lint fixes

q2_pysyndna/__init__.py

@@ -22,3 +22,14 @@
 
 __name__ = 'q2-pysyndna'
 __version__ = _version.get_versions()['version']
+
+__all__ = [__plugin_name__, __package_name__, __description__,
+           __long_description__, __license__, __author__, __email__,
+           __url__, __citations_fname__, SyndnaPoolCsvFormat,
+           SyndnaPoolDirectoryFormat, SyndnaPoolConcentrationTable,
+           LinearRegressionsYamlFormat, LinearRegressionsDirectoryFormat,
+           LinearRegressions, PysyndnaLogFormat, PysyndnaLogDirectoryFormat,
+           PysyndnaLog, TSVLengthFormat, TSVLengthDirectoryFormat, Length,
+           CoordsFormat, CoordsDirectoryFormat, Coords, fit, count_cells,
+           count_copies, view_log, view_fit]
+

q2_pysyndna/_settings.py

@@ -1,4 +1,3 @@
-
 __plugin_name__ = 'pysyndna'
 __package_name__ = 'q2_pysyndna'
 __description__ = 'Plugin to calculate absolute microbial cell counts'
@@ -9,4 +8,4 @@
 __author__ = 'Amanda Birmingham'
 __email__ = '[email protected]'
 __url__ = 'https://github.com/AmandaBirmingham/q2-pysyndna'
-__citations_fname__ = 'citations.bib'
+__citations_fname__ = 'citations.bib'

q2_pysyndna/_visualizer.py

@@ -89,7 +89,7 @@ def _check_context(context: dict) -> dict:
 
 
 def _generate_template_fps(html_fnames: list) -> list:
-    if not INDEX_FNAME in html_fnames:
+    if INDEX_FNAME not in html_fnames:
         html_fnames.append(INDEX_FNAME)
     return list(map(
         lambda page: os.path.join(TEMPLATES, page), html_fnames))

q2_pysyndna/plugin_setup.py

@@ -14,7 +14,6 @@
     LinearRegressionsObjects, LinearRegressions,
     LinearRegressionsYamlFormat, LinearRegressionsDirectoryFormat,
     yaml_fp_to_linear_regressions_yaml_format,
-    dict_to_linear_regressions_yaml_format,
     linear_regressions_directory_format_to_linear_regressions_objects,
     linear_regressions_objects_to_linear_regressions_directory_format)
 from q2_pysyndna._type_format_pysyndna_log import (
@@ -25,14 +24,11 @@
 from q2_pysyndna._type_format_length import (
     Length,
     TSVLengthFormat, TSVLengthDirectoryFormat,
-    length_fp_to_df,
-    df_to_tsv_length_format)
+    length_fp_to_df)
 from q2_pysyndna._type_format_coords import (
     Coords,
     CoordsFormat, CoordsDirectoryFormat,
-    coords_fp_to_df,
-    df_to_coords_format
-)
+    coords_fp_to_df)
 
 # plugin instantiation
 plugin = Plugin(
@@ -108,12 +104,6 @@ def _linear_regressions_yaml_format_to_dict(
     return yaml_fp_to_linear_regressions_yaml_format(str(data))
 
 
-# @plugin.register_transformer
-# def _dict_to_linear_regressions_yaml_format(
-#         data: dict) -> LinearRegressionsYamlFormat:
-#     return dict_to_linear_regressions_yaml_format(data)
-
-
 @plugin.register_transformer
 def _linear_regressions_directory_format_to_linear_regressions_objects(
         data: LinearRegressionsDirectoryFormat) -> LinearRegressionsObjects:
@@ -133,21 +123,11 @@ def _tsv_length_format_to_df(ff: TSVLengthFormat) -> pandas.DataFrame:
     return length_fp_to_df(str(ff))
 
 
-# @plugin.register_transformer
-# def _df_to_tsv_length_format(df: pandas.DataFrame) -> TSVLengthFormat:
-#     return df_to_tsv_length_format(df)
-
-
 @plugin.register_transformer
 def _coords_format_to_df(ff: CoordsFormat) -> pandas.DataFrame:
     return coords_fp_to_df(str(ff))
 
 
-# @plugin.register_transformer
-# def _df_to_coords_format(df: pandas.DataFrame) -> CoordsFormat:
-#     return df_to_coords_format(df)
-
-
 # Method registrations
 plugin.methods.register_function(
     function=q2_pysyndna.fit,

q2_pysyndna/tests/test_type_format_linear_regressions.py

@@ -130,8 +130,8 @@ class TestLinearRegressionsTransformers(TestPluginBase):
 
     LINREGOBJ_1_2_3 = LinearRegressionsObjects(
         linregs_dict=TEST_DICT_1_2_3,
-        log_msgs_list=["The following syndnas were dropped because they had fewer "
-         "than 200 total reads aligned:['p166']"])
+        log_msgs_list=["The following syndnas were dropped because they had "
+                       "fewer than 200 total reads aligned:['p166']"])
 
     @staticmethod
     def compare_linear_regressions_directory_formats(
@@ -254,13 +254,10 @@ def test_linear_regressions_objects_to_linear_regressions_directory_format(
             self):
         rel_fps = ['linear_regressions',
                    'linear_regressions_minimal']
-        abs_fps = [self.get_data_path(rel_fp)
-                     for rel_fp in rel_fps]
+        abs_fps = [self.get_data_path(rel_fp) for rel_fp in rel_fps]
 
         input_objs = [self.LINREGOBJ_1_2_3,
-            LinearRegressionsObjects(
-                self.TEST_DICT_1,
-                [])]
+                      LinearRegressionsObjects(self.TEST_DICT_1,[])]
 
         for i in range(len(abs_fps)):
             abs_fp = abs_fps[i]
@@ -272,4 +269,4 @@ def test_linear_regressions_objects_to_linear_regressions_directory_format(
             for exp_obs_pair in \
                     self.compare_linear_regressions_directory_formats(
                         expected_format, out_format):
-                self.assertEqual(exp_obs_pair[0], exp_obs_pair[1])
+                self.assertEqual(exp_obs_pair[0], exp_obs_pair[1])