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from sgkit .utils import encode_array
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- def test_genee (datadir ):
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+ def test_genee (datadir = "test_genee/" ):
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# Simulated test data was created using https://github.com/ramachandran-lab/genee
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#
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# Edit Simulation.R to create a smaller dataset:
@@ -31,8 +31,8 @@ def test_genee(datadir):
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# write.csv(result, "/path/to/sgkit/sgkit/tests/test_genee/result.csv")
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# write.csv(t(sapply(gene_list, unlist)), "/path/to/sgkit/sgkit/tests/test_genee/gene_list.csv")
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- mydata = pd .read_csv (datadir / "mydata.csv" , index_col = 0 )
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- ld = pd .read_csv (datadir / "ld.csv" , index_col = 0 )
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+ mydata = pd .read_csv (datadir + "mydata.csv" , index_col = 0 )
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+ ld = pd .read_csv (datadir + "ld.csv" , index_col = 0 )
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# This was extracted from gene_list.csv
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gene_list = "1:7,8:14,15:19,20:25,26:35"
@@ -53,7 +53,7 @@ def test_genee(datadir):
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df = genee (ds , ld ).compute ()
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- expected = pd .read_csv (datadir / "result.csv" , index_col = 0 )
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+ expected = pd .read_csv (datadir + "result.csv" , index_col = 0 )
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expected = expected .reset_index ()
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npt .assert_allclose (df ["test_q" ], expected ["test_q" ])
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