cool-seq-tool 0.14.0__tar.gz → 0.14.1__tar.gz

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/.pre-commit-config.yaml

@@ -12,9 +12,9 @@ repos:
       - id: mixed-line-ending
         args: [ --fix=lf ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.12.1
     hooks:
       - id: ruff-format
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
-minimum_pre_commit_version: 4.0.1
+minimum_pre_commit_version: 4.2.0

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.0
+Version: 0.14.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -51,16 +51,16 @@ Requires-Dist: agct>=0.1.0-dev1
 Requires-Dist: polars~=1.0
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
-Requires-Dist: pydantic==2.*
-Requires-Dist: ga4gh.vrs~=2.0.0a10
+Requires-Dist: pydantic<3.0,>=2.0
+Requires-Dist: ga4gh.vrs<3.0,>=2.1.3
 Requires-Dist: wags-tails~=0.3.2
 Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit>=4.0.1; extra == "dev"
+Requires-Dist: pre-commit>=4.2.0; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff==0.8.6; extra == "dev"
+Requires-Dist: ruff==0.12.1; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/pyproject.toml

@@ -31,8 +31,8 @@ dependencies = [
     "polars ~= 1.0",
     "hgvs",
     "biocommons.seqrepo",
-    "pydantic == 2.*",
-    "ga4gh.vrs ~= 2.0.0a10",
+    "pydantic >=2.0,<3.0",
+    "ga4gh.vrs >=2.1.3,<3.0",
     "wags-tails ~= 0.3.2",
     "bioutils",
 ]
@@ -40,11 +40,11 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
-    "pre-commit>=4.0.1",
+    "pre-commit>=4.2.0",
     "ipython",
     "ipykernel",
     "psycopg2-binary",
-    "ruff==0.8.6"
+    "ruff==0.12.1",
 ]
 tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/src/cool_seq_tool/handlers/seqrepo_access.py

@@ -75,9 +75,7 @@ class SeqRepoAccess(SeqRepoDataProxy):
                     f"Start inter-residue coordinate ({start}) is out of index on {ac}"
                 )
             elif error.startswith("stop out of range"):
-                msg = (
-                    f"End inter-residue coordinate ({end}) is out of " f"index on {ac}"
-                )
+                msg = f"End inter-residue coordinate ({end}) is out of index on {ac}"
             else:
                 msg = f"{e}"
             _logger.warning(msg)

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -776,7 +776,7 @@ class ExonGenomicCoordsMapper:
             GRCh38 by default. Will attempt to liftover if starting assembly is GRCh37
         :return: Data for a transcript segment boundary (inter-residue coordinates)
         """
-        params = {key: None for key in GenomicTxSeg.model_fields}
+        params = dict.fromkeys(GenomicTxSeg.model_fields)
 
         # Validate inputs exist in UTA
         if gene:

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/src/cool_seq_tool/mappers/mane_transcript.py

@@ -268,7 +268,7 @@ class ManeTranscript:
         query = f"""
             SELECT alt_ac
             FROM {self.uta_db.schema}.genomic
-            WHERE alt_ac LIKE '{genomic_tx_data.alt_ac.split('.')[0]}%'
+            WHERE alt_ac LIKE '{genomic_tx_data.alt_ac.split(".")[0]}%'
             {order_by_cond}
             """  # noqa: S608
         nc_acs = await self.uta_db.execute_query(query)

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/src/cool_seq_tool/sources/uta_database.py

@@ -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 = [
@@ -325,13 +325,13 @@ class UtaDatabase:
         cds_start_end = await self.execute_query(query)
         if cds_start_end:
             cds_start_end = cds_start_end[0]
-            if cds_start_end[0] is not None and cds_start_end[1] is not None:  # noqa: RET503
+            if cds_start_end[0] is not None and cds_start_end[1] is not None:
                 return cds_start_end[0], cds_start_end[1]
         else:
             _logger.warning(
                 "Unable to get coding start/end site for accession: %s", tx_ac
             )
-            return None
+        return None
 
     async def get_newest_assembly_ac(self, ac: str) -> list[str]:
         """Find accession associated to latest genomic assembly
@@ -352,7 +352,7 @@ class UtaDatabase:
         query = f"""
             SELECT ac
             FROM {self.schema}._seq_anno_most_recent
-            WHERE ac LIKE '{ac.split('.')[0]}%'
+            WHERE ac LIKE '{ac.split(".")[0]}%'
             AND ((descr IS NULL) OR (descr = ''))
             {order_by_cond}
             """  # noqa: S608
@@ -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)

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.0
+Version: 0.14.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -51,16 +51,16 @@ Requires-Dist: agct>=0.1.0-dev1
 Requires-Dist: polars~=1.0
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
-Requires-Dist: pydantic==2.*
-Requires-Dist: ga4gh.vrs~=2.0.0a10
+Requires-Dist: pydantic<3.0,>=2.0
+Requires-Dist: ga4gh.vrs<3.0,>=2.1.3
 Requires-Dist: wags-tails~=0.3.2
 Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit>=4.0.1; extra == "dev"
+Requires-Dist: pre-commit>=4.2.0; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff==0.8.6; extra == "dev"
+Requires-Dist: ruff==0.12.1; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/src/cool_seq_tool.egg-info/requires.txt

@@ -5,17 +5,17 @@ agct>=0.1.0-dev1
 polars~=1.0
 hgvs
 biocommons.seqrepo
-pydantic==2.*
-ga4gh.vrs~=2.0.0a10
+pydantic<3.0,>=2.0
+ga4gh.vrs<3.0,>=2.1.3
 wags-tails~=0.3.2
 bioutils
 
 [dev]
-pre-commit>=4.0.1
+pre-commit>=4.2.0
 ipython
 ipykernel
 psycopg2-binary
-ruff==0.8.6
+ruff==0.12.1
 
 [docs]
 sphinx==6.1.3

{cool_seq_tool-0.14.0 → cool_seq_tool-0.14.1}/tests/handlers/test_seqrepo_access.py

@@ -89,7 +89,7 @@ def test_translate_identifier(test_seqrepo_access):
     resp = test_seqrepo_access.translate_identifier("refseq_152263.3")
     assert resp == (
         [],
-        "SeqRepo unable to get translated identifiers for" " refseq_152263.3",
+        "SeqRepo unable to get translated identifiers for refseq_152263.3",
     )