scvi-tools

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Galen recently added functionality to store arbitrary things there too. There should be a few sentences about what it does.

adamgayoso

Vscode dev containers

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adamgayoso

Possibility of having different number of units in the hidden layers

1

I would like to know if it is possible for the VAE model (in scVI) to have different number of hidden units in each hidden layer. Currently, I am assuming...

gprashant17

There should be a straightforward way to add a random state functionality to scVI with minimal code duplication. This will be helpful in ensuring posterior predictive quantities and de, etc...

adamgayoso

train() arguments not used if train() was previously called

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Since we keep `self.trainer` persistent in train(), running train() again with new arguments for frequency, n_iter_kl_warmup, etc wont be reflected. ```python a = scvi.data.synthetic_iid() m = scvi.model.SCVI(a) m.train(10) print(m.history) #...

galenxing

The current implementation of scANVI only computes the ELBO without relying on the cell states' knowledge for labeled examples (see [here](https://github.com/YosefLab/scvi-tools/blob/master/scvi/core/trainers/annotation.py#L200)). We should fix this behavior and treat labeled and...

PierreBoyeau

Bump minimum Python version to 3.9, test with 3.8 - 3.10.

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Closes #1705. Changes include: - Remove `Literal` compatibility type

martinkim0

Fix links for breast cancer and mouse ob, add deprecation warning.

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Closes #1707.

martinkim0

Update CI workflow to separate static code checking from pytest.

1

Closes #1341.

martinkim0

Replace custom `attrdict` with `ml_collections` implementation.

2

Closes #1690.

martinkim0