cool-seq-tool 0.12.1__tar.gz → 0.13.1__tar.gz

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/.github/workflows/checks.yaml

@@ -56,3 +56,23 @@ jobs:
       - name: Attempt docs build
         working-directory: ./docs
         run: make html
+
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        cmd:
+          - "end-of-file-fixer"
+          - "trailing-whitespace"
+          - "mixed-line-ending"
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: ${{ matrix.cmd }} --all-files

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0  # pre-commit-hooks version
+    rev: v5.0.0  # pre-commit-hooks version
     hooks:
       - id: check-added-large-files
       - id: detect-private-key
@@ -9,10 +9,12 @@ repos:
       - id: check-merge-conflict
       - id: detect-aws-credentials
         args: [ --allow-missing-credentials ]
+      - id: mixed-line-ending
+        args: [ --fix=lf ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.8.6
     hooks:
       - id: ruff-format
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
-minimum_pre_commit_version: 3.7.1
+minimum_pre_commit_version: 4.0.1

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.12.1
+Version: 0.13.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -53,14 +53,14 @@ Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: ga4gh.vrs~=2.0.0a10
-Requires-Dist: wags-tails~=0.2.2
+Requires-Dist: wags-tails~=0.3.2
 Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit>=3.7.1; extra == "dev"
+Requires-Dist: pre-commit>=4.0.1; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff==0.5.0; extra == "dev"
+Requires-Dist: ruff==0.8.6; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -74,6 +74,7 @@ Requires-Dist: sphinx-copybutton==0.5.2; extra == "docs"
 Requires-Dist: sphinxext-opengraph==0.8.2; extra == "docs"
 Requires-Dist: furo==2023.3.27; extra == "docs"
 Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
+Dynamic: license-file
 
 <h1 align="center">
 Cool-Seq-Tool

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
 popd

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/pyproject.toml

@@ -33,13 +33,19 @@ dependencies = [
     "biocommons.seqrepo",
     "pydantic == 2.*",
     "ga4gh.vrs ~= 2.0.0a10",
-    "wags-tails ~= 0.2.2",
+    "wags-tails ~= 0.3.2",
     "bioutils",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = ["pre-commit>=3.7.1", "ipython", "ipykernel", "psycopg2-binary", "ruff==0.5.0"]
+dev = [
+    "pre-commit>=4.0.1",
+    "ipython",
+    "ipykernel",
+    "psycopg2-binary",
+    "ruff==0.8.6"
+]
 tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
     "sphinx==6.1.3",
@@ -110,10 +116,14 @@ lint.select = [
     "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
     "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+    "SLOT",  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
     "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
     "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PLC",  # https://docs.astral.sh/ruff/rules/#convention-c
+    "PLE",  # https://docs.astral.sh/ruff/rules/#error-e_1
+    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
     "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
     "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
@@ -132,14 +142,15 @@ lint.fixable = [
     "PT",
     "RSE",
     "SIM",
+    "PLC",
+    "PLE",
+    "TRY",
     "PERF",
     "FURB",
     "RUF"
 ]
 
 # ANN003 - missing-type-kwargs
-# ANN101 - missing-type-self
-# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -153,26 +164,40 @@ lint.fixable = [
 # E501 - line-too-long*
 # W191 - tab-indentation*
 # S321 - suspicious-ftp-lib-usage
+# PLC0206 - dict-index-missing-items
 # *ignored for compatibility with formatter
 lint.ignore = [
-    "ANN003", "ANN101", "ANN102",
+    "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
     "S321",
+    "PLC0206",
 ]
 
 [tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
-# ANN102 - missing-type-cls
+# D100 - undocumented-public-module
+# D102 - undocumented-public-class
+# D103 - undocumented-public-function
 # N805 - invalid-first-argument-name-for-method
 # F821 - undefined-name
 # F401 - unused-import
 # INP001 - implicit-namespace-package
 # SLF001 - private-member-access
 # ARG001 - unused-function-argument
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "INP001", "SLF001", "ARG001"]
+"tests/*" = [
+    "ANN001",
+    "ANN2",
+    "D100",
+    "D102",
+    "D103",
+    "S101",
+    "INP001",
+    "SLF001",
+    "ARG001"
+]
 "*__init__.py" = ["F401"]
 "src/cool_seq_tool/schemas.py" = ["ANN201", "N805", "ANN001"]
 

