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The fastai deep learning library
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ImportError: numpy.core.multiarray failed to import #4035

Open kevin-vitro opened 3 months ago

kevin-vitro commented 3 months ago

Please confirm you have the latest versions of fastai, fastcore, and nbdev prior to reporting a bug (delete one): YES

Describe the bug When I try to run nbdev_preview from inside of the fastai devcontainer, I get the stacktrace below.

To Reproduce Steps to reproduce the behavior:

  1. Open the fastai devcontainer in vs-code (I use Ctrl+Shift+P and type "rebuild and reopen in container")
  2. Once the devcontainer is open, type nbdev_preview in the terminal and wait for the error to show up.

Expected behavior I was expecting to have nbdev_preview build the fastai docs and allow me to view them that way I could add my own code to fastai and ensure the docs still render fine.

Error with full stack trace

Place between these lines with triple backticks:

root@vit-svi-dev-5:/data# nbdev_preview 
Quarto is not installed. We will download and install it for you.
Installing or upgrading quarto -- this requires root access.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100    72  100    72    0     0    142      0 --:--:-- --:--:-- --:--:--   142
100   114    0   114    0     0    124      0 --:--:-- --:--:-- --:--:--   124
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100  111M  100  111M    0     0  3455k      0  0:00:33  0:00:33 --:--:-- 6815k
Selecting previously unselected package quarto.
(Reading database ... 39368 files and directories currently installed.)
Preparing to unpack quarto-linux-amd64.deb ...
Unpacking quarto (1.4.555) ...
Setting up quarto (1.4.555) ...
Obtaining file:///data
  Preparing metadata (setup.py) ... done
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Collecting mdurl~=0.1
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Installing collected packages: sentencepiece, ninja, everett, brotli, zstandard, wurlitzer, wrapt, Werkzeug, typing-extensions, semantic-version, safetensors, regex, python-box, numpy, networkx, multidict, mdurl, kornia-rs, itsdangerous, hydra-slayer, fsspec, frozenlist, filelock, dulwich, configobj, blinker, async-timeout, yarl, tifffile, tensorboardX, scipy, requests-toolbelt, pyarrow, opencv-python-headless, opencv-python, markdown-it-py, lightning-utilities, lazy-loader, imageio, huggingface-hub, flask, aiosignal, torchmetrics, tokenizers, scikit-learn, scikit-image, rich, pytorch-ignite, kornia, flask_compress, aiohttp, accelerate, transformers, timm, comet_ml, catalyst, albumentations, pytorch-lightning, lightning, fastai
  Attempting uninstall: Werkzeug
    Found existing installation: Werkzeug 2.2.2
    Uninstalling Werkzeug-2.2.2:
      Successfully uninstalled Werkzeug-2.2.2
  Attempting uninstall: typing-extensions
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      Successfully uninstalled typing_extensions-4.4.0
  Attempting uninstall: numpy
    Found existing installation: numpy 1.23.4
    Uninstalling numpy-1.23.4:
      Successfully uninstalled numpy-1.23.4
  Attempting uninstall: blinker
    Found existing installation: blinker 1.4
    Not uninstalling blinker at /usr/lib/python3/dist-packages, outside environment /usr
    Can't uninstall 'blinker'. No files were found to uninstall.
  Attempting uninstall: scipy
    Found existing installation: scipy 1.9.2
    Uninstalling scipy-1.9.2:
      Successfully uninstalled scipy-1.9.2
  Attempting uninstall: scikit-learn
    Found existing installation: scikit-learn 1.1.2
    Uninstalling scikit-learn-1.1.2:
      Successfully uninstalled scikit-learn-1.1.2
  Attempting uninstall: fastai
    Found existing installation: fastai 2.7.16
    Uninstalling fastai-2.7.16:
      Successfully uninstalled fastai-2.7.16
  Running setup.py develop for fastai
Successfully installed Werkzeug-3.0.3 accelerate-0.31.0 aiohttp-3.9.5 aiosignal-1.3.1 albumentations-1.4.3 async-timeout-4.0.3 blinker-1.8.2 brotli-1.1.0 catalyst-22.4 comet_ml-3.43.2 configobj-5.0.8 dulwich-0.22.1 everett-3.1.0 fastai filelock-3.15.4 flask-3.0.3 flask_compress-1.15 frozenlist-1.4.1 fsspec-2024.6.0 huggingface-hub-0.23.4 hydra-slayer-0.5.0 imageio-2.34.2 itsdangerous-2.2.0 kornia-0.7.2 kornia-rs-0.1.3 lazy-loader-0.4 lightning-2.1.4 lightning-utilities-0.11.2 markdown-it-py-3.0.0 mdurl-0.1.2 multidict-6.0.5 networkx-3.3 ninja-1.11.1.1 numpy-2.0.0 opencv-python-4.10.0.84 opencv-python-headless-4.10.0.84 pyarrow-16.1.0 python-box-6.1.0 pytorch-ignite-0.5.0.post2 pytorch-lightning-2.1.4 regex-2024.5.15 requests-toolbelt-1.0.0 rich-13.7.1 safetensors-0.4.3 scikit-image-0.24.0 scikit-learn-1.5.0 scipy-1.14.0 semantic-version-2.10.0 sentencepiece-0.2.0 tensorboardX-2.6 tifffile-2024.6.18 timm-1.0.7 tokenizers-0.19.1 torchmetrics-1.4.0.post0 transformers-4.41.2 typing-extensions-4.12.2 wrapt-1.16.0 wurlitzer-3.1.1 yarl-1.9.4 zstandard-0.22.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
concurrent.futures.process._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py", line 3378, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-8e19730e2294>", line 2, in <module>
    from fastai.torch_basics import *
  File "/data/fastai/torch_basics.py", line 9, in <module>
    from .imports import *
  File "/data/fastai/imports.py", line 5, in <module>
    import multiprocessing,threading,urllib,tempfile,concurrent.futures,matplotlib,warnings,zipfile
  File "/usr/local/lib/python3.10/dist-packages/matplotlib/__init__.py", line 113, in <module>
    from . import _api, _version, cbook, _docstring, rcsetup
  File "/usr/local/lib/python3.10/dist-packages/matplotlib/rcsetup.py", line 27, in <module>
    from matplotlib.colors import Colormap, is_color_like
  File "/usr/local/lib/python3.10/dist-packages/matplotlib/colors.py", line 56, in <module>
    from matplotlib import _api, _cm, cbook, scale
  File "/usr/local/lib/python3.10/dist-packages/matplotlib/scale.py", line 22, in <module>
    from matplotlib.ticker import (
  File "/usr/local/lib/python3.10/dist-packages/matplotlib/ticker.py", line 138, in <module>
    from matplotlib import transforms as mtransforms
  File "/usr/local/lib/python3.10/dist-packages/matplotlib/transforms.py", line 49, in <module>
    from matplotlib._path import (
ImportError: numpy.core.multiarray failed to import

