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msk-mind / luna

Scripts for data processing
https://msk-mind.github.io/luna
Apache License 2.0
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Need a stable new release #394

Open cell-lives opened 1 year ago

cell-lives commented 1 year ago

I'm getting used to luna. After creating the environment with docker, I found a lot of problems when running notebooks in the tutorial.

In 2_tiling-file, the save_tiles command parameters have changed a lot, where --num_cores and --dataset-id parameters are not recognized correctly.

In 3_model-training, the train_tissue_classifier command is even not available. In addition, I reviewed the luna.pathology.cli module in the dev branch and found no definition of train_tissue_classifier.

Later, I tried the release of pyluna 0.3.3 and installed it in the docker image of the luna_tutorial. When trying to run the first code block in 1_dataset-prep, threw an error, "ModuleNotFoundError: No module named 'luna'". however, pip list |grep luna found the pyluna module. When I tried to import the pyluna module by import pyluna, threw an error, "ModuleNotFoundError: No module named 'pyluna'", too.

I think the reason for the above errors and issues is no right stable release or correct branch for user. Therefore, I expect the development team to release a new stable version. Or tell the user in the tutorial which branch they should use to install luna.

armaank commented 1 year ago

Hi - correct! We're working on a new release/version of luna after a major refactor, so the current set of tutorials isn't guaranteed to work. Thanks for your patience. Do you have a specific use case you have in mind for luna that I can address?

To answer your questions in detail, yes, a lot of the CLI arguments have changed - the latest doc build here should have them all documented (for example: https://msk-mind.github.io/luna/cli_reference/pathology/save_tiles/ )

We decided to remove the train_tissue_classifier from luna, so that tutorial will no longer work.

If you want to install luna properly, I'd suggest following steps 1 and 2 here while we work on an official pypi release.

cell-lives commented 1 year ago

Glad to hear from you. First of all, I am using luna to reproduce the results of this paper, Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer. Perhaps you could tell me which branch of luna needs to be used for the reproduction of this paper?

After reproduction, I would like to formally use it in my project. I was wondering what is your timeline for the release of the new version? I might consider waiting for your new version to be released before officially using it.

Looking forward to your reply！