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Installation error: module 'numpy.typing' has no attribute 'NDArray'
See original GitHub issueAfter testing #464 which gave me errors, I noticed that I wasn’t able to reinstall ADS. After the pip install and venv activation, I get this whenever I try to run one of the CLI scripts:
Error:
Traceback (most recent call last):
File "/home/herman/.conda/envs/ads_venv/bin/axondeepseg", line 33, in <module>
sys.exit(load_entry_point('AxonDeepSeg', 'console_scripts', 'axondeepseg')())
File "/home/herman/.conda/envs/ads_venv/bin/axondeepseg", line 25, in importlib_load_entry_point
return next(matches).load()
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/importlib/metadata.py", line 77, in load
module = import_module(match.group('module'))
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 843, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/home/herman/Documents/NEUROPOLY_21/axondeepseg/AxonDeepSeg/segment.py", line 28, in <module>
from AxonDeepSeg.apply_model import axon_segmentation
File "/home/herman/Documents/NEUROPOLY_21/axondeepseg/AxonDeepSeg/apply_model.py", line 8, in <module>
from ivadomed import inference as imed_inference
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/ivadomed/inference.py", line 15, in <module>
from ivadomed.loader.mri3d_subvolume_segmentation_dataset import MRI3DSubVolumeSegmentationDataset
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/ivadomed/loader/mri3d_subvolume_segmentation_dataset.py", line 8, in <module>
from ivadomed import transforms as imed_transforms, postprocessing as imed_postpro
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/ivadomed/transforms.py", line 17, in <module>
import torchio as tio
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/__init__.py", line 10, in <module>
from .transforms import * # noqa: F401, F403
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/transforms/__init__.py", line 1, in <module>
from .transform import Transform
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/transforms/transform.py", line 13, in <module>
from ..data.subject import Subject
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/data/__init__.py", line 1, in <module>
from .queue import Queue
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/data/queue.py", line 10, in <module>
from .sampler import PatchSampler
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/data/sampler/__init__.py", line 2, in <module>
from .label import LabelSampler
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/data/sampler/label.py", line 14, in <module>
class LabelSampler(WeightedSampler):
File "/home/herman/.conda/envs/ads_venv/lib/python3.8/site-packages/torchio/data/sampler/label.py", line 109, in LabelSampler
patch_size: npt.NDArray[np.uint],
AttributeError: module 'numpy.typing' has no attribute 'NDArray'
This is annoying (I don’t really have time to debug this today). Fortunately, I had another venv already setup so I can still use ADS on my laptop. It looks like a dependency problem (maybe some unpinned library was updated? not sure)
pip freeze
absl-py==0.13.0
alabaster==0.7.12
appdirs @ file:///home/conda/feedstock_root/build_artifacts/appdirs_1603108395799/work
argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1640817743617/work
argon2-cffi-bindings @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi-bindings_1649500309442/work
arrow==1.2.2
astor==0.8.1
astroid==2.9.3
asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1618968359944/work
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work
-e git+ssh://git@github.com/axondeepseg/axondeepseg.git@a800e307cfab899a55d7d60db2719c6f29184a95#egg=AxonDeepSeg
Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1655419414885/work
backcall @ file:///home/conda/feedstock_root/build_artifacts/backcall_1592338393461/work
backports.functools-lru-cache @ file:///home/conda/feedstock_root/build_artifacts/backports.functools_lru_cache_1618230623929/work
beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1649463573192/work
bids-validator==1.7.2
binaryornot==0.4.4
bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1656355450470/work
brotlipy @ file:///home/conda/feedstock_root/build_artifacts/brotlipy_1648854175163/work
cachetools==4.2.2
certifi==2020.11.8
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1656782821535/work
chardet==4.0.0
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1655906222726/work
click==8.0.1
cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1653061851209/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1655412516417/work
commonmark==0.9.1
contextlib2 @ file:///home/conda/feedstock_root/build_artifacts/contextlib2_1624848568296/work
cookiecutter==2.1.1
coverage @ file:///home/conda/feedstock_root/build_artifacts/coverage_1654179102739/work
cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1657174007680/work
csv-diff==1.1
cycler==0.10.0
cytoolz==0.11.2
dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1656089485461/work
dataclasses @ file:///home/conda/feedstock_root/build_artifacts/dataclasses_1628958434797/work
debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1649586349877/work
decorator==4.4.2
defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work
Deprecated==1.2.13
dictdiffer==0.8.1
dill @ file:///home/conda/feedstock_root/build_artifacts/dill_1653058582944/work
docopt==0.6.2