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/src/cool_seq_tool/mappers/__init__.py

@@ -6,4 +6,4 @@ from .mane_transcript import ManeTranscript
 from .exon_genomic_coords import ExonGenomicCoordsMapper
 
 
-__all__ = ["AlignmentMapper", "LiftOver", "ManeTranscript", "ExonGenomicCoordsMapper"]
+__all__ = ["AlignmentMapper", "ExonGenomicCoordsMapper", "LiftOver", "ManeTranscript"]

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -1022,11 +1022,8 @@ class ExonGenomicCoordsMapper:
         :return ``True`` if alt_start_i should be used, ``False`` if alt_end_i should
         be used
         """
-        return (
-            is_seg_start
-            and strand == Strand.POSITIVE
-            or not is_seg_start
-            and strand == Strand.NEGATIVE
+        return (is_seg_start and strand == Strand.POSITIVE) or (
+            not is_seg_start and strand == Strand.NEGATIVE
         )
 
     @staticmethod

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/src/cool_seq_tool/resources/status.py

@@ -88,11 +88,11 @@ async def check_status(
         try:
             get_data_file(r)
         except FileNotFoundError:
-            _logger.error(
+            _logger.exception(
                 "%s does not exist at configured location %s", name_lower, declared_path
             )
         except ValueError:
-            _logger.error(
+            _logger.exception(
                 "%s configured at %s is not a valid file.", name_lower, declared_path
             )
         except Exception as e:
@@ -107,8 +107,8 @@ async def check_status(
             chain_file_37_to_38=chain_file_37_to_38,
             chain_file_38_to_37=chain_file_38_to_37,
         )
-    except (FileNotFoundError, ChainfileError) as e:
-        _logger.error("agct converter setup failed: %s", e)
+    except (FileNotFoundError, ChainfileError):
+        _logger.exception("agct converter setup failed")
     except Exception as e:
         _logger.critical("Encountered unexpected error setting up agct: %s", e)
     else:
@@ -116,10 +116,8 @@ async def check_status(
 
     try:
         await UtaDatabase.create(db_url)
-    except (OSError, InvalidCatalogNameError, UndefinedTableError) as e:
-        _logger.error(
-            "Encountered error instantiating UTA at URI %s: %s", UTA_DB_URL, e
-        )
+    except (OSError, InvalidCatalogNameError, UndefinedTableError):
+        _logger.exception("Encountered error instantiating UTA at URI %s", UTA_DB_URL)
     except Exception as e:
         _logger.critical(
             "Encountered unexpected error instantiating UTA from URI %s: %s",
@@ -134,10 +132,10 @@ async def check_status(
             sr = SeqRepo(root_dir=SEQREPO_ROOT_DIR)
         sra = SeqRepoAccess(sr)
         sra.sr["NC_000001.11"][1000:1001]
-    except OSError as e:
-        _logger.error("Encountered error while instantiating SeqRepo: %s", e)
+    except OSError:
+        _logger.exception("Encountered error while instantiating SeqRepo")
     except KeyError:
-        _logger.error("SeqRepo data fetch test failed -- is it populated?")
+        _logger.exception("SeqRepo data fetch test failed -- is it populated?")
     except Exception as e:
         _logger.critical("Encountered unexpected error setting up SeqRepo: %s", e)
     else:

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/src/cool_seq_tool/sources/uta_database.py

@@ -162,11 +162,11 @@ class UtaDatabase:
                     database=self.args.database,
                 )
             except InterfaceError as e:
-                _logger.error(
-                    "While creating connection pool, encountered exception %s", e
+                _logger.exception(
+                    "While creating connection pool, encountered exception"
                 )
                 msg = "Could not create connection pool"
-                raise Exception(msg) from e
+                raise Exception(msg) from e  # noqa: TRY002
 
