From e587f67c73866d4edbf90e1a44b11074912df600 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 4 Jan 2024 02:03:28 +0300
Subject: Add tests for parsing 'phenocovar' files.

---
 tests/r_qtl/test_files/test_phenocovar.zip         | Bin 0 -> 516 bytes
 .../test_files/test_phenocovar_transposed.zip      | Bin 0 -> 567 bytes
 tests/r_qtl/test_r_qtl2_pheno.py                   |  26 +++++++++++++++++++++
 3 files changed, 26 insertions(+)
 create mode 100644 tests/r_qtl/test_files/test_phenocovar.zip
 create mode 100644 tests/r_qtl/test_files/test_phenocovar_transposed.zip

(limited to 'tests')

diff --git a/tests/r_qtl/test_files/test_phenocovar.zip b/tests/r_qtl/test_files/test_phenocovar.zip
new file mode 100644
index 0000000..7b8f079
Binary files /dev/null and b/tests/r_qtl/test_files/test_phenocovar.zip differ
diff --git a/tests/r_qtl/test_files/test_phenocovar_transposed.zip b/tests/r_qtl/test_files/test_phenocovar_transposed.zip
new file mode 100644
index 0000000..e3f9185
Binary files /dev/null and b/tests/r_qtl/test_files/test_phenocovar_transposed.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index 46be469..66850a0 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -31,3 +31,29 @@ def test_parse_pheno_files(filepath, expected):
     with ZipFile(Path(filepath).absolute(), "r") as zfile:
         cdata = rqtl2.control_data(zfile)
         assert tuple(rqtl2.file_data(zfile, "pheno", cdata)) == expected
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/test_phenocovar.zip",
+      ({"pheno": "T0", "time (hrs)": "0"},
+       {"pheno": "T2", "time (hrs)": "0.0333333333333333"},
+       {"pheno": "T4", "time (hrs)": "0.0666666666666667"},
+       {"pheno": "T6", "time (hrs)": "0.1"},
+       {"pheno": "T8", "time (hrs)": "0.133333333333333"})),
+     ("tests/r_qtl/test_files/test_phenocovar_transposed.zip",
+      ({"pheno": "T0", "time (hrs)": "0"},
+       {"pheno": "T2", "time (hrs)": "0.0333333333333333"},
+       {"pheno": "T4", "time (hrs)": "0.0666666666666667"},
+       {"pheno": "T6", "time (hrs)": "0.1"},
+       {"pheno": "T8", "time (hrs)": "0.133333333333333"}))))
+def test_parse_phenocovar_files(filepath, expected):
+    """Test parsing of 'phenocovar' files from the R/qtl2 bundle.
+
+    GIVEN: path to a R/qtl2 bundle
+    WHEN: the 'phenocovar' file is parsed
+    THEN: verify the parsed data is as expected
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        cdata = rqtl2.control_data(zfile)
+        assert tuple(rqtl2.file_data(zfile, "phenocovar", cdata)) == expected
-- 
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