flake8 fixes

q2_katharoseq/__init__.py

@@ -9,4 +9,4 @@
 from ._methods import read_count_threshold, estimating_biomass, biomass_plot
 
 __version__ = _version.get_versions()['version']
-__all__ = ['read_count_threshold', 'estimating_biomass']
+__all__ = ['read_count_threshold', 'estimating_biomass', 'biomass_plot']

q2_katharoseq/_methods.py

@@ -193,6 +193,7 @@ def estimating_biomass(
 
     return filtered
 
+
 def biomass_plot(
         output_dir: str,
         total_reads: qiime2.NumericMetadataColumn,
@@ -228,7 +229,7 @@ def biomass_plot(
     slope = lm.coef_[0]
 
     plt.clf()
-    plt.scatter(x,y, color='black')
+    plt.scatter(x, y, color='black')
     axes = plt.gca()
     x_vals = np.array(axes.get_xlim())
     y_vals = intercept + slope * x_vals

q2_katharoseq/tests/test_method.py

@@ -7,15 +7,16 @@
 from qiime2 import CategoricalMetadataColumn
 from qiime2 import NumericMetadataColumn
 
-from q2_katharoseq import read_count_threshold, estimating_biomass
+from q2_katharoseq import (read_count_threshold,
+                           estimating_biomass,
+                           biomass_plot)
 from q2_katharoseq._methods import allosteric_sigmoid
 from q2_katharoseq._methods import get_threshold
 
 from os.path import dirname, abspath, join
 from inspect import currentframe, getfile
 
 
-
 class KatharoSeqTestCase(TestCase):
 
     def setUp(self):
@@ -54,7 +55,7 @@ def setUp(self):
         self.control = 'classic'
         self.threshold = 50
 
-    def test_outputs_index(self): # OK
+    def test_outputs_index(self):
         with tempfile.TemporaryDirectory() as output_dir:
             read_count_threshold(
                 output_dir,
@@ -68,7 +69,7 @@ def test_outputs_index(self): # OK
             index_fp = os.path.join(output_dir, 'index.html')
             self.assertTrue(os.path.exists(index_fp))
 
-    def test_invalid_threshold(self): # OK 
+    def test_invalid_threshold(self):
         with tempfile.TemporaryDirectory() as output_dir, \
             self.assertRaisesRegex(
                 ValueError,
@@ -99,7 +100,7 @@ def test_invalid_threshold(self): # OK
                 self.table,
                 self.control)
 
-    def test_no_positive_controls_in_col(self): # OK
+    def test_no_positive_controls_in_col(self):
         ind = pd.Index(['s1', 's2', 's3', 's4'],
                        name='sampleid')
         positive_control_column = pd.Series(
@@ -124,7 +125,7 @@ def test_no_positive_controls_in_col(self): # OK
                 self.table,
                 self.control)
 
-    def test_no_positive_controls_in_table(self): # OK
+    def test_no_positive_controls_in_table(self):
         ind = pd.Index(
                 ['s5', 's6', 's7', 's8'],
                 name='sampleid')
@@ -151,14 +152,14 @@ def test_no_positive_controls_in_table(self): # OK
                 table,
                 self.control)
 
-    def test_sigmoid(self): # OK
+    def test_sigmoid(self):
         x = 1.0
         h = 2.0
         k_prime = 3.0
         a = allosteric_sigmoid(x, h, k_prime)
         self.assertTrue(a == .25)
 
-    def test_threshold(self): # OK
+    def test_threshold(self):
         r1 = [3.5, 2.3, 1.3, 3.4]
         r2 = [1.1, 2.2, 1.7, 2.3]
         thresh = 50.0
@@ -168,16 +169,6 @@ def test_threshold(self): # OK
     def test_estimating_biomass(self):
         fp = join(dirname(abspath(getfile(currentframe()))), 'support_files')
 
-        # One line at top of file describing dtype that throws this off
-        # data = pd.read_csv(
-        #     f'{fp}/input_estimating_biomass.tsv', sep='\t', dtype={
-        #         'sample_name': str, 'total_reads': float,
-        #         'control_cell_into_extraction': float,
-        #         'extraction_mass_g': float,
-        #         'positive_control': str})
-
-
-
         data = qiime2.Metadata.load(f'{fp}/input_estimating_biomass.tsv')
 
         obs = estimating_biomass(
@@ -194,7 +185,6 @@ def test_estimating_biomass(self):
             f'{fp}/output_estimating_biomass.tsv', sep='\t', index_col=0)
         pd.testing.assert_frame_equal(obs, exp)
 
-
     def test_biomass_plot(self):
         fp = join(dirname(abspath(getfile(currentframe()))), 'support_files')
 
@@ -207,14 +197,18 @@ def test_biomass_plot(self):
 
         data = qiime2.Metadata.load(f'{fp}/input_estimating_biomass.tsv')
 
-        biomass_plot(
-            total_reads=data.get_column('total_reads'),
-            control_cell_extraction=data.get_column('control_cell_into_extraction'),  # noqa
-            min_total_reads=1150,
-            positive_control_value='True',
-            positive_control_column=data.get_column('positive_control')
-        )
-        self.assertTrue(os.path.exists(index_fp))
+        with tempfile.TemporaryDirectory() as output_dir:
+            biomass_plot(
+                total_reads=data.get_column('total_reads'),
+                control_cell_extraction=data.get_column(
+                    'control_cell_into_extraction'),  # noqa
+                min_total_reads=1150,
+                positive_control_value='True',
+                positive_control_column=data.get_column('positive_control')
+            )
+
+            index_fp = os.path.join(output_dir, 'index.html')
+            self.assertTrue(os.path.exists(index_fp))
 
 
 if __name__ == '__main__':