From 9ab4316ee3c4d3068053c94334c64915514d8664 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 28 Feb 2024 10:55:00 +0300
Subject: tests: Update unit tests: remove use of obsoleted functions.

---
 tests/r_qtl/test_r_qtl2_geno.py  | 19 +++++++++++++++----
 tests/r_qtl/test_r_qtl2_pheno.py | 11 ++++++++---
 2 files changed, 23 insertions(+), 7 deletions(-)

(limited to 'tests')

diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index d3c77e6..a1e69b7 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -273,12 +273,23 @@ def test_parse_founder_geno_files(relpath, expected):
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
-    "filepath,expected",
+    "filepath,member,transposed,expected",
     (("tests/r_qtl/test_files/test_geno.zip",
+      "test_geno.csv",
+      False,
       ("1", "2", "3", "4", "5", "6", "7", "8", "9", "10")),
      ("tests/r_qtl/test_files/test_geno_transposed.zip",
+      "test_geno_transposed.csv",
+      True,
       ("1", "2", "3", "4", "5", "6", "7", "8", "9", "10")),
      ("tests/r_qtl/test_files/test_geno_multiple.zip",
-      ("1", "2", "3", "4", "5", "6", "7", "8", "9", "10"))))
-def test_load_geno_samples(filepath, expected):
-    assert sorted(rqtl2.load_geno_samples(filepath)) == sorted(expected)
+      "test_geno_multiple01.csv",
+      False,
+      ("1", "2", "3", "4", "5")),
+     ("tests/r_qtl/test_files/test_geno_multiple.zip",
+      "test_geno_multiple02.csv",
+      False,
+      ("6", "7", "8", "9", "10"))))
+def test_load_geno_samples(filepath, member, transposed, expected):
+    assert sorted(rqtl2.load_samples(
+        filepath, member, transposed)) == sorted(expected)
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index d31ad54..54244fc 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -61,10 +61,15 @@ def test_parse_phenocovar_files(filepath, expected):
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
-    "filepath,expected",
+    "filepath,member,transposed,expected",
     (("tests/r_qtl/test_files/test_pheno.zip",
+      "test_pheno.csv",
+      False,
       ("1", "2", "3", "4", "5")),
      ("tests/r_qtl/test_files/test_pheno_transposed.zip",
+      "test_pheno_transposed.csv",
+      True,
       ("1", "2", "3", "4", "5"))))
-def test_load_geno_samples(filepath, expected):
-    assert sorted(rqtl2.load_pheno_samples(filepath)) == sorted(expected)
+def test_load_geno_samples(filepath, member, transposed, expected):
+    assert sorted(rqtl2.load_samples(
+        filepath, member, transposed)) == sorted(expected)
-- 
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