Fix a myriad of linter issues

* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes

6 files changed, 31 insertions, 27 deletions

diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 69d4c52..267ced3 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -1,10 +1,10 @@
 """Module contains the tests for correlation"""
+import math
 from unittest import TestCase
 from unittest import mock
+from collections import namedtuple
 
 import pytest
-from collections import namedtuple
-import math
 from numpy.testing import assert_almost_equal
 
 from gn3.computations.correlations import normalize_values
@@ -58,12 +58,12 @@ class DataBase(QueryableMixin):
         """expects the expectede results value to be an array"""
         self.password = password
         self.db_name = db_name
-        self.__query_options = None
+        self.__query_options = None # pylint: disable=[W0238]
         self.results_generator(expected_results)
 
     def execute(self, query_options):
         """method to execute an sql query"""
-        self.__query_options = query_options
+        self.__query_options = query_options # pylint: disable=[W0238]
         return 1
 
     def cursor(self):
diff --git a/tests/unit/computations/test_dictify_by_samples.py b/tests/unit/computations/test_dictify_by_samples.py
index 8a1332f..5cd3eca 100644
--- a/tests/unit/computations/test_dictify_by_samples.py
+++ b/tests/unit/computations/test_dictify_by_samples.py
@@ -1,7 +1,11 @@
+"""Property tests for `gn3.computations.partial_correlations.dictify_by_samples`
+ function"""
 from math import isnan
-import pytest
 from collections.abc import Sequence
+
+import pytest
 from hypothesis import given, strategies as st
+
 from gn3.computations.partial_correlations import dictify_by_samples
 
 
@@ -53,22 +57,22 @@ def check_values(samples, values, variances, row):
         for smp, val, var in zip(samples, values, variances)
         if smp != "")
 
-non_empty_samples = st.lists(
+generated_non_empty_samples = st.lists(
     st.text(min_size=1, max_size=15).map(
         lambda s: s.strip()))
-empty_samples = st.text(
+generated_empty_samples = st.text(
     alphabet=" \t\n\r\f\v", min_size=1, max_size=15).filter(
         lambda s: len(s.strip()) == 0)
-values = st.lists(st.floats())
-variances = st.lists(st.one_of(st.none(), st.floats()))
-other = st.lists(st.integers())
+generated_values = st.lists(st.floats())
+generated_variances = st.lists(st.one_of(st.none(), st.floats()))
+generated_other = st.lists(st.integers())
 
 @pytest.mark.unit_test
 @given(svv=st.tuples(
-    st.lists(non_empty_samples),
-    st.lists(values),
-    st.lists(variances),
-    st.lists(other)))
+    st.lists(generated_non_empty_samples),
+    st.lists(generated_values),
+    st.lists(generated_variances),
+    st.lists(generated_other)))
 def test_dictifify_by_samples_with_nonempty_samples_strings(svv):
     """
     Test for `dictify_by_samples`.
@@ -94,7 +98,7 @@ def test_dictifify_by_samples_with_nonempty_samples_strings(svv):
 @pytest.mark.unit_test
 @given(svv=st.tuples(
     st.lists(
-        st.lists(empty_samples,min_size=1),
+        st.lists(generated_empty_samples,min_size=1),
         min_size=1),
     st.lists(st.lists(st.floats(), min_size=1), min_size=1),
     st.lists(
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
index 0b24489..e4abd2f 100644
--- a/tests/unit/db/test_datasets.py
+++ b/tests/unit/db/test_datasets.py
@@ -15,14 +15,14 @@ class TestDatasetsDBFunctions(TestCase):
     @pytest.mark.unit_test
     def test_retrieve_dataset_name(self):
         """Test that the function is called correctly."""
-        for trait_type, thresh, trait_name, dataset_name, columns, table, expected in [
-                ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName",
+        for trait_type, thresh, dataset_name, columns, table, expected in [
+                ["ProbeSet", 9, "probesetDatasetName",
                  "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze",
                  {"dataset_id": None, "dataset_name": "probesetDatasetName",
                   "dataset_fullname": "probesetDatasetName"}],
-                ["Geno", 3, "genoTraitName", "genoDatasetName",
+                ["Geno", 3, "genoDatasetName",
                  "Id, Name, FullName, ShortName", "GenoFreeze", {}],
-                ["Publish", 6, "publishTraitName", "publishDatasetName",
+                ["Publish", 6, "publishDatasetName",
                  "Id, Name, FullName, ShortName", "PublishFreeze", {}]]:
             db_mock = mock.MagicMock()
             with self.subTest(trait_type=trait_type):
@@ -30,16 +30,15 @@ class TestDatasetsDBFunctions(TestCase):
                     cursor.fetchone.return_value = {}
                     self.assertEqual(
                         retrieve_dataset_name(
-                            trait_type, thresh, trait_name, dataset_name, db_mock),
+                            trait_type, thresh, dataset_name, db_mock),
                         expected)
                     cursor.execute.assert_called_once_with(
-                        "SELECT {cols} "
-                        "FROM {table} "
+                        f"SELECT {columns} "
+                        f"FROM {table} "
                         "WHERE public > %(threshold)s AND "
                         "(Name = %(name)s "
                         "OR FullName = %(name)s "
-                        "OR ShortName = %(name)s)".format(
-                            table=table, cols=columns),
+                        "OR ShortName = %(name)s)",
                         {"threshold": thresh, "name": dataset_name})
 
     @pytest.mark.unit_test
diff --git a/tests/unit/test_data_helpers.py b/tests/unit/test_data_helpers.py
index b6de42e..e7c3ae9 100644
--- a/tests/unit/test_data_helpers.py
+++ b/tests/unit/test_data_helpers.py
@@ -37,7 +37,7 @@ class TestDataHelpers(TestCase):
                 (13, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
                  ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9), ))):
             with self.subTest(n=count, items=items):
-                self.assertEqual(partition_all(count, items), expected)
+                self.assertEqual(tuple(partition_all(count, items)), expected)
 
     @pytest.mark.unit_test
     def test_parse_csv_line(self):
diff --git a/tests/unit/test_db_utils.py b/tests/unit/test_db_utils.py
index dd0cd5d..96ee68f 100644
--- a/tests/unit/test_db_utils.py
+++ b/tests/unit/test_db_utils.py
@@ -2,9 +2,9 @@
 
 from unittest import TestCase
 from unittest import mock
+from types import SimpleNamespace
 
 import pytest
-from types import SimpleNamespace
 
 from gn3.db_utils import database_connector
 from gn3.db_utils import parse_db_url
diff --git a/tests/unit/test_file_utils.py b/tests/unit/test_file_utils.py
index 77fea88..7048d43 100644
--- a/tests/unit/test_file_utils.py
+++ b/tests/unit/test_file_utils.py
@@ -92,7 +92,8 @@ extracting the file"""
         test_dir = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test"
         if not os.path.exists(test_dir):
             os.mkdir(test_dir)
-        open(f"{test_dir}/genotype.txt", "a").close()
+        with open(f"{test_dir}/genotype.txt", "a", encoding="utf8"):
+            pass
         file_loc = cache_ipfs_file(
             ipfs_file=("/ipfs/"
                        "QmQPeNsJPyVWPFDVHb"