Merge branch 'main' into fix-logging

docs/source/conf.py

@@ -60,10 +60,9 @@
 autodoc_preserve_defaults = True
 
 # -- get version -------------------------------------------------------------
-from cool_seq_tool.version import __version__
+from cool_seq_tool import __version__
 
-version = __version__
-release = version
+version = release = __version__
 
 
 # -- linkcode ----------------------------------------------------------------

pyproject.toml

@@ -61,11 +61,10 @@ Source = "https://github.com/genomicmedlab/cool-seq-tool"
 "Bug Tracker" = "https://github.com/genomicmedlab/cool-seq-tool/issues"
 
 [build-system]
-requires = ["setuptools>=64"]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.dynamic]
-version = {attr = "cool_seq_tool.version.__version__"}
+[tool.setuptools_scm]
 
 # Scanning for namespace packages in the ``src`` directory is true by
 # default in pyproject.toml, so you do NOT need to include the

src/cool_seq_tool/__init__.py

@@ -1 +1,10 @@
 """The cool_seq_tool package"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("cool_seq_tool")
+except PackageNotFoundError:
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError

src/cool_seq_tool/api.py

@@ -3,8 +3,8 @@
 from fastapi import FastAPI
 from fastapi.openapi.utils import get_openapi
 
+from cool_seq_tool import __version__
 from cool_seq_tool.routers import SERVICE_NAME, default, mane, mappings
-from cool_seq_tool.version import __version__
 
 app = FastAPI(
     docs_url=f"/{SERVICE_NAME}",

src/cool_seq_tool/schemas.py

@@ -1,7 +1,6 @@
 """Defines attribute constants, useful object structures, and API response schemas."""
 
 import datetime
-import re
 from enum import Enum, IntEnum
 from typing import Literal
 
@@ -10,11 +9,10 @@
     ConfigDict,
     StrictInt,
     StrictStr,
-    field_validator,
     model_validator,
 )
 
-from cool_seq_tool.version import __version__
+from cool_seq_tool import __version__
 
 _now = str(datetime.datetime.now(tz=datetime.timezone.utc))
 
@@ -276,17 +274,6 @@ class ServiceMeta(BaseModelForbidExtra):
         "https://github.com/GenomicMedLab/cool-seq-tool"
     )
 
-    @field_validator("version")
-    def validate_version(cls, v):
-        """Check version matches semantic versioning regex pattern.
-        https://semver.org/#is-there-a-suggested-regular-expression-regex-to-check-a-semver-string
-        """
-        version_regex = r"^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$"
-        if not re.match(version_regex, v):
-            msg = f"Invalid version {v}"
-            raise ValueError(msg)
-        return v
-
     model_config = ConfigDict(
         json_schema_extra={
             "example": {

src/cool_seq_tool/utils.py

@@ -3,8 +3,8 @@
 import datetime
 import logging
 
+from cool_seq_tool import __version__
 from cool_seq_tool.schemas import ResidueMode, ServiceMeta
-from cool_seq_tool.version import __version__
 
 _logger = logging.getLogger(__name__)
 

tests/mappers/test_exon_genomic_coords.py

@@ -1,7 +1,6 @@
 """Module for testing that Cool Seq Tool works correctly."""
 
 import copy
-import re
 from datetime import datetime
 
 import pytest
@@ -303,8 +302,7 @@ def check_service_meta(actual):
     :param ServiceMeta actual: Actual service metadata
     """
     assert actual.name == "cool_seq_tool"
-    version_regex = r"^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$"
-    assert bool(re.match(version_regex, actual.version))
+    # pydantic checks that version is a string
     assert isinstance(actual.response_datetime, datetime)
     assert actual.url == "https://github.com/GenomicMedLab/cool-seq-tool"