lint

q2_qsip2/_wrangling.py

@@ -5,10 +5,8 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-import pandas as pd
 
-from collections import namedtuple
-from typing import NamedTuple, Optional
+from typing import Optional
 
 import qiime2
 
@@ -166,7 +164,7 @@ def _handle_metadata(
         metadata_type='source',
         extracted=extracted
     )
-    sample_metadata =_validate_metadata_columns(
+    sample_metadata = _validate_metadata_columns(
         sample_metadata,
         sample_column_mapping,
         metadata_type='sample',

q2_qsip2/plugin_setup.py

@@ -8,7 +8,7 @@
 
 import importlib
 
-from qiime2.plugin import Bool, Citations, List, Metadata, Plugin, Str
+from qiime2.plugin import Citations, List, Metadata, Plugin, Str
 from q2_types.feature_table import FeatureTable, Frequency
 
 from q2_qsip2 import __version__

q2_qsip2/tests/test_wrangling.py

@@ -41,7 +41,7 @@ def test_extract_source_metadata(self):
             'source-level-data': ['x', 'y'],
         })
 
-        self.assertTrue( exp.equals(extracted) )
+        self.assertTrue(exp.equals(extracted))
 
     def metadata_to_validate(self):
         df = pd.DataFrame({
@@ -58,6 +58,7 @@ def metadata_column_mapping(self):
             'isotope': None,
             'isotopolog': 'my-isotopolog-col',
         }
+
     def test_validate_metadata_columns(self):
         metadata = self.metadata_to_validate()
         columns_mapping = self.metadata_column_mapping()

q2_qsip2/types/_deferred_setup/_transformers.py

@@ -1,10 +1,15 @@
-import pandas as pd
+# ----------------------------------------------------------------------------
+# Copyright (c) 2024, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
 from rpy2.robjects.methods import RS4
 
 import pickle
 
-import qiime2
-
 from q2_qsip2.plugin_setup import plugin
 from q2_qsip2.types import QSIP2DataFormat
 

q2_qsip2/types/_formats.py

@@ -5,12 +5,11 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-import pandas as pd
+
 import rpy2.robjects as ro
 
 import pickle
 
-import qiime2
 from qiime2.plugin import ValidationError
 import qiime2.plugin.model as model
 

q2_qsip2/types/_types.py

@@ -6,7 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from qiime2.plugin import SemanticType, ValidationError
+from qiime2.plugin import SemanticType
 
 
 QSIP2Data = SemanticType('QSIP2Data')

q2_qsip2/types/tests/test_formats.py

@@ -8,7 +8,6 @@
 
 import biom
 import pandas as pd
-from pandas.testing import assert_frame_equal
 import rpy2.robjects as ro
 from rpy2.robjects.methods import RS4
 

q2_qsip2/types/tests/test_transformers.py

@@ -5,15 +5,13 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-import pandas as pd
-from pandas.testing import assert_frame_equal
+
 import rpy2.robjects as ro
 from rpy2.robjects.methods import RS4
 
 import importlib.resources
 import pickle
 
-import qiime2
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_qsip2.types import QSIP2DataFormat

q2_qsip2/visualizers/_helpers.py

@@ -1,21 +1,20 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2024, QIIME2.
+# Copyright (c) 2024, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-import rpy2.robjects as ro
 from rpy2.robjects.packages import importr
 
 import importlib.resources
 from pathlib import Path
 import shutil
-import tempfile
 
 ggplot2 = importr('ggplot2')
 
+
 def _ggplot2_object_to_visualization(
     ggplot2_obj: object, output_dir: Path, width: int, height: int
 ) -> None:

q2_qsip2/visualizers/_visualizers.py

@@ -18,6 +18,7 @@
 
 qsip2 = importr('qSIP2')
 
+
 def plot_weighted_average_densities(
     output_dir: str, qsip_data: RS4, group: Optional[str] = None
 ) -> None:

q2_qsip2/visualizers/tests/test_visualizers.py

@@ -8,7 +8,6 @@
 
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_qsip2.visualizers._visualizers import plot_weighted_average_density
 
 class VisualizerTests(TestPluginBase):
     package = 'q2_qsip2.visualizers.tests'

q2_qsip2/workflow.py

@@ -6,8 +6,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 import biom
-import pandas as pd
-import rpy2
 import rpy2.robjects as ro
 from rpy2.robjects.packages import importr
 from rpy2.robjects.methods import RS4
@@ -20,7 +18,6 @@
 from q2_qsip2._wrangling import (
     _construct_column_mapping,
     _handle_metadata,
-    _extract_source_metadata
 )
 
 qsip2 = importr('qSIP2')
@@ -35,7 +32,6 @@ def standard_workflow(
     return table
 
 
-
 def create_qsip_data(
     table: biom.Table,
     sample_metadata: qiime2.Metadata,
@@ -119,9 +115,9 @@ def create_qsip_data(
            table_df, feature_id='ASV'
         )
         R_qsip_obj = qsip2.qsip_data(
-            source_data = R_source_obj,
-            sample_data = R_sample_obj,
-            feature_data = R_feature_obj
+            source_data=R_source_obj,
+            sample_data=R_sample_obj,
+            feature_data=R_feature_obj
         )
 
     return R_qsip_obj