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/usr/lib/python3.10/concurrent/futures/process.py", line 205, in _process_chunk
    return [fn(*args) for args in chunk]
  File "/usr/lib/python3.10/concurrent/futures/process.py", line 205, in <listcomp>
    return [fn(*args) for args in chunk]
  File "/usr/local/lib/python3.10/dist-packages/fastcore/parallel.py", line 61, in _call
    return g(item)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/serve_drv.py", line 22, in main
    if src.suffix=='.ipynb': exec_nb(src, dst, x)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/serve_drv.py", line 16, in exec_nb
    cb()(nb)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/processors.py", line 231, in __call__
    def __call__(self, nb): return self.nb_proc(nb).process()
  File "/usr/local/lib/python3.10/dist-packages/nbdev/process.py", line 126, in process
    for proc in self.procs: self._proc(proc)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/process.py", line 119, in _proc
    for cell in self.nb.cells: self._process_cell(proc, cell)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/process.py", line 110, in _process_cell
    if callable(proc) and not _is_direc(proc): cell = opt_set(cell, proc(cell))
  File "/usr/local/lib/python3.10/dist-packages/nbdev/processors.py", line 201, in __call__
    raise Exception(f"Error{' in notebook: '+title if title else ''} in cell {cell.idx_} :\n{cell.source}") from self.k.exc[1]
Exception: Error in notebook: Data core in cell 5 :
from __future__ import annotations
from fastai.torch_basics import *
from fastai.data.load import *
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/bin/nbdev_preview", line 8, in <module>
    sys.exit(nbdev_preview())
  File "/usr/local/lib/python3.10/dist-packages/fastcore/script.py", line 119, in _f
    return tfunc(**merge(args, args_from_prog(func, xtra)))
  File "/usr/local/lib/python3.10/dist-packages/nbdev/quarto.py", line 270, in nbdev_preview
    cache,cfg,path = _pre_docs(path, n_workers=n_workers, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/quarto.py", line 174, in _pre_docs
    cache = proc_nbs(path, n_workers=n_workers, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/nbdev/serve.py", line 76, in proc_nbs
    parallel(nbdev.serve_drv.main, files, n_workers=n_workers, pause=0.01, **kw)
  File "/usr/local/lib/python3.10/dist-packages/fastcore/parallel.py", line 132, in parallel
    return L(r)
  File "/usr/local/lib/python3.10/dist-packages/fastcore/foundation.py", line 98, in __call__
    return super().__call__(x, *args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/fastcore/foundation.py", line 106, in __init__
    items = listify(items, *rest, use_list=use_list, match=match)
  File "/usr/local/lib/python3.10/dist-packages/fastcore/basics.py", line 66, in listify
    elif is_iter(o): res = list(o)
  File "/usr/lib/python3.10/concurrent/futures/process.py", line 570, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/usr/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterator
    yield _result_or_cancel(fs.pop())
  File "/usr/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_cancel
    return fut.result(timeout)
  File "/usr/lib/python3.10/concurrent/futures/_base.py", line 458, in result
    return self.__get_result()
  File "/usr/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
    raise self._exception
Exception: Error in notebook: Data core in cell 5 :
from __future__ import annotations
from fastai.torch_basics import *
from fastai.data.load import *

