fixed test errors

Author: kaseylove

tests/test_flow.py

@@ -15,8 +15,6 @@ def test_invalid_yaml_path(tmp_path: Path):
         _ = flow.load_csv_with_metadata("", tmp_path / "nonexistent.yaml")
     with pytest.raises(flow.YamlError):
         _ = flow.load_csv_with_metadata("", "wells")
-    with pytest.raises(flow.YamlError):
-        _ = flow.load_single_csv_with_metadata("", tmp_path / "nonexistent.yaml")
 
 
 def test_invalid_yaml_formatting(tmp_path: Path):
@@ -599,9 +597,7 @@ def test_csv_no_metadata(tmp_path: Path):
     df.sort_values(by="condition", inplace=True, ignore_index=True)
 
     data = [["A1", "singlets", 1, 2], ["G12", "singlets", 10, 20]]
-    df_manual = pd.DataFrame(
-        data, columns=["condition", "population", "channel1", "channel2"]
-    )
+    df_manual = pd.DataFrame(data, columns=["condition", "population", "channel1", "channel2"])
     assert df.equals(df_manual)
 
 
@@ -638,4 +634,4 @@ def test_csv_no_metadata_invalid_custom_regex(tmp_path: Path):
 
     regex = r"^.*export_(?P<construct>.+)_(?P<dox>.+)_(?P<day>.+)_(?P<population>.+)\.csv"
     with pytest.raises(flow.RegexError):
-        _ = flow.load_csv(str(tmp_path), regex)
+        _ = flow.load_csv(str(tmp_path), regex)

tests/test_qpcr.py

@@ -22,13 +22,11 @@ def test_single_csv(tmp_path: Path):
     with open(str(tmp_path / "data.csv"), "w") as f:
         f.write("""well,channel1,channel2\nA1,1,2""")
     yaml_path = str(tmp_path) + "/test.yaml"
-    df = qpcr.load_single_csv_with_metadata(str(tmp_path)+ "/data.csv", yaml_path)
+    df = qpcr.load_single_csv_with_metadata(str(tmp_path) + "/data.csv", yaml_path)
     df.sort_values(by="well", inplace=True, ignore_index=True)
 
     data = [["A1", 1, 2, "cond1"]]
-    df_manual = pd.DataFrame(
-        data, columns=["well", "channel1", "channel2", "condition"]
-    )
+    df_manual = pd.DataFrame(data, columns=["well", "channel1", "channel2", "condition"])
     assert df.equals(df_manual)
 
 
@@ -47,13 +45,13 @@ def test_single_csv_kwargs(tmp_path: Path):
     with open(str(tmp_path / "data.txt"), "w") as f:
         f.write("""well\tchannel1\tchannel2\nA1\t1\t2""")
     yaml_path = str(tmp_path) + "/test.yaml"
-    df = qpcr.load_single_csv_with_metadata(str(tmp_path)+ "/data.txt", yaml_path, csv_kwargs=dict(sep='\t'))
+    df = qpcr.load_single_csv_with_metadata(
+        str(tmp_path) + "/data.txt", yaml_path, csv_kwargs={"delimiter": ","}
+    )
     df.sort_values(by="well", inplace=True, ignore_index=True)
 
     data = [["A1", 1, 2, "cond1"]]
-    df_manual = pd.DataFrame(
-        data, columns=["well", "channel1", "channel2", "condition"]
-    )
+    df_manual = pd.DataFrame(data, columns=["well", "channel1", "channel2", "condition"])
     assert df.equals(df_manual)
 
 
@@ -72,17 +70,18 @@ def test_single_csv_well_column(tmp_path: Path):
     with open(str(tmp_path / "data.csv"), "w") as f:
         f.write("""my_well,channel1,channel2\nA1,1,2""")
     yaml_path = str(tmp_path) + "/test.yaml"
-    df = qpcr.load_single_csv_with_metadata(str(tmp_path)+ "/data.csv", yaml_path, well_column='my_well')
+    df = qpcr.load_single_csv_with_metadata(
+        str(tmp_path) + "/data.csv", yaml_path, well_column="my_well"
+    )
     df.sort_values(by="my_well", inplace=True, ignore_index=True)
 