docutils @ file:///home/conda/feedstock_root/build_artifacts/docutils_1648737565474/work
entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1643888246732/work
et-xmlfile==1.0.1
executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1646044401614/work
fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/python-fastjsonschema_1641751198313/work/dist
file-tree @ file:///home/conda/feedstock_root/build_artifacts/file-tree_1653476294379/work
file-tree-fsl @ file:///home/conda/feedstock_root/build_artifacts/file-tree-fsl_1637872818453/work
filelock==3.0.12
flit_core @ file:///home/conda/feedstock_root/build_artifacts/flit-core_1645629044586/work/source/flit_core
formulaic==0.3.4
fsleyes @ file:///home/conda/feedstock_root/build_artifacts/fsleyes_1655300643563/work
fsleyes-props @ file:///home/conda/feedstock_root/build_artifacts/fsleyes-props_1619018550148/work
fsleyes-widgets @ file:///home/conda/feedstock_root/build_artifacts/fsleyes-widgets_1651273083908/work
fslpy @ file:///home/conda/feedstock_root/build_artifacts/fslpy_1656585277233/work
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1653010523205/work
future @ file:///home/conda/feedstock_root/build_artifacts/future_1649010148304/work
google-auth==1.32.1
google-auth-oauthlib==0.4.4
grpcio==1.38.1
h5py==2.10.0
humanize==4.2.3
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1642433548627/work
imagecodecs @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs_1655137610845/work
imageio==2.9.0
imagesize @ file:///home/conda/feedstock_root/build_artifacts/imagesize_1656939531508/work
importlib-metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1653252793585/work
importlib-resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1655356668708/work
indexed-gzip @ file:///home/conda/feedstock_root/build_artifacts/indexed_gzip_1653574409039/work
iniconfig @ file:///home/conda/feedstock_root/build_artifacts/iniconfig_1603384189793/work
interface-meta==1.3.0
ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1655369107642/work
ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1653754926575/work
ipython-genutils==0.2.0
ipywidgets @ file:///home/conda/feedstock_root/build_artifacts/ipywidgets_1655973868664/work
isodate @ file:///home/conda/feedstock_root/build_artifacts/isodate_1639582763789/work
isort==5.10.1
ivadomed==2.9.5
jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1649067097809/work
Jinja2==3.1.2
jinja2-time==0.2.0
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1633637554808/work
jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema-meta_1656454091745/work
jupyter @ file:///home/conda/feedstock_root/build_artifacts/jupyter_1637233111631/work
jupyter-client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1654730843242/work
jupyter-console @ file:///home/conda/feedstock_root/build_artifacts/jupyter_console_1655961255101/work
jupyter-core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1652365251650/work
jupyterlab-pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1649936611996/work
jupyterlab-widgets @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_widgets_1655961217661/work
kiwisolver==1.3.1
lazy-object-proxy==1.7.1
locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work
loguru==0.6.0
Markdown==3.3.4
MarkupSafe==2.1.1
matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1611858708474/work
matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1631080358261/work
mccabe==0.6.1
mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1635844675081/work
mpld3 @ file:///home/conda/feedstock_root/build_artifacts/mpld3_1653674415912/work
nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1656688109017/work
nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert-meta_1649676641343/work
nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1651607001005/work
nest-asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1648959695634/work
networkx==2.5.1
nibabel @ file:///home/conda/feedstock_root/build_artifacts/nibabel_1644264968592/work
notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1654636967533/work
num2words==0.5.10
numpy==1.20.3
oauthlib==3.1.1
onnxruntime==1.7.0
opencv-contrib-python==4.6.0.66
opencv-python-headless==4.6.0.66
openpyxl @ file:///home/conda/feedstock_root/build_artifacts/openpyxl_1632332968451/work
packaging==20.9
pandas==1.4.3
pandocfilters @ file:///home/conda/feedstock_root/build_artifacts/pandocfilters_1631603243851/work
parse @ file:///home/conda/feedstock_root/build_artifacts/parse_1610612363844/work
parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1638334955874/work
partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1617910651905/work
pathlib2 @ file:///home/conda/feedstock_root/build_artifacts/pathlib2_1649684025223/work
patsy==0.5.1
pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1602535608087/work
pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1657007156214/work
pipenv==2020.11.15
platformdirs==2.5.1
pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1648772598846/work
pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1643032624649/work
prettytable @ file:///home/conda/feedstock_root/build_artifacts/prettytable_1651787307815/work
progressbar2 @ file:///home/conda/feedstock_root/build_artifacts/progressbar2_1643742461370/work
prometheus-client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1649447152425/work
