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test: resolve deprecation warnings #413

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Merged
korikuzma merged 1 commit into from
Jul 16, 2025
Merged

test: resolve deprecation warnings #413

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5 changes: 4 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ dev = [
"psycopg2-binary",
"ruff==0.12.1",
]
tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
tests = ["pytest", "pytest-cov", "pytest-asyncio", "mock"]
docs = [
"sphinx==6.1.3",
"sphinx-autodoc-typehints==1.22.0",
Expand Down Expand Up @@ -81,6 +81,9 @@ build-backend = "setuptools.build_meta"
"cool_seq_tool.resources" = ["transcript_mapping.tsv"]

[tool.pytest.ini_options]
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "session"
asyncio_default_test_loop_scope = "session"
addopts = "--cov=src --cov-report term-missing"
testpaths = ["tests"]

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10 changes: 0 additions & 10 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
"""Provide utilities for test cases."""

import asyncio

import pytest

from cool_seq_tool import CoolSeqTool
Expand All @@ -10,14 +8,6 @@
from cool_seq_tool.sources.uta_database import GenomicAlnData, GenomicTxMetadata


@pytest.fixture(scope="session")
def event_loop(request):
"""Create an instance of the default event loop for each test case."""
loop = asyncio.get_event_loop_policy().new_event_loop()
yield loop
loop.close()


@pytest.fixture(scope="session")
def test_cool_seq_tool():
"""Create CoolSeqTool test fixture"""
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10 changes: 5 additions & 5 deletions tests/mappers/test_mane_transcript.py
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Expand Up @@ -298,8 +298,8 @@ async def test_g_to_c(

def test_set_liftover(test_mane_transcript, genomic_tx_data):
"""Test that _set_liftover works correctly."""
cpy = genomic_tx_data.copy(deep=True)
expected = genomic_tx_data.copy(deep=True)
cpy = genomic_tx_data.model_copy(deep=True)
expected = genomic_tx_data.model_copy(deep=True)
test_mane_transcript._set_liftover(cpy, "alt_pos_range", "chr7", "GRCh38")
expected.alt_pos_range = (140739811, 140739946)
assert cpy == expected
Expand All @@ -311,8 +311,8 @@ def test_set_liftover(test_mane_transcript, genomic_tx_data):
@pytest.mark.asyncio
async def test_liftover_to_38(test_mane_transcript, genomic_tx_data):
"""Test that liftover_to_38 works correctly."""
cpy = genomic_tx_data.copy(deep=True)
expected = genomic_tx_data.copy(deep=True)
cpy = genomic_tx_data.model_copy(deep=True)
expected = genomic_tx_data.model_copy(deep=True)
await test_mane_transcript._liftover_to_38(cpy)
expected.alt_ac = "NC_000007.14"
expected.alt_pos_change_range = (140739903, 140739903)
Expand Down Expand Up @@ -675,7 +675,7 @@ async def test_g_to_grch38(test_mane_transcript, grch38_egfr, grch38_braf):
resp = await test_mane_transcript.g_to_grch38(
"NC_000007.13", 55259515, 55259515, get_mane_genes=False
)
grch38_egfr_no_genes = grch38_egfr.copy()
grch38_egfr_no_genes = grch38_egfr.model_copy()
grch38_egfr_no_genes.mane_genes = []
assert resp == grch38_egfr_no_genes

Expand Down