Outdated Requirements

[scjjb]

Hello, I just wanted to let you know that your environment as defined in requirements.txt no longer works because of a couple of updates to packages:

• zarr v3 removed ZipStore (this one is specifically an inference issue)
• segmentation-models-pytorch v0.3 removed init(..., use_batchnorm=True) from Conv2dReLU.
• timm is tricky for a couple of reasons, I couldn't figure out a version that was new enough to have convnextv2_tiny.fcmae_ft_in22k_in1k but old enough to have timm.models.layers.activations; this might actually be a problem in the version of segmentation_models_pytorch but I'm not sure

I haven't manage to resolve the timm/segmentation-models-pytorch issue so I'm not sure if there's any other issues.

Would you please be able to provide a requirements.txt with specific package versions to help to follow your work?

Thank you!

[eliasbaumann]

Hey, I updated the requirements in the inference repo, if you have time, could you try this for requirements.txt:

openslide-python==1.3.1
scikit-image==0.22.0
scikit-learn==1.3.2
scipy==1.11.4
opencv-python==4.8.1.78
pandas==2.1.3
tqdm
itk==5.4.0
matplotlib==3.8.2
mahotas@ git+https://github.com/luispedro/mahotas.git@f7edeb22a4b47e6c5200c008a8e7386067d72443
pandas==2.1.3
jupyterlab==4.0.9
zarr==2.16.1
tifffile==2023.9.26
h5py==3.10.0
segmentation-models-pytorch==0.1.0
networkx==2.8.7
libpysal==4.9.2
Pillow==9.3.0
shapely==2.0.2
staintools==2.1.2
albumentations==1.3.1
spams-bin==2.6.8
toml==0.10.2
numcodecs==0.12.1
imagecodecs==2023.9.18
timm==0.9.6
geojson==3.1.0
pylibCZIrw==4.1.3