solo

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Dependency conflict: lightning 2.1.4 and scvi-tools 1.1.2

1

When I try installing all the `solo` dependencies from `requirements.txt` with `conda`/`mamba`, the following clash is reported: ``` error libmamba Could not solve for environment specs The following packages are...

jpintar

AttributeError: 'numpy.ndarray' object has no attribute 'loc' when running solo on the test dataset

1

Dear developer team of Solo: I'm very sorry to bother you but I'm having a small problem running Solo on the GitHub test data . When I run Solo on...

dstyaaaaaa

Hi I'm trying to run the following: ``` import scanpy as sc adata = sc.read_10x_h5("sample_filtered_feature_bc_matrix.h5", gex_only=False) hdata = adata[:, adata.var.index.isin(["HTO_C0301", "HTO_C0302"])].copy() from solo import hashsolo hashsolo.hashsolo(hdata., number_of_noise_barcodes=1) ``` And it...

zktuong

Implement a proper logger

1

Implement a proper logger. Print statements aren't great

njbernstein

Problem with hashsolo

10

Hi, I just ran my solo analysis and now i need the information a bout which of my cells was predicted to be a doublet and so forth. If i...

Kani0n

Create notebook showing how to use and the benefits of Solo

1

cc: @vjojic

njbernstein

Add batching to Solo

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currently, users must manually break up their dataset if it contains multiple sample. We can help them by running Solo for them per batch. The main issue with this is...

njbernstein

Dependencies are too strict

1

Would it be possible to use `>=` instead of `==` in the package dependencies? As it stands, each time a package is updated, these dependencies will have to be updated...

JoshLoecker

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.2 to 4.66.3. Release notes Sourced from tqdm's releases. tqdm v4.66.3 stable cli: eval safety (fixes CVE-2024-34062, GHSA-g7vv-2v7x-gj9p) Commits 4e613f8 Merge pull request from GHSA-g7vv-2v7x-gj9p b53348c cli:...

dependabot[bot]

ImportError: cannot import name 'LightningLoggerBase' from 'pytorch_lightning.loggers'

1

Hi, how do you make software work? ``` solo -h Traceback (most recent call last): File "/root/miniconda3/envs/solo/bin/solo", line 5, in from solo.solo import main File "/root/miniconda3/envs/solo/lib/python3.12/site-packages/solo/solo.py", line 17, in import...

zznx