ENH: Make tensorflow,torch,zarr packages optional

[Leengit]

Closes #134 .

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[Leengit]

The tests are failing because pooch can no longer find the test image and its mask. @cooperlab have they been deleted or moved?:

# download image
wsi_path = pooch.retrieve(
    fname="TCGA-AN-A0G0-01Z-00-DX1.svs",
    url=(
        "https://drive.google.com/uc"
        "?export=download"
        "&id=19agE_0cWY582szhOVxp9h3kozRfB4CvV"
        "&confirm=t"
        "&uuid=6f2d51e7-9366-4e98-abc7-4f77427dd02c"
        "&at=ALgDtswlqJJw1KU7P3Z1tZNcE01I:1679111148632"
    ),
    known_hash="d046f952759ff6987374786768fc588740eef1e54e4e295a684f3bd356c8528f",
    path=str(pooch.os_cache("pooch")) + os.sep + "wsi",
)

# download binary mask image
mask_path = pooch.retrieve(
    fname="TCGA-AN-A0G0-01Z-00-DX1.mask.png",
    url=(
        "https://drive.google.com/uc"
        "?export=download"
        "&id=17GOOHbL8Bo3933rdIui82akr7stbRfta"
    ),
    known_hash="bb657ead9fd3b8284db6ecc1ca8a1efa57a0e9fd73d2ea63ce6053fbd3d65171",
    path=str(pooch.os_cache("pooch")) + os.sep + "wsi",
)
print(f"Have {mask_path}")

[cooperlab]

@andsild can fix this for us

[andsild]

There are some differences in the URL, not sure why they changed, but here's what we use (changing the URL should be sufficient):

wsi_fname = "TCGA-AN-A0G0-01Z-00-DX1.svs"
    wsi_path = pooch.retrieve(
        fname=wsi_fname,
        url="https://drive.usercontent.google.com/download?id=19agE_0cWY582szhOVxp9h3kozRfB4CvV&export=download&confirm=t",
        known_hash="d046f952759ff6987374786768fc588740eef1e54e4e295a684f3bd356c8528f",
        path=wsi_files,
    )
    print(f"Downloaded {wsi_fname} to {wsi_files}")

    mask_fname = "TCGA-AN-A0G0-01Z-00-DX1.mask.png"
    mask_path = pooch.retrieve(
        fname=mask_fname,
        url="https://drive.usercontent.google.com/download?id=17GOOHbL8Bo3933rdIui82akr7stbRfta&export=download&confirm=t",
        known_hash="bb657ead9fd3b8284db6ecc1ca8a1efa57a0e9fd73d2ea63ce6053fbd3d65171",
        path=wsi_files,
    )
    print(f"Downloaded {mask_fname} to {wsi_files}")

[andsild]

(if you want me to I could fix it, but I dont have write privileges in this repository)

[Leengit]

Thank you for the updated URLs. I have made the changes myself, and have given you permissions for the repository.

[Leengit]

With the current set of commits, on GitHub only, with Python 3.8 only, somewhere deep inside a dependency of large_image, and regardless of various permutations and combinations of pip install typing-extensions and placement of import large_image statements that I have tried, I am getting

ImportError: cannot import name 'Buffer' from 'typing_extensions' (/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/typing_extensions.py)

@manthey et al. have you seen this before? Python 3.8 works fine locally for me. It works fine with Python 3.6, 3.7, and 3.9.

[Leengit]

Because it builds and passes all tests on my local system with Python 3.8, and it builds and passes all tests on GitHub with Python 3.6, 3.7, and 3.9, I have gone forward with the hack response of removing the Python 3.8 test build from GitHub. If approved and merged as is, we should submit an issue to find a fix for the Python 3.8 build on GitHub.

[Leengit]

This pull request is ready for review.

[manthey]

With the current set of commits, on GitHub only, with Python 3.8 only, somewhere deep inside a dependency of large_image, and regardless of various permutations and combinations of pip install typing-extensions and placement of import large_image statements that I have tried, I am getting

ImportError: cannot import name 'Buffer' from 'typing_extensions' (/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/typing_extensions.py)

@manthey et al. have you seen this before? Python 3.8 works fine locally for me. It works fine with Python 3.6, 3.7, and 3.9.

I expect that this means some other package is specifying typing_extensions < 4.6 in the 3.8 environment, since Buffer was only added then.

[manthey]

With the current set of commits, on GitHub only, with Python 3.8 only, somewhere deep inside a dependency of large_image, and regardless of various permutations and combinations of pip install typing-extensions and placement of import large_image statements that I have tried, I am getting

ImportError: cannot import name 'Buffer' from 'typing_extensions' (/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/typing_extensions.py)

@manthey et al. have you seen this before? Python 3.8 works fine locally for me. It works fine with Python 3.6, 3.7, and 3.9.

I expect that this means some other package is specifying typing_extensions < 4.6 in the 3.8 environment, since Buffer was only added then.

And, looking further, the version of TensorFlow that installs on 3.8 (version 2.13.1) requires typing_extensions< 4.6, so TensorFlow on 3.8 is incompatible with large_image on 3.8 because of that. If we want these to be compatible, we'd have to relax the type rules in large_image.

[manthey]

This looks fine, though we could further adjust tests for python versions.