77from sgkit .utils import encode_array
88
99
10- def test_genee (datadir ):
10+ def test_genee (datadir = "test_genee/" ):
1111 # Simulated test data was created using https://github.com/ramachandran-lab/genee
1212 #
1313 # Edit Simulation.R to create a smaller dataset:
@@ -31,8 +31,8 @@ def test_genee(datadir):
3131 # write.csv(result, "/path/to/sgkit/sgkit/tests/test_genee/result.csv")
3232 # write.csv(t(sapply(gene_list, unlist)), "/path/to/sgkit/sgkit/tests/test_genee/gene_list.csv")
3333
34- mydata = pd .read_csv (datadir / "mydata.csv" , index_col = 0 )
35- ld = pd .read_csv (datadir / "ld.csv" , index_col = 0 )
34+ mydata = pd .read_csv (datadir + "mydata.csv" , index_col = 0 )
35+ ld = pd .read_csv (datadir + "ld.csv" , index_col = 0 )
3636
3737 # This was extracted from gene_list.csv
3838 gene_list = "1:7,8:14,15:19,20:25,26:35"
@@ -53,7 +53,7 @@ def test_genee(datadir):
5353
5454 df = genee (ds , ld ).compute ()
5555
56- expected = pd .read_csv (datadir / "result.csv" , index_col = 0 )
56+ expected = pd .read_csv (datadir + "result.csv" , index_col = 0 )
5757 expected = expected .reset_index ()
5858
5959 npt .assert_allclose (df ["test_q" ], expected ["test_q" ])
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