prompt-toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1656332401605/work
protobuf==3.20.1
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1653089172347/work
ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work
py @ file:///home/conda/feedstock_root/build_artifacts/py_1636301881863/work
pyasn1==0.4.8
pyasn1-modules==0.2.8
pybids==0.15.1
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work
pydicom @ file:///home/conda/feedstock_root/build_artifacts/pydicom_1648584438356/work
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1650904496387/work
pylint==2.12.2
PyOpenGL @ file:///home/conda/feedstock_root/build_artifacts/pyopengl_1652285526610/work
pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1643496850550/work
pyparsing==2.4.7
Pypubsub==4.0.3
PyQt5==5.15.4
PyQt5-sip==12.9.0
pyrsistent @ file:///home/conda/feedstock_root/build_artifacts/pyrsistent_1649013354401/work
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1648857275402/work
pytest==7.1.2
pytest-cov @ file:///home/conda/feedstock_root/build_artifacts/pytest-cov_1633356845954/work
python-dateutil==2.8.1
python-slugify==6.1.2
python-utils @ file:///home/conda/feedstock_root/build_artifacts/python-utils_1654078983092/work
pytz==2021.1
PyWavelets==1.1.1
PyYAML==6.0
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1656183564873/work
qtconsole @ file:///home/conda/feedstock_root/build_artifacts/qtconsole-base_1654465674650/work
QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1651524593465/work
raven==6.10.0
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1656534056640/work
requests-oauthlib==1.3.0
rich @ file:///home/conda/feedstock_root/build_artifacts/rich_1653400695283/work
rsa==4.7.2
Rtree @ file:///home/conda/feedstock_root/build_artifacts/rtree_1649367609955/work
scikit-image @ file:///home/conda/feedstock_root/build_artifacts/scikit-image_1638363134145/work
scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1639497510391/work
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1653073867187/work
seaborn==0.11.2
Send2Trash @ file:///home/conda/feedstock_root/build_artifacts/send2trash_1628511208346/work
SimpleITK==2.1.1.2
sip @ file:///home/conda/feedstock_root/build_artifacts/sip_1646101181167/work
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
snowballstemmer @ file:///home/conda/feedstock_root/build_artifacts/snowballstemmer_1637143057757/work
soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1638550740809/work
Sphinx @ file:///home/conda/feedstock_root/build_artifacts/sphinx_1655452194084/work
sphinx-rtd-theme @ file:///home/conda/feedstock_root/build_artifacts/sphinx_rtd_theme_1617698677674/work
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp @ file:///home/conda/feedstock_root/build_artifacts/sphinxcontrib-htmlhelp_1621704829796/work
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml @ file:///home/conda/feedstock_root/build_artifacts/sphinxcontrib-serializinghtml_1649380998999/work
SQLAlchemy==1.3.24
stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1655315839047/work
tabulate @ file:///home/conda/feedstock_root/build_artifacts/tabulate_1655900837660/work
tensorboard==2.9.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1652790603425/work
text-unidecode==1.3
textual @ file:///home/conda/feedstock_root/build_artifacts/textual_1653135219208/work
threadpoolctl==2.2.0
tifffile==2021.7.2
tinycss2 @ file:///home/conda/feedstock_root/build_artifacts/tinycss2_1637612658783/work
toml==0.10.2
tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work
toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1636177962100/work
torch==1.8.1+cpu
torchio==0.18.82
torchvision==0.9.1+cpu
tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1656937829196/work
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1649051611147/work
traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1655411388954/work
trimesh @ file:///home/conda/feedstock_root/build_artifacts/trimesh_1651880120104/work
typing_extensions==4.1.1
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1647489083693/work
virtualenv-clone==0.5.4
wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1600965781394/work
webencodings==0.5.1
Werkzeug==2.0.1
widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1655939017940/work
wrapt==1.13.3
wxnatpy @ file:///home/conda/feedstock_root/build_artifacts/wxnatpy_1633683489436/work
wxPython==4.1.1
xarray @ file:///home/conda/feedstock_root/build_artifacts/xarray_1646254587173/work
xnat @ file:///home/conda/feedstock_root/build_artifacts/xnat_1649668041065/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1649012893348/work
Issue Analytics
- State:
- Created a year ago
- Comments:7 (7 by maintainers)
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Yes, I agree. I deleted the venv, reinstalled everything for the 100th time and it finally works. Not sure what happened but I’ll close this now.
Can you check what version you’re uninstalling in your env? Maybe fixing it to 1.23.x in the installation would be a better solution if that’s the case?
The stranger thing (hehe) about this is that our linux CI isn’t catching this issue, so it really sounds something on your end. To be really sure, if you can, maybe you could create a new temporary user in your OS so that your really start with a “clean” installation. If it works there and not in your regular OS user, then it might just be a quirk in your current setup 😕