style: Format tests

open2c · Apr 6, 2024 · 744dc33 · 744dc33
1 parent c2d9930
commit 744dc33
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Showing 6 changed files with 65 additions and 109 deletions.
diff --git a/tests/test_core_checks.py b/tests/test_core_checks.py
@@ -56,10 +56,7 @@ def test_is_cataloged():
         columns=["chrom", "start", "end", "funny_view_region"],
     )
     assert is_cataloged(
-        df,
-        view_df,
-        df_view_col="funny_view_region",
-        view_name_col="funny_name"
+        df, view_df, df_view_col="funny_view_region", view_name_col="funny_name"
     )
 
 
@@ -131,8 +128,8 @@ def test_is_contained():
         cols=["chrom1", "start1", "end1"],
         cols_view=["CHROM", "START", "END"],
         df_view_col="VIEW_REGION",
-        view_name_col="NAME"
-        )
+        view_name_col="NAME",
+    )
 
     with pytest.raises(TypeError):
         # cols and view_cols are not passed as an arguments
@@ -219,19 +216,16 @@ def test_is_covering():
         columns=["chrom1", "start1", "end1"],
     )
     chromsizes = pd.DataFrame(
-        [
-            ["chr1", 0, 9, "chr1p"],
-            ["chr1", 11, 20, "chr1q"]
-        ],
+        [["chr1", 0, 9, "chr1p"], ["chr1", 11, 20, "chr1q"]],
         columns=["CHROM", "START", "END", "NAME"],
-        )
+    )
     assert is_covering(
-                        df1,
-                        chromsizes,
-                        cols=["chrom1", "start1", "end1"],
-                        cols_view=["CHROM", "START", "END"],
-                        view_name_col="NAME"
-                    )
+        df1,
+        chromsizes,
+        cols=["chrom1", "start1", "end1"],
+        cols_view=["CHROM", "START", "END"],
+        view_name_col="NAME",
+    )
 
     with pytest.raises(ValueError):
         # cols and view_cols are not passed as an arguments
@@ -274,19 +268,16 @@ def test_is_tiling():
         columns=["chrom1", "start1", "end1", "view_region"],
     )
     chromsizes = pd.DataFrame(
-        [
-            ["chr1", 0, 9, "chr1p"],
-            ["chr1", 11, 20, "chr1q"]
-        ],
+        [["chr1", 0, 9, "chr1p"], ["chr1", 11, 20, "chr1q"]],
         columns=["CHROM", "START", "END", "NAME"],
-        )
+    )
     assert is_tiling(
-                        df1,
-                        chromsizes,
-                        cols=["chrom1", "start1", "end1"],
-                        cols_view=["CHROM", "START", "END"],
-                        view_name_col="NAME"
-                    )
+        df1,
+        chromsizes,
+        cols=["chrom1", "start1", "end1"],
+        cols_view=["CHROM", "START", "END"],
+        view_name_col="NAME",
+    )
 
     with pytest.raises(KeyError):
         # cols and view_cols are not passed as an arguments
@@ -477,7 +468,7 @@ def test_is_sorted():
         view_name_col="FRUIT",
         df_view_col="FRUIT",
         cols=["CHROM", "START", "END"],
-        cols_view=["CHROM", "START", "END"]
+        cols_view=["CHROM", "START", "END"],
     )
 
     with pytest.raises(ValueError):

diff --git a/tests/test_core_specs.py b/tests/test_core_specs.py
@@ -1,4 +1,3 @@
-
 import numpy as np
 import pandas as pd
 import pytest

diff --git a/tests/test_extras.py b/tests/test_extras.py
@@ -34,8 +34,7 @@ def test_make_chromarms():
         cols_mids=["chromosome", "loc"],
     )
     pd.testing.assert_frame_equal(
-        result,
-        arms.rename(columns={"chrom": "chromosome", "start": "lo", "end": "hi"})
+        result, arms.rename(columns={"chrom": "chromosome", "start": "lo", "end": "hi"})
     )
 
     # test passing 2 columns
@@ -52,9 +51,7 @@ def test_make_chromarms():
 
     # test for passing Series or dict
     result = bioframe.make_chromarms(
-        pd.Series({"chrX": 8}),
-        mids,
-        cols_mids=["chromosome", "loc"]
+        pd.Series({"chrX": 8}), mids, cols_mids=["chromosome", "loc"]
     )
     pd.testing.assert_frame_equal(arms, result)
 
