pin compatible numpy version // crash in wkcuber with Python 3.8

[boergens]

Ubuntu 20.04 WSL, fresh environment

(env) boergens@DESKTOP-4L0H931:~/wkcuber$ python -m wkcuber --scale 11.24,11.24,25 /mnt/c/Users/Kevin/Desktop/sample_40_prescan_488-1.tif asdf
Traceback (most recent call last):
  File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/wkcuber/__main__.py", line 17, in <module>
    from .converter import create_parser as create_conversion_parser
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/wkcuber/converter.py", line 24, in <module>
    from .convert_nifti import create_parser as create_nifti_parser
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/wkcuber/convert_nifti.py", line 6, in <module>
    import nibabel as nib
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/nibabel/__init__.py", line 65, in <module>
    from . import nifti1 as ni1
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/nibabel/nifti1.py", line 26, in <module>
    from .quaternions import fillpositive, quat2mat, mat2quat
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/nibabel/quaternions.py", line 31, in <module>
    MAX_FLOAT = np.maximum_sctype(np.float)
  File "/home/boergens/wkcuber/env/lib/python3.8/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float'

(env) boergens@DESKTOP-4L0H931:~/wkcuber/env/lib/python3.8/site-packages$ ls
GitPython-3.1.30.dist-info                    fsspec-2022.11.0.dist-info          pygments
PIL                                           git                                 pylab.py
Pillow-8.4.0.dist-info                        gitdb                               pyparsing
Pillow.libs                                   gitdb-4.0.10.dist-info              pyparsing-3.0.9.dist-info
PyWavelets-1.4.1.dist-info                    google                              python_dateutil-2.8.2.dist-info
PyYAML-6.0.dist-info                          google_auth-2.15.0-py3.9-nspkg.pth  python_dotenv-0.19.2.dist-info
Pygments-2.14.0.dist-info                     google_auth-2.15.0.dist-info        pywt
__pycache__                                   h11                                 requests
_cffi_backend.cpython-38-x86_64-linux-gnu.so  h11-0.12.0.dist-info                requests-2.28.1.dist-info
_yaml                                         httpcore                            requests_oauthlib
aiohttp                                       httpcore-0.13.7.dist-info           requests_oauthlib-1.3.1.dist-info
aiohttp-3.8.3.dist-info                       httpx                               rfc3986
aiosignal                                     httpx-0.18.2.dist-info              rfc3986-1.5.0.dist-info
aiosignal-1.3.1.dist-info                     idna                                rich
anyio                                         idna-3.4.dist-info                  rich-10.16.2.dist-info
anyio-3.6.2.dist-info                         imagecodecs                         rsa
asciitree                                     imagecodecs-2022.12.24.dist-info    rsa-4.9.dist-info
asciitree-0.3.3.egg-info                      imagecodecs.libs                    scikit_image-0.18.3.dist-info
async_timeout                                 imageio                             scikit_image.libs
async_timeout-4.0.2.dist-info                 imageio-2.24.0.dist-info            scikit_learn-0.24.2.dist-info
attr                                          joblib                              scikit_learn.libs
attrs                                         joblib-1.2.0.dist-info              scipy
attrs-21.4.0.dist-info                        kiwisolver                          scipy-1.10.0.dist-info
boltons                                       kiwisolver-1.4.4.dist-info          scipy.libs
boltons-21.0.0.dist-info                      kubernetes                          setuptools
cachetools                                    kubernetes-23.6.0.dist-info         setuptools-44.0.0.dist-info
cachetools-5.2.1.dist-info                    loxun-2.0.egg-info                  six-1.16.0.dist-info
cattr                                         loxun.py                            six.py
cattrs                                        matplotlib                          skimage
cattrs-22.2.0.dist-info                       matplotlib-3.6.2-py3.8-nspkg.pth    sklearn
certifi                                       matplotlib-3.6.2.dist-info          smmap
certifi-2022.12.7.dist-info                   mpl_toolkits                        smmap-5.0.0.dist-info
cffi                                          multidict                           sniffio
cffi-1.15.1.dist-info                         multidict-6.0.4.dist-info           sniffio-1.3.0.dist-info
charset_normalizer                            natsort                             tests
charset_normalizer-2.1.1.dist-info            natsort-6.2.1.dist-info             threadpoolctl-3.1.0.dist-info
cluster_tools                                 networkx                            threadpoolctl.py
cluster_tools-0.11.1.dist-info                networkx-2.8.8.dist-info            tifffile
colorama                                      nibabel                             tifffile-2022.10.10.dist-info
colorama-0.4.6.dist-info                      nibabel-2.5.2.dist-info             typing_extensions-4.4.0.dist-info
commonmark                                    nisext                              typing_extensions.py
commonmark-0.9.1.dist-info                    numcodecs                           universal_pathlib-0.0.19.dist-info
contourpy                                     numcodecs-0.11.0.dist-info          upath
contourpy-1.0.6.dist-info                     numpy                               urllib3
cycler-0.11.0.dist-info                       numpy-1.24.1.dist-info              urllib3-1.26.13.dist-info
cycler.py                                     numpy.libs                          webknossos
czifile                                       oauthlib                            webknossos-0.11.1.dist-info
czifile-2019.7.2.dist-info                    oauthlib-3.2.2.dist-info            websocket
dateutil                                      packaging                           websocket_client-1.4.2.dist-info
dotenv                                        packaging-23.0.dist-info            wkcuber
easy_install.py                               pip                                 wkcuber-0.11.1.dist-info
entrypoints-0.4.dist-info                     pip-20.0.2.dist-info                wkw
entrypoints.py                                pkg_resources                       wkw-1.1.18.dist-info
exceptiongroup                                pkg_resources-0.0.0.dist-info       yaml
exceptiongroup-1.1.0.dist-info                psutil                              yarl
fasteners                                     psutil-5.9.4.dist-info              yarl-1.8.2.dist-info
fasteners-0.18.dist-info                      pyasn1                              zarr
fontTools                                     pyasn1-0.4.8.dist-info              zarr-2.13.3.dist-info
fonttools-4.38.0.dist-info                    pyasn1_modules                      zipp
frozenlist                                    pyasn1_modules-0.2.8.dist-info      zipp-3.11.0.dist-info
frozenlist-1.3.3.dist-info                    pycparser
fsspec                                        pycparser-2.21.dist-info

Let me know if you need further info

[jstriebel]

Hi, sorry for the issue. Please try a numpy version <=1.20, it seems like np.float vanished in recent versions. We'll fix it in the code as well to support newer versions.

[boergens]

Hi, that worked, thank you for your help!