test: resolve deprecation warnings (#413)

unpin pytest-asyncio

Author: korikuzma

pyproject.toml

@@ -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",
@@ -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"]
 

tests/conftest.py

@@ -1,7 +1,5 @@
 """Provide utilities for test cases."""
 
-import asyncio
-
 import pytest
 
 from cool_seq_tool import CoolSeqTool
@@ -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"""

tests/mappers/test_mane_transcript.py

@@ -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
@@ -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)
@@ -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