Merge branch 'staging' into new-paginate

.pre-commit-config.yaml

@@ -1,14 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v1.4.0
+    rev: v4.6.0  # pre-commit-hooks version
     hooks:
       - id: check-added-large-files
       - id: detect-private-key
       - id: trailing-whitespace
       - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.2.0  # ruff version
     hooks:
       - id: ruff-format
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
+minimum_pre_commit_version: 3.7.1

Pipfile

@@ -26,7 +26,7 @@ pytest = "*"
 pytest-cov = "*"
 pytest-asyncio = "*"
 mock = "*"
-pre-commit = "*"
+pre-commit = ">=3.7.1"
 ruff = "==0.2.0"
 ipykernel = "*"
 jupyterlab = "*"

docs/source/conf.py

@@ -70,9 +70,9 @@
 autodoc_preserve_defaults = True
 
 # -- get version -------------------------------------------------------------
-from importlib.metadata import version
+from metakb import __version__
 
-release = version = version("metakb")
+release = version = __version__
 
 # -- linkcode ----------------------------------------------------------------
 def linkcode_resolve(domain, info):

pyproject.toml

@@ -43,7 +43,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 tests = ["pytest", "pytest-cov", "mock", "pytest-asyncio"]
-dev = ["pre-commit", "ruff==0.2.0"]
+dev = ["pre-commit>=3.7.1", "ruff==0.2.0"]
 notebooks = ["ipykernel", "jupyterlab"]
 docs = [
     "sphinx==6.1.3",
@@ -68,11 +68,10 @@ Source = "https://github.com/cancervariants/metakb"
 metakb = "metakb.cli:cli"
 
 [build-system]
-requires = ["setuptools>=64"]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.dynamic]
-version = {attr = "metakb.version.__version__"}
+[tool.setuptools_scm]
 
 [tool.setuptools.packages.find]
 where = ["src"]

src/metakb/__init__.py

@@ -1,7 +1,16 @@
 """The MetaKB package."""
+from importlib.metadata import PackageNotFoundError, version
 from pathlib import Path
 
 APP_ROOT = Path(__file__).resolve().parents[0]
 
 # default date format for all saved data files
 DATE_FMT = "%Y%m%d"
+
+
+try:
+    __version__ = version("metakb")
+except PackageNotFoundError:
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError

src/metakb/main.py

@@ -6,6 +6,7 @@
 from fastapi import FastAPI, Query
 from fastapi.openapi.utils import get_openapi
 
+from metakb import __version__
 from metakb.log_handle import configure_logs
 from metakb.query import PaginationParamError, QueryHandler
 from metakb.schemas.api import (
@@ -15,7 +16,6 @@
     SearchStudiesService,
     ServiceMeta,
 )
-from metakb.version import __version__
 
 query = QueryHandler()
 

src/metakb/schemas/api.py

@@ -3,8 +3,8 @@
 
 from pydantic import BaseModel, ConfigDict, StrictStr
 
+from metakb import __version__
 from metakb.schemas.variation_statement import VariantTherapeuticResponseStudy
-from metakb.version import __version__
 
 
 class ServiceMeta(BaseModel):