@@ -196,11 +193,11 @@ def test_frac_gc():
 
 def test_seq_gc():
 
-    assert (0 == bioframe.seq_gc("AT"))
-    assert (np.isnan( bioframe.seq_gc("NNN")))
-    assert (1 == bioframe.seq_gc("NGnC"))
-    assert (0.5 == bioframe.seq_gc("GTCA"))
-    assert (0.25 == bioframe.seq_gc("nnnNgTCa", mapped_only=False))
+    assert 0 == bioframe.seq_gc("AT")
+    assert np.isnan(bioframe.seq_gc("NNN"))
+    assert 1 == bioframe.seq_gc("NGnC")
+    assert 0.5 == bioframe.seq_gc("GTCA")
+    assert 0.25 == bioframe.seq_gc("nnnNgTCa", mapped_only=False)
     with pytest.raises(ValueError):
         bioframe.seq_gc(["A", "T"])
     with pytest.raises(ValueError):

diff --git a/tests/test_ops_select.py b/tests/test_ops_select.py
@@ -6,33 +6,24 @@
 
 def test_select():
     df = pd.DataFrame(
-        [["chrX", 3, 8],
-         ["chr1", 4, 5],
-         ["chrX", 1, 5]],
+        [["chrX", 3, 8], ["chr1", 4, 5], ["chrX", 1, 5]],
         columns=["chrom", "start", "end"],
     )
 
-    result = pd.DataFrame(
-        [["chr1", 4, 5]],
-        columns=["chrom", "start", "end"]
-    )
+    result = pd.DataFrame([["chr1", 4, 5]], columns=["chrom", "start", "end"])
     pd.testing.assert_frame_equal(
         result, bioframe.select(df, "chr1:4-10").reset_index(drop=True)
     )
 
     result = pd.DataFrame(
-        [["chrX", 3, 8],
-         ["chrX", 1, 5]],
-         columns=["chrom", "start", "end"]
+        [["chrX", 3, 8], ["chrX", 1, 5]], columns=["chrom", "start", "end"]
     )
     pd.testing.assert_frame_equal(
         result, bioframe.select(df, "chrX").reset_index(drop=True)
     )
 
     result = pd.DataFrame(
-        [["chrX", 3, 8],
-         ["chrX", 1, 5]],
-         columns=["chrom", "start", "end"]
+        [["chrX", 3, 8], ["chrX", 1, 5]], columns=["chrom", "start", "end"]
     )
     pd.testing.assert_frame_equal(
         result, bioframe.select(df, "chrX:4-6").reset_index(drop=True)
@@ -52,14 +43,11 @@ def test_select__with_colnames():
     ### select with non-standard column names
     new_names = ["chr", "chrstart", "chrend"]
     df = pd.DataFrame(
-        [["chrX", 3, 8],
-         ["chr1", 4, 5],
-         ["chrX", 1, 5]],
+        [["chrX", 3, 8], ["chr1", 4, 5], ["chrX", 1, 5]],
         columns=new_names,
     )
     result = pd.DataFrame(
-        [["chrX", 3, 8],
-         ["chrX", 1, 5]],
+        [["chrX", 3, 8], ["chrX", 1, 5]],
         columns=new_names,
     )
     pd.testing.assert_frame_equal(
@@ -94,47 +82,32 @@ def test_select__with_nulls():
 
 def test_select__mask_indices_labels():
     df = pd.DataFrame(
-        [["chrX", 3, 8],
-         ["chr1", 4, 5],
-         ["chrX", 1, 5]],
+        [["chrX", 3, 8], ["chr1", 4, 5], ["chrX", 1, 5]],
         columns=["chrom", "start", "end"],
     )
 
     region = "chr1:4-10"
-    answer = pd.DataFrame(
-        [["chr1", 4, 5]],
-        columns=["chrom", "start", "end"]
-    )
+    answer = pd.DataFrame([["chr1", 4, 5]], columns=["chrom", "start", "end"])
 
     result = bioframe.select(df, region)
-    pd.testing.assert_frame_equal(
-        answer, result.reset_index(drop=True)
-    )
+    pd.testing.assert_frame_equal(answer, result.reset_index(drop=True))
     mask = bioframe.select_mask(df, region)
-    pd.testing.assert_frame_equal(
-        answer, df.loc[mask].reset_index(drop=True)
-    )
+    pd.testing.assert_frame_equal(answer, df.loc[mask].reset_index(drop=True))
     labels = bioframe.select_labels(df, region)
-    pd.testing.assert_frame_equal(
-        answer, df.loc[labels].reset_index(drop=True)
-    )
+    pd.testing.assert_frame_equal(answer, df.loc[labels].reset_index(drop=True))
     idx = bioframe.select_indices(df, region)
-    pd.testing.assert_frame_equal(
-        answer, df.iloc[idx].reset_index(drop=True)
-    )
+    pd.testing.assert_frame_equal(answer, df.iloc[idx].reset_index(drop=True))
 