     @classmethod
     async def create(
@@ -221,7 +221,7 @@ class UtaDatabase:
                WHERE table_schema = '{self.schema}'
                AND table_name = 'genomic'
             );
-            """  # noqa: S608
+            """
         genomic_table_exists = await self.execute_query(check_table_exists)
         genomic_table_exists = genomic_table_exists[0].get("exists")
         if genomic_table_exists is None:
@@ -250,7 +250,7 @@ class UtaDatabase:
                         LEFT JOIN {self.schema}.exon_aln ea ON
                             (((te.exon_id = ea.tx_exon_id) AND
                             (ae.exon_id = ea.alt_exon_id))));
-                """  # noqa: S608
+                """
             await self.execute_query(create_genomic_table)
 
             indexes = [
@@ -499,7 +499,7 @@ class UtaDatabase:
             AND {start_pos} BETWEEN {pos_q}
             AND {end_pos} BETWEEN {pos_q}
             {order_by_cond}
-            """  # noqa: S608
+            """
         result = await self.execute_query(query)
         if not result:
             _logger.warning("Unable to find transcript alignment for query: %s", query)
@@ -852,8 +852,8 @@ class UtaDatabase:
 
         try:
             assembly = Assembly(assembly)
-        except ValueError as e:
-            _logger.error(e)
+        except ValueError:
+            _logger.exception("Unable to parse %s as an Assembly", assembly)
             return None
 
         return chromosome, assembly
@@ -924,11 +924,11 @@ class UtaDatabase:
 
         try:
             get_secret_value_response = client.get_secret_value(SecretId=secret_name)
-        except ClientError as e:
+        except ClientError:
             # For a list of exceptions thrown, see
             # https://docs.aws.amazon.com/secretsmanager/latest/apireference/API_GetSecretValue.html
-            _logger.error(e)
-            raise e
+            _logger.exception("Encountered AWS client error fetching UTA DB secret")
+            raise
         else:
             return get_secret_value_response["SecretString"]
 

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.12.1
+Version: 0.13.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -53,14 +53,14 @@ Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: ga4gh.vrs~=2.0.0a10
-Requires-Dist: wags-tails~=0.2.2
+Requires-Dist: wags-tails~=0.3.2
 Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit>=3.7.1; extra == "dev"
+Requires-Dist: pre-commit>=4.0.1; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff==0.5.0; extra == "dev"
+Requires-Dist: ruff==0.8.6; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -74,6 +74,7 @@ Requires-Dist: sphinx-copybutton==0.5.2; extra == "docs"
 Requires-Dist: sphinxext-opengraph==0.8.2; extra == "docs"
 Requires-Dist: furo==2023.3.27; extra == "docs"
 Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
+Dynamic: license-file
 
 <h1 align="center">
 Cool-Seq-Tool

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/src/cool_seq_tool.egg-info/requires.txt

@@ -7,15 +7,15 @@ hgvs
 biocommons.seqrepo
 pydantic==2.*
 ga4gh.vrs~=2.0.0a10
-wags-tails~=0.2.2
+wags-tails~=0.3.2
 bioutils
 
 [dev]
-pre-commit>=3.7.1
+pre-commit>=4.0.1
 ipython
 ipykernel
 psycopg2-binary
-ruff==0.5.0
+ruff==0.8.6
 
 [docs]
 sphinx==6.1.3

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/tests/mappers/test_alignment.py

@@ -111,7 +111,7 @@ def hras_t2a():
     return _expected
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_cds_start(test_alignment_mapper):
     """Test that _get_cds_start method works correctly"""
     # Valid
@@ -125,7 +125,7 @@ async def test_get_cds_start(test_alignment_mapper):
     assert w == "Accession NM_004333.6293702 not found in UTA db"
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_c(test_alignment_mapper, braf_v600e_c, egfr_l858r_c):
     """Test that p_to_c works as expected"""
     # BRAF V600E
@@ -164,7 +164,7 @@ async def test_p_to_c(test_alignment_mapper, braf_v600e_c, egfr_l858r_c):
     }
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_c_invalid(test_alignment_mapper):
     """Test invalid queries for p_to_c method"""
     # Invalid protein accession
@@ -175,7 +175,7 @@ async def test_p_to_c_invalid(test_alignment_mapper):
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_c_to_g(
     test_alignment_mapper,
     braf_v600e_grch37,
@@ -227,7 +227,7 @@ async def test_c_to_g(
         assert resp == expected, params
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_c_to_g_invalid(test_alignment_mapper):
     """Test invalid queries for c_to_g method"""
     # Should not expect to find anything given these two positions
@@ -262,7 +262,7 @@ async def test_c_to_g_invalid(test_alignment_mapper):
     assert w == "c_start_pos and c_end_pos are not a valid range for the codon(s)"
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_g(
     test_alignment_mapper,
     braf_v600e_grch37,
@@ -350,7 +350,7 @@ async def test_p_to_g(
         assert resp == hras_t2a(assembly), params
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_g_invalid(test_alignment_mapper):
     """Test invalid queries for p_to_g method"""
     # Invalid protein accession

