.2.0)
Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.9/dist-packages (from jinja2->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (2.1.2)
Requirement already satisfied: pandocfilters>=1.4.1 in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (1.5.0)
Requirement already satisfied: entrypoints>=0.2.2 in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.4)
Requirement already satisfied: bleach in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (6.0.0)
Requirement already satisfied: defusedxml in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.7.1)
Requirement already satisfied: jupyterlab-pygments in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.2.2)
Requirement already satisfied: mistune<2,>=0.8.1 in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.8.4)
Requirement already satisfied: beautifulsoup4 in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (4.11.2)
Requirement already satisfied: lxml in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (4.9.2)
Requirement already satisfied: tinycss2 in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (1.2.1)
Requirement already satisfied: nbclient>=0.5.0 in /usr/local/lib/python3.9/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.7.2)
Requirement already satisfied: jsonschema>=2.6 in /usr/local/lib/python3.9/dist-packages (from nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (4.3.3)
Requirement already satisfied: fastjsonschema in /usr/local/lib/python3.9/dist-packages (from nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (2.16.3)
Requirement already satisfied: attrs>=17.4.0 in /usr/local/lib/python3.9/dist-packages (from jsonschema>=2.6->nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (22.2.0)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /usr/local/lib/python3.9/dist-packages (from jsonschema>=2.6->nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.19.3)
Requirement already satisfied: cffi>=1.0.1 in /usr/local/lib/python3.9/dist-packages (from argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (1.15.1)
Requirement already satisfied: soupsieve>1.2 in /usr/local/lib/python3.9/dist-packages (from beautifulsoup4->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (2.4)
Requirement already satisfied: webencodings in /usr/local/lib/python3.9/dist-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (0.5.1)
Requirement already satisfied: pycparser in /usr/local/lib/python3.9/dist-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.7.0->piml) (2.21)
Building wheels for collected packages: lime
  Building wheel for lime (setup.py) ... done
  Created wheel for lime: filename=lime-0.2.0.1-py3-none-any.whl size=283859 sha256=977759970aaaf5e3c539ceb4ea229ba921e34294642260690da4c7fac6e0c3ca
  Stored in directory: /root/.cache/pip/wheels/ed/d7/c9/5a0130d06d6310bc6cbe55220e6e72dcb8c4eff9a478717066
Successfully built lime
Installing collected packages: pure-eval, executing, slicer, prompt-toolkit, progressbar2, numpy, natsort, matplotlib-inline, llvmlite, jedi, dill, asttokens, stack-data, numba, pygam, momentchi2, ipython, dcor, shap, lime, piml
  Attempting uninstall: prompt-toolkit
    Found existing installation: prompt-toolkit 2.0.10
    Uninstalling prompt-toolkit-2.0.10:
      Successfully uninstalled prompt-toolkit-2.0.10
  Attempting uninstall: progressbar2
    Found existing installation: progressbar2 3.38.0
    Uninstalling progressbar2-3.38.0:
      Successfully uninstalled progressbar2-3.38.0
  Attempting uninstall: numpy
    Found existing installation: numpy 1.22.4
    Uninstalling numpy-1.22.4:
      Successfully uninstalled numpy-1.22.4
  Attempting uninstall: natsort
    Found existing installation: natsort 5.5.0
    Uninstalling natsort-5.5.0:
      Successfully uninstalled natsort-5.5.0
  Attempting uninstall: llvmlite
    Found existing installation: llvmlite 0.39.1
    Uninstalling llvmlite-0.39.1:
      Successfully uninstalled llvmlite-0.39.1
  Attempting uninstall: numba
    Found existing installation: numba 0.56.4
    Uninstalling numba-0.56.4:
      Successfully uninstalled numba-0.56.4
  Attempting uninstall: ipython
    Found existing installation: ipython 7.9.0
    Uninstalling ipython-7.9.0:
      Successfully uninstalled ipython-7.9.0
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
google-colab 1.0.0 requires ipython~=7.9.0, but you have ipython 8.11.0 which is incompatible.
Successfully installed asttokens-2.2.1 dcor-0.6 dill-0.3.6 executing-1.2.0 ipython-8.11.0 jedi-0.18.2 lime-0.2.0.1 llvmlite-0.36.0 matplotlib-inline-0.1.6 momentchi2-0.1.8 natsort-8.3.1 numba-0.53.1 numpy-1.24.2 piml-0.4.3 progressbar2-4.2.0 prompt-toolkit-3.0.38 pure-eval-0.2.2 pygam-0.9.0 shap-0.41.0 slicer-0.0.7 stack-data-0.6.2

