From 6b008c08928736f90db4f620535db22db71b0adc Mon Sep 17 00:00:00 2001
From: Michal Ziemski <mziemski@ethz.ch>
Date: Wed, 6 Sep 2023 16:30:06 +0200
Subject: [PATCH] Linting

---
 q2_types_genomics/kaiju/_format.py         | 14 ++++++++------
 q2_types_genomics/kaiju/_type.py           |  5 +++--
 q2_types_genomics/kaiju/tests/test_type.py |  4 +++-
 setup.py                                   |  4 +++-
 4 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/q2_types_genomics/kaiju/_format.py b/q2_types_genomics/kaiju/_format.py
index dead660..a485d8c 100644
--- a/q2_types_genomics/kaiju/_format.py
+++ b/q2_types_genomics/kaiju/_format.py
@@ -34,15 +34,17 @@ def _validate_n_records(self, n=None):
                 if not line[0].isnumeric() or not line[1].isnumeric():
                     raise ValidationError(
                         "NCBI taxonomy nodes file must contain a numeric "
-                        "taxonomy ID in the first two columns, found non-numeric "
-                        f"value on line {i + 1}."
+                        "taxonomy ID in the first two columns, found "
+                        f"non-numeric value on line {i + 1}."
                     )
                 for col in (5, 7, 9, 10, 11):
-                    if not line[col].isnumeric() or not int(line[col]) in (0, 1):
+                    if not line[col].isnumeric() or \
+                            not int(line[col]) in (0, 1):
                         raise ValidationError(
-                            "NCBI taxonomy nodes file must contain 0 or 1 in columns "
-                            "6, 8, 10, 11, and 12, found a non-allowed value on line "
-                            f"{i + 1}, column {col + 1}: {line[col]}."
+                            "NCBI taxonomy nodes file must contain 0 or 1 "
+                            "in columns 6, 8, 10, 11, and 12, found a "
+                            f"non-allowed value on line {i + 1}, column "
+                            f"{col + 1}: {line[col]}."
                         )
 
     def _validate_(self, level):
diff --git a/q2_types_genomics/kaiju/_type.py b/q2_types_genomics/kaiju/_type.py
index cb3dec1..169a023 100644
--- a/q2_types_genomics/kaiju/_type.py
+++ b/q2_types_genomics/kaiju/_type.py
@@ -5,7 +5,6 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-from q2_types.sample_data import SampleData
 from qiime2.plugin import SemanticType
 
 from . import KaijuDBDirectoryFormat
@@ -16,4 +15,6 @@
 
 plugin.register_semantic_types(KaijuDB)
 
-plugin.register_semantic_type_to_format(KaijuDB, artifact_format=KaijuDBDirectoryFormat)
+plugin.register_semantic_type_to_format(
+    KaijuDB, artifact_format=KaijuDBDirectoryFormat
+)
diff --git a/q2_types_genomics/kaiju/tests/test_type.py b/q2_types_genomics/kaiju/tests/test_type.py
index 3a0ee9b..10cf15f 100644
--- a/q2_types_genomics/kaiju/tests/test_type.py
+++ b/q2_types_genomics/kaiju/tests/test_type.py
@@ -20,7 +20,9 @@ def test_kaijudb_semantic_type_registration(self):
         self.assertRegisteredSemanticType(KaijuDB)
 
     def test_kaijudb_semantic_type_to_format_registration(self):
-        self.assertSemanticTypeRegisteredToFormat(KaijuDB, KaijuDBDirectoryFormat)
+        self.assertSemanticTypeRegisteredToFormat(
+            KaijuDB, KaijuDBDirectoryFormat
+        )
 
 
 if __name__ == "__main__":
diff --git a/setup.py b/setup.py
index 9983c25..3ff94b1 100644
--- a/setup.py
+++ b/setup.py
@@ -21,7 +21,9 @@
     license="BSD-3-Clause",
     url="https://github.com/bokulich-lab/q2-types-genomics",
     entry_points={
-        "qiime2.plugins": ["q2-types-genomics=q2_types_genomics.plugin_setup:plugin"]
+        "qiime2.plugins": [
+            "q2-types-genomics=q2_types_genomics.plugin_setup:plugin"
+        ]
     },
     package_data={
         'q2_types_genomics': ['citations.bib'],