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/tests/mappers/test_exon_genomic_coords.py

@@ -704,7 +704,7 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
         assert len(actual.errors) > 0
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_all_exon_coords(
     test_egc_mapper, nm_152263_exons, nm_152263_exons_genomic_coords
 ):
@@ -724,7 +724,7 @@ async def test_get_all_exon_coords(
     assert resp == []
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_start_end_exon_coords(test_egc_mapper):
     """Test that _get_start_end_exon_coords works correctly."""
     resp = await test_egc_mapper._get_start_end_exon_coords(
@@ -761,7 +761,7 @@ async def test_get_start_end_exon_coords(test_egc_mapper):
     assert resp == (None, None, ["Transcript does not exist in UTA: NM_1234.5"])
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_adjacent_exon(
     test_egc_mapper,
     nm_152263_exons_genomic_coords,
@@ -864,7 +864,7 @@ def test_use_alt_start_i(test_egc_mapper):
     assert not resp
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_genomic_to_transcript_fusion_context(
     test_egc_mapper,
     zbtb10_exon3_end,
@@ -1003,7 +1003,7 @@ async def test_genomic_to_transcript_fusion_context(
     genomic_tx_seg_service_checks(resp, gusbp3_exon5_start)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_alt_ac_start_and_end(
     test_egc_mapper, tpm3_1_8_start_genomic, tpm3_1_8_end_genomic
 ):
@@ -1038,7 +1038,7 @@ async def test_get_alt_ac_start_and_end(
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_get_exons_coords(test_egc_mapper, nm_152263_exons_genomic_coords):
     """Test that _get_all_exon_coords works correctly."""
     resp = await test_egc_mapper._get_all_exon_coords("NM_152263.4", "NC_000001.11")
@@ -1049,7 +1049,7 @@ async def test_get_get_exons_coords(test_egc_mapper, nm_152263_exons_genomic_coo
     assert resp == []
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_genomic_to_transcript(test_egc_mapper, tpm3_exon1, tpm3_exon8):
     """Test that _genomic_to_tx_segment method works correctly."""
     resp = await test_egc_mapper._genomic_to_tx_segment(
@@ -1145,7 +1145,7 @@ async def test_genomic_to_transcript(test_egc_mapper, tpm3_exon1, tpm3_exon8):
     genomic_tx_seg_checks(resp, tpm3_exon8)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_tpm3(
     test_egc_mapper,
     tpm3_exon1_exon8,
@@ -1214,7 +1214,7 @@ async def test_tpm3(
     genomic_tx_seg_service_checks(t_to_g_resp, tpm3_exon8_g)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_braf(test_egc_mapper, mane_braf):
     """Test BRAF genomic_to_tx_segment and
     tx_segment_to_genomic.
@@ -1248,7 +1248,7 @@ async def test_braf(test_egc_mapper, mane_braf):
     genomic_tx_seg_service_checks(t_to_g_resp, expected)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_wee1(test_egc_mapper, wee1_exon2_exon11, mane_wee1_exon2_exon11):
     """Test WEE1 genomic_to_tx_segment and
     tx_segment_to_genomic.
@@ -1312,7 +1312,7 @@ async def test_wee1(test_egc_mapper, wee1_exon2_exon11, mane_wee1_exon2_exon11):
     genomic_tx_seg_service_checks(t_to_g_resp, mane_wee1_exon2_exon11)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_transcript_to_genomic(
     test_egc_mapper,
     tpm3_exon1_g,
@@ -1398,7 +1398,7 @@ async def test_transcript_to_genomic(
     genomic_tx_seg_service_checks(resp, expected)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_valid_inputs(test_egc_mapper, eln_grch38_intronic):
     """Test that valid inputs don"t return any errors"""
     inputs = {
@@ -1462,7 +1462,7 @@ async def test_valid_inputs(test_egc_mapper, eln_grch38_intronic):
     genomic_tx_seg_service_checks(resp, eln_grch38_intronic)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_invalid(test_egc_mapper):
     """Test that invalid queries return `None`."""
     resp = await test_egc_mapper.genomic_to_tx_segment(