 
 def test_select__query_intervals_are_half_open():
-    df = pd.DataFrame({
-        "chrom": ["chr1", "chr1",
-                  "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"],
-        "start": [0, 10,
-                  10, 20, 30, 40, 50, 60],
-        "end":  [10, 20,
-                 20, 30, 40, 50, 60, 70],
-        "name": ["a", "b",
-                 "A", "B", "C", "D", "E", "F"],
-    })
+    df = pd.DataFrame(
+        {
+            "chrom": ["chr1", "chr1", "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"],
+            "start": [0, 10, 10, 20, 30, 40, 50, 60],
+            "end": [10, 20, 20, 30, 40, 50, 60, 70],
+            "name": ["a", "b", "A", "B", "C", "D", "E", "F"],
+        }
+    )
 
     result = bioframe.select(df, "chr1")
     assert (result["name"] == ["a", "b"]).all()
@@ -172,16 +145,14 @@ def test_select__query_intervals_are_half_open():
 
 def test_select__with_point_intervals():
     # Dataframe containing "point intervals"
-    df = pd.DataFrame({
-        "chrom": ["chr1", "chr1",
-                  "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"],
-        "start": [0, 10,
-                  10, 20, 30, 40, 50, 60],
-        "end":  [10, 10,
-                 20, 30, 40, 50, 50, 70],
-        "name": ["a", "b",
-                 "A", "B", "C", "D", "E", "F"],
-    })
+    df = pd.DataFrame(
+        {
+            "chrom": ["chr1", "chr1", "chr2", "chr2", "chr2", "chr2", "chr2", "chr2"],
+            "start": [0, 10, 10, 20, 30, 40, 50, 60],
+            "end": [10, 10, 20, 30, 40, 50, 50, 70],
+            "name": ["a", "b", "A", "B", "C", "D", "E", "F"],
+        }
+    )
     result = bioframe.select(df, "chr1")
     assert (result["name"] == ["a", "b"]).all()
 
@@ -213,9 +184,7 @@ def test_select__with_point_intervals():
 def test_select__with_points():
     # Dataframe of points
     df = pd.DataFrame(
-        [["chrX", 3, "A"],
-         ["chr1", 4, "C"],
-         ["chrX", 1, "B"]],
+        [["chrX", 3, "A"], ["chr1", 4, "C"], ["chrX", 1, "B"]],
         columns=["chrom", "pos", "name"],
     )
 

diff --git a/tests/test_resources.py b/tests/test_resources.py
@@ -11,9 +11,7 @@ def test_fetch_chromsizes():
         assert chromsizes.name == "length"
         assert len(chromsizes) == 25
 
-        chromsizes_df = bioframe.fetch_chromsizes(
-            db, provider=provider, as_bed=True
-        )
+        chromsizes_df = bioframe.fetch_chromsizes(db, provider=provider, as_bed=True)
         assert isinstance(chromsizes_df, pd.DataFrame)
         assert list(chromsizes_df.columns) == ["chrom", "start", "end"]
         assert len(chromsizes_df) == 25

diff --git a/tests/test_vis.py b/tests/test_vis.py
@@ -28,11 +28,13 @@ def test_to_ucsc_colorstring():
     with pytest.raises(ValueError):
         bioframe.to_ucsc_colorstring("notacolor")
 
-    df = bioframe.from_any([
-        ["chr1", 0, 10, "red"],
-        ["chr1", 10, 20, "blue"],
-        ["chr2", 0, 10, "green"],
-        ["chr2", 10, 20, None],
-    ])
+    df = bioframe.from_any(
+        [
+            ["chr1", 0, 10, "red"],
+            ["chr1", 10, 20, "blue"],
+            ["chr2", 0, 10, "green"],
+            ["chr2", 10, 20, None],
+        ]
+    )
     df["itemRgb"] = df["name"].apply(bioframe.to_ucsc_colorstring)
     assert df["itemRgb"].tolist() == ["255,0,0", "0,0,255", "0,128,0", "0"]