     data = [["A1", 1, 2, "A1", "cond1"]]
-    df_manual = pd.DataFrame(
-        data, columns=["my_well", "channel1", "channel2", "well", "condition"]
-    )
+    df_manual = pd.DataFrame(data, columns=["my_well", "channel1", "channel2", "well", "condition"])
     assert df.equals(df_manual)
     # Reload specifying columns
-    df = qpcr.load_single_csv_with_metadata(str(tmp_path)+ "/data.csv", yaml_path, well_column='my_well',
-                                            columns=['channel1'])
+    df = qpcr.load_single_csv_with_metadata(
+        str(tmp_path) + "/data.csv", yaml_path, well_column="my_well", columns=["channel1"]
+    )
     assert "channel1" in df.columns
     assert "channel2" not in df.columns
 
@@ -102,13 +101,15 @@ def test_single_csv_invalid_well_column(tmp_path: Path):
     with open(str(tmp_path / "data.csv"), "w") as f:
         f.write("""my_well,channel1,channel2\nA1,1,2""")
     yaml_path = str(tmp_path) + "/test.yaml"
-    
+
     with pytest.raises(qpcr.ColumnError):
-        _ = qpcr.load_single_csv_with_metadata(str(tmp_path) + "/data.csv", yaml_path, well_column='other_well')
+        _ = qpcr.load_single_csv_with_metadata(
+            str(tmp_path) + "/data.csv", yaml_path, well_column="other_well"
+        )
 
 
 def test_single_csv_invalid_path(tmp_path: Path):
-    os.mkdir(tmp_path/'my_dir')
+    os.mkdir(tmp_path / "my_dir")
     with open(str(tmp_path / "test.yaml"), "w") as f:
         f.write(
             """
@@ -119,12 +120,22 @@ def test_single_csv_invalid_path(tmp_path: Path):
         )
 
     with pytest.raises(qpcr.DataPathError):
-        _ = qpcr.load_single_csv_with_metadata(str(tmp_path) + "/my_dir", str(tmp_path) + "/test.yaml")
+        _ = qpcr.load_single_csv_with_metadata(
+            str(tmp_path) + "/my_dir", str(tmp_path) + "/test.yaml"
+        )
+
+
+def test_invalid_yaml_path(tmp_path: Path):
+    """
+    Tests that invalid .yaml files throw errors
+    """
+    with pytest.raises(qpcr.YamlError):
+        _ = qpcr.load_single_csv_with_metadata("", tmp_path / "nonexistent.yaml")
 
 
 def test_qpcr_default(tmp_path: Path):
     """
-    Tests that a file with the qPCR default output can be loaded, 
+    Tests that a file with the qPCR default output can be loaded,
     and that it overrides previous kwargs
     """
     with open(str(tmp_path / "test.yaml"), "w") as f:
@@ -138,15 +149,18 @@ def test_qpcr_default(tmp_path: Path):
     with open(str(tmp_path / "data.txt"), "w") as f:
         f.write("""Nonsense first line\nPos\tCp\textra channel\nA1\t1\t2""")
     yaml_path = str(tmp_path) + "/test.yaml"
-    df = qpcr.load_single_csv_with_metadata(str(tmp_path)+ "/data.txt", yaml_path, 
-                                            well_column='bad_well', columns=['old_col'], csv_kwargs={'delimiter': ','}, 
-                                            is_default=True)
+    df = qpcr.load_single_csv_with_metadata(
+        str(tmp_path) + "/data.txt",
+        yaml_path,
+        well_column="bad_well",
+        columns=["old_col"],
+        csv_kwargs={"delimiter": ","},
+        is_default=True,
+    )
     df.sort_values(by="well", inplace=True, ignore_index=True)
 
     data = [["A1", 1, "A1", "cond1"]]
-    df_manual = pd.DataFrame(
-        data, columns=["Pos", "Cp", "well", "condition"]
-    )
+    df_manual = pd.DataFrame(data, columns=["Pos", "Cp", "well", "condition"])
     assert df.equals(df_manual)
 