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/tests/mappers/test_mane_transcript.py

@@ -232,7 +232,7 @@ def test_p_to_c_pos(test_mane_transcript):
     assert c_pos == (2241, 2252)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_c(test_mane_transcript):
     """Test that _p_to_c method works correctly."""
     # Amino Acid Substitution
@@ -271,7 +271,7 @@ async def test_p_to_c(test_mane_transcript):
     assert pos == expected_pos
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_c_to_g(test_mane_transcript, nm_004333v6_g):
     """Test that _c_to_g method works correctly."""
     tx_ac = "NM_004333.6"
@@ -279,7 +279,7 @@ async def test_c_to_g(test_mane_transcript, nm_004333v6_g):
     assert g == nm_004333v6_g
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_g_to_c(
     test_mane_transcript, braf_mane_data, nm_004333v6_g, braf_v600e_mane_c
 ):
@@ -308,7 +308,7 @@ def test_set_liftover(test_mane_transcript, genomic_tx_data):
     assert cpy == expected
 
 
-@pytest.mark.asyncio()
+@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)
@@ -326,7 +326,7 @@ def test_get_mane_p(test_mane_transcript, braf_mane_data, braf_v600e_mane_p):
     assert mane_p == braf_v600e_mane_p
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_mane_p(test_mane_transcript, braf_v600e_mane_p, egfr_l858r_mane_p):
     """Test that p_to_mane_p method works correctly."""
     # BRAF V600E RefSeq Accessions
@@ -404,7 +404,7 @@ async def test_p_to_mane_p(test_mane_transcript, braf_v600e_mane_p, egfr_l858r_m
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_c_to_mane_c(test_mane_transcript, braf_v600e_mane_c, egfr_l858r_mane_c):
     """Test that c_to_mane_p method works correctly."""
     # BRAF V600E RefSeq Accessions
@@ -503,7 +503,7 @@ def test_get_prioritized_transcripts_from_gene(
         assert resp == ["NM_004333.6", "NM_001374258.2", "NM_001378472.1"]
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_longest_compatible_transcript(test_mane_transcript):
     """Test that get_longest_compatible_transcript method works as expected"""
     mane_transcripts = {
@@ -669,7 +669,7 @@ async def test_get_longest_compatible_transcript(test_mane_transcript):
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_g_to_grch38(test_mane_transcript, grch38_egfr, grch38_braf):
     """Test that g_to_grch38 method works correctly."""
     resp = await test_mane_transcript.g_to_grch38(
@@ -705,7 +705,7 @@ async def test_g_to_grch38(test_mane_transcript, grch38_egfr, grch38_braf):
     assert resp == grch38_braf
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_g_to_mane_c(test_mane_transcript, egfr_l858r_mane_c, braf_v600e_mane_c):
     """Test that g_to_mane_c method works correctly."""
     mane_c = await test_mane_transcript.g_to_mane_c(
@@ -789,7 +789,7 @@ async def test_g_to_mane_c(test_mane_transcript, egfr_l858r_mane_c, braf_v600e_m
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_grch38_to_mane_c_p(
     test_mane_transcript,
     braf_v600e_mane_p,
@@ -913,7 +913,7 @@ async def test_grch38_to_mane_c_p(
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_valid(test_mane_transcript):
     """Test that valid queries do not raise any exceptions"""
     resp = await test_mane_transcript.get_mane_transcript(
@@ -937,7 +937,7 @@ async def test_valid(test_mane_transcript):
     assert resp
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_no_matches(test_mane_transcript):
     """Test that invalid queries return None."""
     # Invalid ENST version

