flake8

gneiss/plot/tests/test_decompose.py

@@ -137,17 +137,17 @@ def test_proportion_plot(self):
                                    num_features, denom_features,
                                    self.feature_metadata,
                                    label_col='phylum')
-        res = np.vstack([l.get_xydata() for l in ax1.get_lines()])
+        res = np.vstack([L.get_xydata() for L in ax1.get_lines()])
         exp = np.array([0., 0., 1., 1., 2., 2., 3., 3.])
 
         npt.assert_allclose(res[:, 1], exp, verbose=True)
 
-        res = np.vstack([l.get_xydata() for l in ax2.get_lines()])
+        res = np.vstack([L.get_xydata() for L in ax2.get_lines()])
         exp = np.array([0., 0., 1., 1., 2., 2., 3., 3.])
 
         npt.assert_allclose(res[:, 1], exp, verbose=True)
 
-        res = [l._text for l in ax2.get_yticklabels()]
+        res = [L._text for L in ax2.get_yticklabels()]
         exp = ['p__bar', 'p__bar', 'p__tar', 'p__far']
         self.assertListEqual(res, exp)
 
@@ -162,17 +162,17 @@ def test_proportion_plot_order(self):
                                    num_features, denom_features,
                                    self.feature_metadata,
                                    label_col='phylum')
-        res = np.vstack([l.get_xydata() for l in ax1.get_lines()])
+        res = np.vstack([L.get_xydata() for L in ax1.get_lines()])
         exp = np.array([0., 0., 1., 1., 2., 2., 3., 3.])
 
         npt.assert_allclose(res[:, 1], exp, atol=1e-2, rtol=1e-2, verbose=True)
 
-        res = np.vstack([l.get_xydata() for l in ax2.get_lines()])
+        res = np.vstack([L.get_xydata() for L in ax2.get_lines()])
         exp = np.array([0., 0., 1., 1., 2., 2., 3., 3.])
 
         npt.assert_allclose(res[:, 1], exp, atol=1e-2, rtol=1e-2, verbose=True)
 
-        res = [l._text for l in ax2.get_yticklabels()]
+        res = [L._text for L in ax2.get_yticklabels()]
         exp = ['p__bar', 'p__bar', 'p__far', 'p__tar']
         self.assertListEqual(res, exp)
 
@@ -189,17 +189,17 @@ def test_proportion_plot_order_figure(self):
                                    num_features, denom_features,
                                    self.feature_metadata,
                                    label_col='phylum', axes=axes)
-        res = np.vstack([l.get_xydata() for l in ax1.get_lines()])
+        res = np.vstack([L.get_xydata() for L in ax1.get_lines()])
         exp = np.array([0., 0., 1., 1., 2., 2., 3., 3.])
 
         npt.assert_allclose(res[:, 1], exp, atol=1e-2, rtol=1e-2, verbose=True)
 
-        res = np.vstack([l.get_xydata() for l in ax2.get_lines()])
+        res = np.vstack([L.get_xydata() for L in ax2.get_lines()])
         exp = np.array([0., 0., 1., 1., 2., 2., 3., 3.])
 
         npt.assert_allclose(res[:, 1], exp, atol=1e-2, rtol=1e-2, verbose=True)
 
-        res = [l._text for l in ax2.get_yticklabels()]
+        res = [L._text for L in ax2.get_yticklabels()]
         exp = ['p__bar', 'p__bar', 'p__far', 'p__tar']
         self.assertListEqual(res, exp)
 
@@ -214,7 +214,7 @@ def test_proportion_plot_original_labels(self):
                                    num_features, denom_features,
                                    axes=axes)
 
-        res = [l._text for l in ax2.get_yticklabels()]
+        res = [L._text for L in ax2.get_yticklabels()]
         exp = ['A', 'B', 'D', 'C']
         self.assertListEqual(res, exp)
 

gneiss/plot/tests/test_heatmap.py

@@ -112,7 +112,7 @@ def test_basic_line_width(self):
 
         # Test to see if the lineages of the tree are ok
         lines = list(fig.get_axes()[1].get_lines())
-        widths = [l.get_lw() for l in lines]
+        widths = [L.get_lw() for L in lines]
         np.allclose(widths, [1.0] * len(widths))
 
     def test_highlights(self):

gneiss/util.py

@@ -412,19 +412,19 @@ def block_diagonal(ncols, nrows, nblocks):
     return mat
 
 
-def _shift(l, n):
+def _shift(L, n):
     """ Creates the band table by iteratively shifting a single vector.
 
     Parameters
     ----------
-    l : array
+    L : array
        Vector to be shifted
     n : int
        Max number of shifts
     """
-    sl = l
+    sl = L
 
-    table = [l]
+    table = [L]
 
     if n == 0:
         return table