 
@@ -164,17 +178,15 @@ def test_qpcr_default_real_data(tmp_path: Path):
         """
         )
     with open(str(tmp_path / "data.txt"), "w") as f:
-        f.write("""Experiment: 2025.08.07_galloway-gaprun-lib-quant_KL  Selected Filter: SYBR Green I / HRM Dye (465-510)
+        f.write("""Experiment: 2025.08.07_galloway-gaprun-lib-quant_KL  Filter: SYBR Green I
                 Include	Color	Pos	Name	Cp	Concentration	Standard	Status
                 True	255	A1	Sample 1	27.23		0	""")
     yaml_path = str(tmp_path) + "/test.yaml"
-    df = qpcr.load_single_csv_with_metadata(str(tmp_path)+ "/data.txt", yaml_path, is_default=True)
+    df = qpcr.load_single_csv_with_metadata(str(tmp_path) + "/data.txt", yaml_path, is_default=True)
     df.sort_values(by="well", inplace=True, ignore_index=True)
 
     data = [["A1", 27.23, "A1", "cond1"]]
-    df_manual = pd.DataFrame(
-        data, columns=["Pos", "Cp", "well", "condition"]
-    )
+    df_manual = pd.DataFrame(data, columns=["Pos", "Cp", "well", "condition"])
     assert df.equals(df_manual)
 
 
@@ -196,7 +208,6 @@ def test_plates(tmp_path: Path):
         )
     with open(str(tmp_path / sub_dir[0] / "plate1.csv"), "w") as f:
         f.write("""well,channel1,channel2\nA1,1,2\nG12,10,20""")
-    
 
     with open(str(tmp_path / sub_dir[1] / "test.yaml"), "w") as f:
         f.write(
@@ -207,12 +218,12 @@ def test_plates(tmp_path: Path):
         """
         )
     with open(str(tmp_path / sub_dir[1] / "plate2.csv"), "w") as f:
-        f.write("""well,channel1,channel2\nA1,3,4\nG12,30,""""")
+        f.write("""well,channel1,channel2\nA1,3,4\nG12,30,""" "")
 
     # Call function
     plates = pd.DataFrame(
         {
-            "data_path": [Path(tmp_path / d / f'plate{i+1}.csv') for i,d in enumerate(sub_dir)],
+            "data_path": [Path(tmp_path / d / f"plate{i+1}.csv") for i, d in enumerate(sub_dir)],
             "yaml_path": [Path(tmp_path / d / "test.yaml") for d in sub_dir],
             "extra_metadata": ["meta1", "meta2"],
         }
@@ -229,8 +240,10 @@ def test_plates(tmp_path: Path):
     df_manual = pd.DataFrame(
         data, columns=["condition", "channel1", "channel2", "well", "extra_metadata"]
     )
-    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
-    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
+    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis="columns")
+    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(
+        axis="columns"
+    )
     assert df.equals(df_manual)
 
     df = qpcr.load_plates_with_metadata(plates, filename_regex=r"plate(?P<plate>\d+)\.csv")
@@ -243,8 +256,10 @@ def test_plates(tmp_path: Path):
     df_manual = pd.DataFrame(
         data, columns=["condition", "channel1", "channel2", "well", "extra_metadata", "plate"]
     )
-    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
-    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
+    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis="columns")
+    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(
+        axis="columns"
+    )
     assert df.equals(df_manual)
 
 
@@ -253,7 +268,7 @@ def test_plates_valid_base_path(tmp_path: Path):
     Tests that several plates can be loaded using a valid base_path
     """
     # Create data
-    os.mkdir(tmp_path/"dir")
+    os.mkdir(tmp_path / "dir")
     with open(str(tmp_path / "dir" / "test1.yaml"), "w") as f:
         f.write(
             """
@@ -264,7 +279,6 @@ def test_plates_valid_base_path(tmp_path: Path):
         )
     with open(str(tmp_path / "dir" / "plate1.csv"), "w") as f:
         f.write("""well,channel1,channel2\nA1,1,2\nG12,10,20""")
-    
 
     with open(str(tmp_path / "dir" / "test2.yaml"), "w") as f:
         f.write(
@@ -285,7 +299,7 @@ def test_plates_valid_base_path(tmp_path: Path):
             "extra_metadata": ["meta1", "meta2"],
         }
     )
-    df = qpcr.load_plates_with_metadata(plates, base_path=(tmp_path/"dir"))
+    df = qpcr.load_plates_with_metadata(plates, base_path=(tmp_path / "dir"))
 
