Adding versioning + auto alembic upgrade + upgrade/downgrade debug fo…

_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '1.0.7.dev7+gfc28f13.d20240910'
+__version_tuple__ = version_tuple = (1, 0, 7, 'dev7', 'gfc28f13.d20240910')

entrypoint.sh

@@ -14,5 +14,5 @@ if [[ -v C3G_INIT_DB ]]; then
   echo instanciating data base
   flask  --app $APP   init-db $DB_OPS
 fi
-
+alembic upgrade head
 gunicorn "project_tracking:create_app()"  "${@}"

migration/alembic/versions/d1dc98f61aee_major_changes.py

@@ -137,6 +137,9 @@ def downgrade() -> None:
     op.drop_column('experiment', 'ext_src')
     op.drop_column('experiment', 'ext_id')
     op.rename_table('specimen', 'patient')
+    op.drop_column('patient', 'ext_src')
+    op.drop_column('patient', 'ext_id')
+    op.add_column('patient', sa.Column('fms_id', sa.VARCHAR(), autoincrement=False, nullable=True))
     op.drop_table('reference')
     sa.Enum('VALID', 'ON_HOLD', 'INVALID', name='stateenum').drop(op.get_bind())
     # ### end Alembic commands ###

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["hatchling"]
+requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [tool.pytest.ini_options]
@@ -13,9 +13,15 @@ testpaths = [
 run.branch = true
 run.source = ["project_tracking"]
 
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "_version.py"
+
 [project]
 name = "project_tracking"
-version = "0.0.1"
+dynamic = ["version"]
 authors = [
   { name="P-O Quirion", email="[email protected]" },
   { name="Paul Streteowich", email="[email protected]" },