(chore) reformatted tests

wfondrie · Sep 7, 2024 · 3214c24 · 3214c24
1 parent 1809edd
commit 3214c24
Show file tree

Hide file tree

Showing 5 changed files with 70 additions and 57 deletions.
diff --git a/tests/system_tests/test_cli.py b/tests/system_tests/test_cli.py
@@ -69,7 +69,6 @@ def test_basic_cli(tmp_path, scope_files):
     assert targets_psms_df.iloc[0, 5] == "sp|P10809|CH60_HUMAN"
 
 
-
 def test_cli_options(tmp_path, scope_files):
     """Test non-defaults"""
     params = [

diff --git a/tests/unit_tests/test_confidence.py b/tests/unit_tests/test_confidence.py
@@ -178,7 +178,7 @@ def test_assign_confidence_parquet(psm_df_1000_parquet, tmp_path):
         assign_confidence(
             [copy.copy(psms_disk)],
             prefixes=[None],
-            descs=None, # should default to [True] as in the first case
+            descs=None,  # should default to [True] as in the first case
             dest_dir=tmp_path,
             max_workers=4,
             eval_fdr=0.02,

diff --git a/tests/unit_tests/test_parser_parquet.py b/tests/unit_tests/test_parser_parquet.py
@@ -10,32 +10,34 @@
 def std_parquet(tmp_path):
     """Create a standard pin file"""
     out_file = tmp_path / "std_pin.parquet"
-    df = pd.DataFrame([
-        {
-            "sPeCid": "DefaultDirection",
-            "LaBel": "0",
-            "pepTide": "-",
-            "sCore": "-",
-            "scanNR": "1",
-            "pRoteins": "-",
-        },
-        {
-            "sPeCid": "a",
-            "LaBel": "1",
-            "pepTide": "ABC",
-            "sCore": "5",
-            "scanNR": "2",
-            "pRoteins": "protein1",
-        },
-        {
-            "sPeCid": "b",
-            "LaBel": "-1",
-            "pepTide": "CBA",
-            "sCore": "10",
-            "scanNR": "3",
-            "pRoteins": "decoy_protein1",
-        },
-    ])
+    df = pd.DataFrame(
+        [
+            {
+                "sPeCid": "DefaultDirection",
+                "LaBel": "0",
+                "pepTide": "-",
+                "sCore": "-",
+                "scanNR": "1",
+                "pRoteins": "-",
+            },
+            {
+                "sPeCid": "a",
+                "LaBel": "1",
+                "pepTide": "ABC",
+                "sCore": "5",
+                "scanNR": "2",
+                "pRoteins": "protein1",
+            },
+            {
+                "sPeCid": "b",
+                "LaBel": "-1",
+                "pepTide": "CBA",
+                "sCore": "10",
+                "scanNR": "3",
+                "pRoteins": "decoy_protein1",
+            },
+        ]
+    )
     df.to_parquet(out_file, index=False)
     return out_file
 

diff --git a/tests/unit_tests/test_streaming.py b/tests/unit_tests/test_streaming.py
@@ -15,14 +15,18 @@
 @pytest.fixture
 def readers_to_merge():
     # Prepare two dataframe readers
-    df1 = pd.DataFrame({
-        "foo": [1, 3, 4, 5, 8, 10],
-        "bar": [20, 6, 3, 2, 1, 0],
-    })
-    df2 = pd.DataFrame({
-        "foo": [2, 2, 6, 9, 11, 13, 15],
-        "bar": [18, 16, 13, 6, 5, 5, 0],
-    })
+    df1 = pd.DataFrame(
+        {
+            "foo": [1, 3, 4, 5, 8, 10],
+            "bar": [20, 6, 3, 2, 1, 0],
+        }
+    )
+    df2 = pd.DataFrame(
+        {
+            "foo": [2, 2, 6, 9, 11, 13, 15],
+            "bar": [18, 16, 13, 6, 5, 5, 0],
+        }
+    )
     reader1 = DataFrameReader(df1)
     reader2 = DataFrameReader(df2)
     return [reader1, reader2]
@@ -31,14 +35,18 @@ def readers_to_merge():
 @pytest.fixture
 def readers_to_join():
     # Prepare two dataframe readers
-    df1 = pd.DataFrame({
-        "foo": [1, 3, 4, 5, 8, 10],
-        "bar": [20, 6, 3, 2, 1, 0],
-    })
-    df2 = pd.DataFrame({
-        "baz": [11, 13, 14, 15, 18, 110],
-        "quux": [220, 26, 23, 22, 21, 20],
-    })
+    df1 = pd.DataFrame(
+        {
+            "foo": [1, 3, 4, 5, 8, 10],
+            "bar": [20, 6, 3, 2, 1, 0],
+        }
+    )
+    df2 = pd.DataFrame(
+        {
+            "baz": [11, 13, 14, 15, 18, 110],
+            "quux": [220, 26, 23, 22, 21, 20],
+        }
+    )
     reader1 = DataFrameReader(df1)
     reader2 = DataFrameReader(df2)
     return [reader1, reader2]
@@ -51,10 +59,12 @@ def test_merged_tabular_data_reader(readers_to_merge):
     )
     pd.testing.assert_frame_equal(
         reader.read(),
-        pd.DataFrame({
-            "foo": [1, 2, 2, 3, 4, 5, 6, 8, 9, 10, 11, 13, 15],
-            "bar": [20, 18, 16, 6, 3, 2, 13, 1, 6, 0, 5, 5, 0],
-        }),
+        pd.DataFrame(
+            {
+                "foo": [1, 2, 2, 3, 4, 5, 6, 8, 9, 10, 11, 13, 15],
+                "bar": [20, 18, 16, 6, 3, 2, 13, 1, 6, 0, 5, 5, 0],
+            }
+        ),
     )
 
     # Check that chunked read works

diff --git a/tests/unit_tests/test_writer_flashlfq.py b/tests/unit_tests/test_writer_flashlfq.py
@@ -29,15 +29,17 @@ def test_basic(mock_conf, tmp_path):
     """Test that the basic output works"""
     conf = mock_conf
     df = pd.read_table(mokapot.to_flashlfq(conf, tmp_path / "test.txt"))
-    expected = pd.DataFrame({
-        "File Name": ["c.mzML"] * 2,
-        "Base Sequence": ["ABCDXYZ", "ABCDEFG"],
-        "Full Sequence": ["B.ABCD[+2.817]XYZ.A", "ABCDE(shcah8)FG"],
-        "Peptide Monoisotopic Mass": [1, 2],
-        "Scan Retention Time": [1.0, 2.0],
-        "Precursor Charge": [2, 3],
-        "Protein Accession": ["A|B|C; B|C|A", "A|B|C"],
-    })
+    expected = pd.DataFrame(
+        {
+            "File Name": ["c.mzML"] * 2,
+            "Base Sequence": ["ABCDXYZ", "ABCDEFG"],
+            "Full Sequence": ["B.ABCD[+2.817]XYZ.A", "ABCDE(shcah8)FG"],
+            "Peptide Monoisotopic Mass": [1, 2],
+            "Scan Retention Time": [1.0, 2.0],
+            "Precursor Charge": [2, 3],
+            "Protein Accession": ["A|B|C; B|C|A", "A|B|C"],
+        }
+    )
 
     pd.testing.assert_frame_equal(df, expected)