{cool_seq_tool-0.12.1 → cool_seq_tool-0.13.1}/tests/sources/test_uta_database.py

@@ -44,7 +44,7 @@ def data_from_result():
     return GenomicTxData(**params)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_cds_start_end(test_db):
     """Test that get_cds_start_end works correctly."""
     expected = (61, 2362)
@@ -58,7 +58,7 @@ async def test_get_cds_start_end(test_db):
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_newest_assembly_ac(test_db):
     """Test that get_newest_assembly_ac works correctly."""
     resp = await test_db.get_newest_assembly_ac("NC_000007.13")
@@ -77,7 +77,7 @@ async def test_get_newest_assembly_ac(test_db):
     assert resp == []
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_validate_genomic_ac(test_db):
     """Test that validate_genomic_ac"""
     resp = await test_db.validate_genomic_ac("NC_000007.13")
@@ -87,7 +87,7 @@ async def test_validate_genomic_ac(test_db):
     assert resp is False
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_validate_gene_exists(test_db):
     """Test validate_gene_symbol"""
     resp = await test_db.gene_exists("TPM3")
@@ -97,7 +97,7 @@ async def test_validate_gene_exists(test_db):
     assert resp is False
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_validate_transcript_exists(test_db):
     """Tests validate_transcript"""
     resp = await test_db.transcript_exists("NM_152263.3")
@@ -107,7 +107,7 @@ async def test_validate_transcript_exists(test_db):
     assert resp is False
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_ac_descr(test_db):
     """Test that get_ac_descr works correctly."""
     resp = await test_db.get_ac_descr("NC_000007.13")
@@ -117,7 +117,7 @@ async def test_get_ac_descr(test_db):
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_tx_exon_aln_v_data(test_db, tx_exon_aln_v_data):
     """Test that get_tx_exon_aln_v_data"""
     resp = await test_db.get_tx_exon_aln_v_data(
@@ -165,14 +165,14 @@ async def test_get_tx_exon_aln_v_data(test_db, tx_exon_aln_v_data):
     ]
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_data_from_result(test_db, tx_exon_aln_v_data, data_from_result):
     """Test that data_from_result works correctly."""
     resp = test_db.data_from_result(tx_exon_aln_v_data)
     assert resp == data_from_result
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_mane_c_genomic_data(test_db):
     """Test that get_mane_c_genomic_data works correctly."""
     resp = await test_db.get_mane_c_genomic_data(
@@ -196,7 +196,7 @@ async def test_mane_c_genomic_data(test_db):
     assert resp == GenomicTxMetadata(**expected_params)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_genomic_tx_data(test_db, genomic_tx_data):
     """Test that get_genomic_tx_data works correctly."""
     resp = await test_db.get_genomic_tx_data("NM_004333.4", (2145, 2145))
@@ -216,7 +216,7 @@ async def test_get_genomic_tx_data(test_db, genomic_tx_data):
     assert resp == GenomicTxMetadata(**expected_params)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_ac_from_gene(test_db):
     """Test that get_ac_from_gene works correctly."""
     resp = await test_db.get_ac_from_gene("BRAF")
@@ -229,7 +229,7 @@ async def test_get_ac_from_gene(test_db):
     assert resp == []
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_gene_from_ac(test_db):
     """Tet that get_gene_from_ac works correctly."""
     resp = await test_db.get_gene_from_ac("NC_000007.13", 140453136, None)
@@ -245,7 +245,7 @@ async def test_get_gene_from_ac(test_db):
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_transcripts_from_gene(test_db):
     """Test that get_transcripts works correctly."""
     resp = await test_db.get_transcripts(start_pos=2145, end_pos=2145, gene="BRAF")
@@ -281,7 +281,7 @@ async def test_get_transcripts_from_gene(test_db):
     assert len(resp) == 0
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_chr_assembly(test_db):
     """Test that get_chr_assembly works correctly."""
     resp = await test_db.get_chr_assembly("NC_000007.13")
@@ -295,7 +295,7 @@ async def test_get_chr_assembly(test_db):
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_c_ac(test_db):
     """Test that p_to_c_ac works correctly."""
     resp = await test_db.p_to_c_ac("NP_004324.2")
@@ -308,7 +308,7 @@ async def test_p_to_c_ac(test_db):
     assert resp == []
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_alt_ac_start_or_end(
     test_db, tpm3_1_8_start_genomic, tpm3_1_8_end_genomic
 ):
@@ -330,7 +330,7 @@ async def test_get_alt_ac_start_or_end(
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_mane_transcripts_from_genomic_pos(test_db):
     """Test that get_mane_transcripts_from_genomic_pos works correctly"""
     resp = await test_db.get_transcripts_from_genomic_pos("NC_000007.14", 140753336)