     # Check against manual output
     data = [
@@ -297,18 +311,20 @@ def test_plates_valid_base_path(tmp_path: Path):
     df_manual = pd.DataFrame(
         data, columns=["condition", "channel1", "channel2", "well", "extra_metadata"]
     )
-    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
-    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
+    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis="columns")
+    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(
+        axis="columns"
+    )
     assert df.equals(df_manual)
 
 
 def test_plates_df_regex(tmp_path: Path):
     """
-    Tests that several plates can be loaded using a valid filename_regex 
+    Tests that several plates can be loaded using a valid filename_regex
     for each plate
     """
     # Create data
-    os.mkdir(tmp_path/"dir")
+    os.mkdir(tmp_path / "dir")
     with open(str(tmp_path / "dir" / "test1.yaml"), "w") as f:
         f.write(
             """
@@ -319,7 +335,6 @@ def test_plates_df_regex(tmp_path: Path):
         )
     with open(str(tmp_path / "dir" / "2025_plate1.csv"), "w") as f:
         f.write("""well,channel1,channel2\nA1,1,2\nG12,10,20""")
-    
 
     with open(str(tmp_path / "dir" / "test2.yaml"), "w") as f:
         f.write(
@@ -337,11 +352,14 @@ def test_plates_df_regex(tmp_path: Path):
         {
             "data_path": ["2025_plate1.csv", "plate2_2026.csv"],
             "yaml_path": ["test1.yaml", "test2.yaml"],
-            "filename_regex": [r"(?P<date>\d+)_plate(?P<plate>\d+)\.csv", r"plate(?P<plate>\d+)_(?P<date>\d+)\.csv"],
+            "filename_regex": [
+                r"(?P<date>\d+)_plate(?P<plate>\d+)\.csv",
+                r"plate(?P<plate>\d+)_(?P<date>\d+)\.csv",
+            ],
             "extra_metadata": ["meta1", "meta2"],
         }
     )
-    df = qpcr.load_plates_with_metadata(plates, base_path=(tmp_path/"dir"))
+    df = qpcr.load_plates_with_metadata(plates, base_path=(tmp_path / "dir"))
 
     # Check against manual output
     data = [
@@ -351,10 +369,22 @@ def test_plates_df_regex(tmp_path: Path):
         ["cond1", 30, 40, "G12", "meta2", "2026", r"plate(?P<plate>\d+)_(?P<date>\d+)\.csv", "2"],
     ]
     df_manual = pd.DataFrame(
-        data, columns=["condition", "channel1", "channel2", "well", "extra_metadata", "date", "filename_regex", "plate"]
+        data,
+        columns=[
+            "condition",
+            "channel1",
+            "channel2",
+            "well",
+            "extra_metadata",
+            "date",
+            "filename_regex",
+            "plate",
+        ],
+    )
+    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis="columns")
+    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(
+        axis="columns"
     )
-    df = df.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
-    df_manual = df_manual.sort_values(by=["extra_metadata", "well"], ignore_index=True).sort_index(axis='columns')
     assert df.equals(df_manual)
 
 
@@ -363,7 +393,7 @@ def test_plates_invalid_regex(tmp_path: Path):
     Tests that error is raised if plate filename doesn't match passed regex
     """
     # Create data
-    os.mkdir(tmp_path/"dir")
+    os.mkdir(tmp_path / "dir")
     with open(str(tmp_path / "dir" / "test.yaml"), "w") as f:
         f.write(
             """
@@ -386,8 +416,11 @@ def test_plates_invalid_regex(tmp_path: Path):
         }
     )
     with pytest.raises(qpcr.RegexError):
-        _ = qpcr.load_plates_with_metadata(plates, base_path=(tmp_path/"dir"), 
-                                           filename_regex=r"plate(?P<plate>\d+)_(?P<date>\d+)\.csv")
+        _ = qpcr.load_plates_with_metadata(
+            plates,
+            base_path=(tmp_path / "dir"),
+            filename_regex=r"plate(?P<plate>\d+)_(?P<date>\d+)\.csv",
+        )
 
 
 def test_plates_invalid_df():
@@ -401,4 +434,4 @@ def test_plates_invalid_df():
     df_list = [df1, df2, df3]
     for df in df_list:
         with pytest.raises(qpcr.GroupsError):
-            _ = qpcr.load_plates_with_metadata(df)
+            _ = qpcr.load_plates_with_metadata(df)