diff --git a/README.md b/README.md index a036842..3fd0c20 100644 --- a/README.md +++ b/README.md @@ -19,12 +19,9 @@ The package has been renamed to `wsi`. While the repository is private, make sure you [exchange SSH keys of the machine with Github.com](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account). -Then simply install with `pip`: +Then simply install with `pip` (make sure you have a recent enough version with `pip install pip -U`: ```bash -# pip install git+ssh://git@github.com:rendeirolab/wsi.git -git clone git@github.com:rendeirolab/wsi.git -cd wsi -pip install . +pip install git+https://github.com/rendeirolab/wsi.git ``` Note that the package uses setuptols-scm for version control and therefore the installation source needs to be a git repository (a zip file of source code won't work). @@ -125,6 +122,16 @@ gdata = slide.as_torch_geometric_data(feats, coords) # from existing features a gdata = slide.as_torch_geometric_data(model_name='resnet18') # without ``` +## Development + +`wsi` will not be providing new features and future maintenance will be restricted to bugs. Please refer to our newer project [Lazyslide](https://github.com/rendeirolab/LazySlide) for a more modern, interoperable package for the analysis of whole-slide images. + + +To contribute bug maintenance, clone the repository, open an issue in the [issue tracker](https://github.com/rendeirolab/wsi/issues), and submit a pull request. +``` +git clone git@github.com:rendeirolab/wsi.git +``` + ## Reference Please cite the [paper of the original authors](https://www.nature.com/articles/s41551-020-00682-w): diff --git a/wsi/wsi.py b/wsi/wsi.py index ec425ba..a57ec20 100755 --- a/wsi/wsi.py +++ b/wsi/wsi.py @@ -1843,7 +1843,7 @@ def inference( """ from typing import cast import torch - from tqdm_loggable.auto import tqdm + from tqdm.auto import tqdm if isinstance(model, torch.nn.Module): model = cast(torch.nn.Module, model)