Full error of the seond cell:

from piml import Experiment
exp = Experiment()

---------------------------------------------------------------------------
SystemError                               Traceback (most recent call last)
Cell In[2], line 1
----> 1 from piml import Experiment

File /usr/local/lib/python3.9/dist-packages/piml/__init__.py:1
----> 1 from .api import Experiment
      2 from .diagnoser.utils import twosample_test
      4 __all__ = ['Experiment']

File piml/api.py:16, in init piml.api()

File piml/dashboard/data_panel.py:12, in init piml.dashboard.data_panel()

File piml/workflow/data_api.py:8, in init piml.workflow.data_api()

File piml/data/base.py:14, in init piml.data.base()

File piml/data/data_selector.py:11, in init piml.data.data_selector()

File /usr/local/lib/python3.9/dist-packages/dcor/__init__.py:13
     10 import os as _os
     11 import pathlib as _pathlib
---> 13 from . import distances, homogeneity, independence
     14 from ._dcor import (
     15     DistanceCovarianceMethod as DistanceCovarianceMethod,
     16     Stats as Stats,
   (...)
     27     u_distance_stats_sqr as u_distance_stats_sqr,
     28 )
     29 from ._dcor_internals import (
     30     double_centered as double_centered,
     31     mean_product as mean_product,
   (...)
     35     u_projection as u_projection,
     36 )

File /usr/local/lib/python3.9/dist-packages/dcor/independence.py:14
     11 import numpy as np
     12 import scipy.stats
---> 14 from ._dcor import u_distance_correlation_sqr
     15 from ._dcor_internals import (
     16     _check_same_n_elements,
     17     _distance_matrix_generic,
   (...)
     22     u_product,
     23 )
     24 from ._hypothesis import HypothesisTest, _permutation_test_with_sym_matrix

File /usr/local/lib/python3.9/dist-packages/dcor/_dcor.py:35
     32 from dcor._dcor_internals import _af_inv_scaled
     34 from ._dcor_internals import _dcov_from_terms, _dcov_terms_naive
---> 35 from ._fast_dcov_avl import _distance_covariance_sqr_terms_avl
     36 from ._fast_dcov_mergesort import _distance_covariance_sqr_terms_mergesort
     37 from ._utils import ArrayType, CompileMode, _sqrt, get_namespace

File /usr/local/lib/python3.9/dist-packages/dcor/_fast_dcov_avl.py:18
      7 import warnings
      8 from typing import (
      9     TYPE_CHECKING,
     10     Any,
   (...)
     15     overload,
     16 )
---> 18 import numba
     19 import numpy as np
     20 from numba import boolean, float64, int64

File /usr/local/lib/python3.9/dist-packages/numba/__init__.py:43
     39 from numba.core.decorators import (cfunc, generated_jit, jit, njit, stencil,
     40                                    jit_module)
     42 # Re-export vectorize decorators and the thread layer querying function
---> 43 from numba.np.ufunc import (vectorize, guvectorize, threading_layer,
     44                             get_num_threads, set_num_threads)
     46 # Re-export Numpy helpers
     47 from numba.np.numpy_support import carray, farray, from_dtype

File /usr/local/lib/python3.9/dist-packages/numba/np/ufunc/__init__.py:3
      1 # -*- coding: utf-8 -*-
----> 3 from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize
      4 from numba.np.ufunc._internal import PyUFunc_None, PyUFunc_Zero, PyUFunc_One
      5 from numba.np.ufunc import _internal, array_exprs

File /usr/local/lib/python3.9/dist-packages/numba/np/ufunc/decorators.py:3
      1 import inspect
----> 3 from numba.np.ufunc import _internal
      4 from numba.np.ufunc.parallel import ParallelUFuncBuilder, ParallelGUFuncBuilder
      6 from numba.core.registry import TargetRegistry

SystemError: initialization of _internal failed without raising an exception
faradawn commented 1 year ago

Resolved by using numpy 1.23.1 instead of 1.24.2! Specifically, I added the following two lines after !pip install piml

!pip uninstall numpy -y
!pip install numpy==1.23.1

Thanks.

PS: love the great work of PiML in making neural nets interpretable in an easy way!

faradawn commented 1 year ago

Can solve the issue by

!pip uninstall numpy -y
!pip install numpy==1.23.1
ZebinYang commented 1 year ago

Hi @faradawn

Thanks for reporting this issue.

Temporarily, the corresponding version requirements are added in each example notebook. In the next release, such requirements will be enforced automatically when installing PiML.