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biolab / orange3-single-cell

🍊🔬 Orange add-on for gene expression of single cell data
https://singlecell.biolab.si/
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[ENH] Load data: Add data loader for H5AD format #356

Closed pavlin-policar closed 5 years ago

pavlin-policar commented 5 years ago
Issue

The load data widget does not support the h5ad format. This format is by far the nicest and fastest format I've used for sparse gene expression matrices. scanpy and seurat both support this format.

Description of changes

Add an H5AD reader.

Includes
JakaKokosar commented 5 years ago

Hm.. anndata is not available trough conda-forge channel (it is on bioconda channel). This means we will brake recipe build for the next release.

Support for multiple channels in recipes is not supported: https://github.com/conda/conda-build/pull/3656

Maybe we should just throw a warning if anndata can not be imported.

pavlin-policar commented 5 years ago

Is it possible to specify additional conda channels when building the package? anndata is available on conda through bioconda (taken from their readme: conda install anndata -c bioconda). I don't actually think this is possible, unforuntately.

It seems to me that this is constantly popping up. Isn't there some way to manually install the package through pip using build.sh?

JakaKokosar commented 5 years ago

https://github.com/conda-forge/staged-recipes/pull/9398

I have added you to be a maintainer, please confirm in PR.

JakaKokosar commented 5 years ago

This looks good to me! Also, the recipe tests pass and will hopefully be merged soon.

@VesnaT Can you maybe quickly look at it and merge if OK?

pavlin-policar commented 5 years ago

Actually, since we’re on the topic of licenses could we make sure that anndata is properly licensed so we can include it into our orange without making things complicated? Does anyone know who we could talk to about this?

On Tue, 3 Sep 2019 at 14:04, Jaka notifications@github.com wrote:

This looks good to me! Also, the recipe tests pass and will hopefully be merged soon.

@VesnaT https://github.com/VesnaT Can you maybe quickly look at it and merge if OK?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biolab/orange3-single-cell/pull/356?email_source=notifications&email_token=ABL5ZJ276V4L6AJ2EM7CCJDQHZHEFA5CNFSM4IS76MSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5X62ZI#issuecomment-527428965, or mute the thread https://github.com/notifications/unsubscribe-auth/ABL5ZJY53W5BQZD65A72OTDQHZHEFANCNFSM4IS76MSA .

JakaKokosar commented 5 years ago

What is wrong with the current license?

pavlin-policar commented 5 years ago

Never mind, I checked the license and it's got the BSD-3 clause, which should be fine.

A year or so ago there was a discussion in the lab about licensing and we had to be careful about which packages were added to dependencies because of this. I don't really know if that lead anywhere, but it's better to check this before adding a potentially non-commercially licensed software package to dependencies. But like I said, this one has BSD-3, which should be fine.