HenriquesLab / ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
MIT License
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2D_Noise2Void fail to initialize on Colab #258

Closed alexcarisey closed 1 year ago

alexcarisey commented 1 year ago

Hello, Even the latest version of Noise2Void doesn't seem to be able to run on Colab. My guess is that it's due to broken dependencies and version conflicts maybe? While running the first cell I get the output pasted at the bottom of this message. I attempted to use numpy 1.20 but that breaks TensorFlow 2.5. Is someone else also noticing this behavior? I'm open to suggestions or ideas of things to try!

Thanks! -Alex

     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 454.4/454.4 MB 3.2 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.0/132.0 KB 18.2 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 69.2 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 98.3 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.0/4.0 MB 43.9 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 88.6 MB/s eta 0:00:00
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  Preparing metadata (setup.py) ... done
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 462.4/462.4 KB 41.7 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.6/5.6 MB 112.3 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.0/6.0 MB 119.2 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 116.2 MB/s eta 0:00:00
  Building wheel for termcolor (setup.py) ... done
  Building wheel for wrapt (setup.py) ... done
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.
xarray 2022.12.0 requires numpy>=1.20, but you have numpy 1.19.5 which is incompatible.
xarray-einstats 0.5.1 requires numpy>=1.20, but you have numpy 1.19.5 which is incompatible.
pydantic 1.10.7 requires typing-extensions>=4.2.0, but you have typing-extensions 3.7.4.3 which is incompatible.
optax 0.1.4 requires typing-extensions>=3.10.0, but you have typing-extensions 3.7.4.3 which is incompatible.
ml-dtypes 0.0.4 requires numpy>1.20, but you have numpy 1.19.5 which is incompatible.
matplotlib 3.7.1 requires numpy>=1.20, but you have numpy 1.19.5 which is incompatible.
librosa 0.10.0.post2 requires numpy!=1.22.0,!=1.22.1,!=1.22.2,>=1.20.3, but you have numpy 1.19.5 which is incompatible.
librosa 0.10.0.post2 requires typing-extensions>=4.1.1, but you have typing-extensions 3.7.4.3 which is incompatible.
jaxlib 0.4.7+cuda11.cudnn86 requires numpy>=1.21, but you have numpy 1.19.5 which is incompatible.
jax 0.4.7 requires numpy>=1.21, but you have numpy 1.19.5 which is incompatible.
grpcio-status 1.48.2 requires grpcio>=1.48.2, but you have grpcio 1.34.1 which is incompatible.
google-cloud-bigquery 3.4.2 requires grpcio<2.0dev,>=1.47.0, but you have grpcio 1.34.1 which is incompatible.
flax 0.6.8 requires typing-extensions>=4.1.1, but you have typing-extensions 3.7.4.3 which is incompatible.
cupy-cuda11x 11.0.0 requires numpy<1.26,>=1.20, but you have numpy 1.19.5 which is incompatible.
cmdstanpy 1.1.0 requires numpy>=1.21, but you have numpy 1.19.5 which is incompatible.
chex 0.1.7 requires typing-extensions>=4.2.0; python_version < "3.11", but you have typing-extensions 3.7.4.3 which is incompatible.
bokeh 2.4.3 requires typing-extensions>=3.10.0, but you have typing-extensions 3.7.4.3 which is incompatible.
astropy 5.2.2 requires numpy>=1.20, but you have numpy 1.19.5 which is incompatible.
arviz 0.15.1 requires numpy>=1.20.0, but you have numpy 1.19.5 which is incompatible.
arviz 0.15.1 requires typing-extensions>=4.1.0, but you have typing-extensions 3.7.4.3 which is incompatible.
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 301.1/301.1 KB 24.0 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
  Building wheel for h5py (setup.py) ... done
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.
tensorflow 2.5.0 requires h5py~=3.1.0, but you have h5py 2.10.0 which is incompatible.
arviz 0.15.1 requires numpy>=1.20.0, but you have numpy 1.19.5 which is incompatible.
arviz 0.15.1 requires typing-extensions>=4.1.0, but you have typing-extensions 3.7.4.3 which is incompatible.
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.5/47.5 KB 5.5 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 109.5/109.5 KB 15.0 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 69.6/69.6 KB 9.1 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.1/36.1 MB 41.1 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 519.4/519.4 KB 45.8 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 84.1 MB/s eta 0:00:00
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.
tensorflow 2.5.0 requires h5py~=3.1.0, but you have h5py 2.10.0 which is incompatible.
tensorflow 2.5.0 requires numpy~=1.19.2, but you have numpy 1.24.2 which is incompatible.
optax 0.1.4 requires typing-extensions>=3.10.0, but you have typing-extensions 3.7.4.3 which is incompatible.
numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 1.24.2 which is incompatible.
librosa 0.10.0.post2 requires typing-extensions>=4.1.1, but you have typing-extensions 3.7.4.3 which is incompatible.
flax 0.6.8 requires typing-extensions>=4.1.1, but you have typing-extensions 3.7.4.3 which is incompatible.
chex 0.1.7 requires typing-extensions>=4.2.0; python_version < "3.11", but you have typing-extensions 3.7.4.3 which is incompatible.
bokeh 2.4.3 requires typing-extensions>=3.10.0, but you have typing-extensions 3.7.4.3 which is incompatible.
arviz 0.15.1 requires typing-extensions>=4.1.0, but you have typing-extensions 3.7.4.3 which is incompatible.
  Preparing metadata (setup.py) ... done
  Building wheel for wget (setup.py) ... done
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 272.5/272.5 KB 20.9 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 377.8/377.8 KB 28.9 MB/s eta 0:00:00
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.7/50.7 KB 7.1 MB/s eta 0:00:00
--------
alexcarisey commented 1 year ago

Modifying the following versions requirements in the initialization cell fixed the issue: