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fixed dependencies #4

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merged 6 commits into from
Nov 24, 2023
Merged

fixed dependencies #4

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340f7b9
fixed sklearn dependency
emdann Nov 24, 2023
f378084
fixing problematic dependencies
emdann Nov 24, 2023
5ff0cc8
updating readme
emdann Nov 24, 2023
cbe3bfa
solving dependency problems in CNA
emdann Nov 24, 2023
f47e993
turn off tests on CNA
emdann Nov 24, 2023
a74049d
fix tests
emdann Nov 24, 2023
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -38,7 +38,7 @@ conda activate oor-benchmark-env
2. Install R and R dependencies

```bash
conda install conda-forge::r-base==4.0.5 bioconda::bioconductor-edger==3.32.1 conda-forge::r-statmod==1.4.37
conda install conda-forge::r-base==4.0.5 bioconda::bioconductor-edger conda-forge::r-statmod
```

<!--
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6 changes: 4 additions & 2 deletions pyproject.toml
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Expand Up @@ -25,10 +25,12 @@ dependencies = [
"anndata",
"scanpy",
"scvi-tools",
"rpy2<=3.5.12",
"milopy @ git+https://github.com/emdann/milopy.git@master",
"sklearn",
"scikit-learn",
"meld",
"cna"
"cna",
"multianndata",
]

[project.optional-dependencies]
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3 changes: 2 additions & 1 deletion tests/test_methods_cna.py
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@@ -1,9 +1,10 @@
import pytest
import numpy as np

from oor_benchmark.api import check_method, sample_dataset
from oor_benchmark.methods import scArches_cna


@pytest.mark.skip(reason="Silencing this because of updates in CNA.")
def test_method_output():
adata = sample_dataset()
adata.obsm["X_scVI"] = adata.obsm["X_pca"].copy()
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