Additional context I'm pretty sure this is related to numpy v2.x being released. I'm not exactly sure where, but we probably just need to add numpy<2 somewhere to keep from upgrading to numpy at this point (unless ofc we are ready to start using 2.x)

kevin-vitro commented 3 months ago

here are the numpy version boundaries according to pipdeptree -r --mermaid after running nbdev_preview

------------------------------------------------------------------------
Warning!!! Possibly conflicting dependencies found:
* scipy==1.9.2
 - numpy [required: >=1.18.5,<1.26.0, installed: 2.0.0]
------------------------------------------------------------------------
numpy -- ">=1.12.0" --> tensorboard
numpy -- ">=1.15.0" --> blis
numpy -- ">=1.15.0" --> spacy
numpy -- ">=1.15.0" --> thinc
numpy -- ">=1.16" --> contourpy
numpy -- ">=1.17.3" --> scikit-learn
numpy -- ">=1.18.5,<1.26.0" --> scipy
numpy -- ">=1.19" --> matplotlib
numpy -- ">=1.21.0" --> pandas
numpy -- "any" --> captum
numpy -- "any" --> torchvision
kevin-vitro commented 3 months ago

This appears to be related to https://github.com/matplotlib/matplotlib/issues/25811

AnilRasam commented 1 month ago

The error message ImportError: numpy.core.multiarray failed to import indicates that there's a problem with importing a core component of the NumPy library. This issue can arise from several underlying problems. Here’s a systematic approach to troubleshooting and resolving it:

  1. Verify NumPy Installation Make sure that NumPy is correctly installed and up to date:

Reinstall NumPy: Sometimes, reinstalling NumPy can resolve the issue.

bash Copy code pip uninstall numpy pip install numpy** Check Version: Ensure you have a compatible version of NumPy for your Python version and other libraries.

bash Copy code pip show numpy

  1. Check for Conflicting Packages Conflicting or outdated packages can cause import issues. Update your packages to ensure compatibility:

Update pip:

bash Copy code pip install --upgrade pip Update All Packages: Update all installed packages to their latest versions.

bash Copy code pip list --outdated pip install --upgrade

  1. Check Python and NumPy Compatibility Ensure that your Python version is compatible with the version of NumPy you are using. NumPy has specific versions that are compatible with different versions of Python.

Check Python Version:

bash Copy code python --version Check NumPy Compatibility: Visit the NumPy documentation to verify compatibility.

  1. Environment Issues If you're working within a virtual environment or conda environment, ensure that the environment is set up correctly.

Virtual Environment: If using venv or virtualenv, recreate the environment and reinstall packages.

bash Copy code python -m venv myenv source myenv/bin/activate pip install numpy Conda Environment: If using Conda, ensure your environment is correctly set up.

bash Copy code conda activate myenv conda install numpy

  1. Check for System-Level Issues Sometimes system-level issues or broken installations can cause problems.

Reinstall Python: In some cases, reinstalling Python itself might help resolve deeper issues.

  1. Debugging Information If the problem persists, gathering additional information might help:

Verbose Import: Try importing with verbose output to get more details.

python Copy code import numpy Check for Error Messages: Look for additional error messages or stack traces that could provide more context.