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

2 files changed, 19 insertions, 15 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(