test unit for extract ri from comment

tests/test_data_extract_ri.py

@@ -0,0 +1,35 @@
+import pytest
+import pandas as pd
+from RIAssigner.data import PandasData, MatchMSData
+
+import os
+
+here = os.path.abspath(os.path.dirname(__file__))
+testdata_dir = os.path.join(here, 'data', 'ri_from_comment')
+
+@pytest.fixture
+def reference_data_csv(request):
+    filename = f'peaks_with_rt_ref_{request.param}.csv'
+    df_reference = pd.read_csv(os.path.join(testdata_dir, filename))
+    return df_reference['retention_index'].tolist()
+
+@pytest.mark.parametrize("reference_data_csv, comment_string", [("SemiStdNP", "SemiStdNP"), ("StdNP", "StdNP"), ("StdPolar", "StdPolar")], indirect=["reference_data_csv"])
+def test_extract_ri_from_csv_comment(reference_data_csv, comment_string):
+    query = PandasData(os.path.join(testdata_dir, 'nist_to_ri_2mols.csv'), "csv", rt_unit="seconds")
+    query.extract_ri_from_comment(comment_string)
+    assert query.retention_indices.tolist() == reference_data_csv
+
+@pytest.fixture
+def reference_data_msp(request):
+    filename = f'peaks_with_rt_ref_{request.param}_msp.csv'
+    df_reference = pd.read_csv(os.path.join(testdata_dir, filename), header=None, usecols=[0])
+    comment_parts = df_reference.loc[df_reference[0].str.startswith('COMMENT')][0].str.split()
+    comment = [part for sublist in comment_parts for part in sublist]
+    ri = [float(part.split('=')[1].split('/')[0]) for part in comment if part.startswith(request.param)]
+    return ri
+
+@pytest.mark.parametrize("reference_data_msp, comment_string", [("SemiStdNP", "SemiStdNP"), ("StdNP", "StdNP"), ("StdPolar", "StdPolar")], indirect=["reference_data_msp"])
+def test_extract_ri_from_msp_comment(reference_data_msp, comment_string):
+    query = MatchMSData(os.path.join(testdata_dir, 'NIST_EI_MS_2mols.msp'), "msp", rt_unit="min")
+    query.extract_ri_from_comment(comment_string)
+    assert query.retention_indices == reference_data_msp