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-rw-r--r--tests/unit/computations/test_correlation.py8
-rw-r--r--tests/unit/computations/test_dictify_by_samples.py26
-rw-r--r--tests/unit/db/test_datasets.py17
-rw-r--r--tests/unit/test_data_helpers.py2
-rw-r--r--tests/unit/test_db_utils.py2
-rw-r--r--tests/unit/test_file_utils.py3
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"
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 15:24:15 +0000