Merge pull request #17 from thehyve/poetry2-upgrade

Poetry2 upgrade

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## v0.3.1
+
+Internal changes:
+- Upgraded to Poetry 2.
+- Upgraded dev and test dependencies.
+- Updated metadata in pyproject.toml file.
+- Use Python >= 3.9 type hints.
+- Added __version__ variable
+
 ## v0.3.0
 
 New (for CDM 5.4 onwards):

pyproject.toml

@@ -1,11 +1,12 @@
-[tool.poetry]
+[project]
 name = "omop-cdm"
-version = "0.3.0"
+version = "0.3.1"
 description = "SQLAlchemy ORM of the OHDSI OMOP CDM"
 authors = [
-    "Spayralbe <[email protected]>",
+    {name = "Spayralbe", email = "[email protected]"},
 ]
 readme = "README.md"
+requires-python = ">=3.9,<4.0"
 classifiers = [
     "Intended Audience :: Developers",
     "Operating System :: OS Independent",
@@ -20,34 +21,31 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: Implementation :: CPython",
 ]
+dependencies = [
+    "sqlalchemy >= 2.0",
+]
 
-[tool.poetry.urls]
+[project.urls]
 "Repository" = "https://github.com/thehyve/omop-cdm"
 "Documentation" = "https://github.com/thehyve/omop-cdm/blob/main/docs/README.md"
 "Bug Tracker" = "https://github.com/thehyve/omop-cdm/issues"
 "Changelog" = "https://github.com/thehyve/omop-cdm/blob/main/CHANGELOG.md"
 
-[tool.poetry.dependencies]
-python = "^3.9"
-sqlalchemy = "^2.0.4"
-
 [tool.poetry.group.dev.dependencies]
-nox = "^2024.4.15"
-ruff = "^0.3.2"
-pre-commit = "^3.5.0"
+nox = "^2024.10.9"
+ruff = "^0.9.3"
+pre-commit = "^4.1.0"
 
 [tool.poetry.group.test.dependencies]
-pytest = "^8.1.1"
-pytest-cov = "^4.1.0"
-testcontainers = {version = ">=3.7.1", extras = ["postgres"]}
+pytest = "^8.3.4"
+pytest-cov = "^6.0.0"
+testcontainers = "^4.9.1"
 psycopg2-binary = "^2.9.9"
 
-
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core>=2.0"]
 build-backend = "poetry.core.masonry.api"
 
-
 [tool.pytest.ini_options]
 addopts = "--import-mode=importlib"
 pythonpath = [

src/omop_cdm/__init__.py

@@ -1 +1,7 @@
+"""OMOP CDM SQLAlchemy model."""
+
+import importlib.metadata
+
 from omop_cdm.constants import NAMING_CONVENTION
+
+__version__ = importlib.metadata.version("omop-cdm")

src/omop_cdm/dynamic/cdm54/clinical_data.py

@@ -2,7 +2,7 @@
 
 import datetime
 import decimal
-from typing import List, Optional
+from typing import Optional
 
 from sqlalchemy import BigInteger, Date, DateTime, ForeignKey, Integer, Numeric, String, Text
 from sqlalchemy.ext.declarative import declared_attr
@@ -229,71 +229,71 @@ def race_source_concept(cls) -> Mapped["Concept"]:
         return relationship("Concept", foreign_keys="Person.race_source_concept_id")
 
     @declared_attr
-    def observation_periods(cls) -> Mapped[List["ObservationPeriod"]]:
+    def observation_periods(cls) -> Mapped[list["ObservationPeriod"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def visit_occurrences(cls) -> Mapped[List["VisitOccurrence"]]:
+    def visit_occurrences(cls) -> Mapped[list["VisitOccurrence"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def visit_details(cls) -> Mapped[List["VisitDetail"]]:
+    def visit_details(cls) -> Mapped[list["VisitDetail"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def condition_occurrences(cls) -> Mapped[List["ConditionOccurrence"]]:
+    def condition_occurrences(cls) -> Mapped[list["ConditionOccurrence"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def drug_exposures(cls) -> Mapped[List["DrugExposure"]]:
+    def drug_exposures(cls) -> Mapped[list["DrugExposure"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def procedure_occurrences(cls) -> Mapped[List["ProcedureOccurrence"]]:
+    def procedure_occurrences(cls) -> Mapped[list["ProcedureOccurrence"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def device_exposures(cls) -> Mapped[List["DeviceExposure"]]:
+    def device_exposures(cls) -> Mapped[list["DeviceExposure"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def measurements(cls) -> Mapped[List["Measurement"]]:
+    def measurements(cls) -> Mapped[list["Measurement"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def observations(cls) -> Mapped[List["Observation"]]:
+    def observations(cls) -> Mapped[list["Observation"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
     def death(cls) -> Mapped["Death"]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def notes(cls) -> Mapped[List["Note"]]:
+    def notes(cls) -> Mapped[list["Note"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def specimens(cls) -> Mapped[List["Specimen"]]:
+    def specimens(cls) -> Mapped[list["Specimen"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def payer_plan_periods(cls) -> Mapped[List["PayerPlanPeriod"]]:
+    def payer_plan_periods(cls) -> Mapped[list["PayerPlanPeriod"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def drug_eras(cls) -> Mapped[List["DrugEra"]]:
+    def drug_eras(cls) -> Mapped[list["DrugEra"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def dose_eras(cls) -> Mapped[List["DoseEra"]]:
+    def dose_eras(cls) -> Mapped[list["DoseEra"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def condition_eras(cls) -> Mapped[List["ConditionEra"]]:
+    def condition_eras(cls) -> Mapped[list["ConditionEra"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
     @declared_attr
-    def episodes(cls) -> Mapped[List["Episode"]]:
+    def episodes(cls) -> Mapped[list["Episode"]]:
         return relationship(back_populates="person", cascade="all, delete-orphan")
 
 

src/omop_cdm/regular/cdm531/__init__.py

@@ -62,39 +62,39 @@
 
 __all__ = [
     "Base",
-    "Person",
-    "Death",
-    "Note",
-    "Measurement",
-    "NoteNlp",
-    "Observation",
-    "Specimen",
-    "VisitDetail",
-    "ConditionOccurrence",
-    "DeviceExposure",
-    "DrugExposure",
-    "FactRelationship",
-    "ObservationPeriod",
-    "ProcedureOccurrence",
-    "VisitOccurrence",
     "CareSite",
-    "Location",
-    "Provider",
-    "Cost",
-    "PayerPlanPeriod",
-    "DoseEra",
-    "DrugEra",
-    "ConditionEra",
-    "Metadata",
     "CdmSource",
-    "Vocabulary",
-    "SourceToConceptMap",
     "Concept",
     "ConceptAncestor",
     "ConceptClass",
     "ConceptRelationship",
     "ConceptSynonym",
+    "ConditionEra",
+    "ConditionOccurrence",
+    "Cost",
+    "Death",
+    "DeviceExposure",
     "Domain",
+    "DoseEra",
+    "DrugEra",
+    "DrugExposure",
     "DrugStrength",
+    "FactRelationship",
+    "Location",
+    "Measurement",
+    "Metadata",
+    "Note",
+    "NoteNlp",
+    "Observation",
+    "ObservationPeriod",
+    "PayerPlanPeriod",
+    "Person",
+    "ProcedureOccurrence",
+    "Provider",
     "Relationship",
+    "SourceToConceptMap",
+    "Specimen",
+    "VisitDetail",
+    "VisitOccurrence",
+    "Vocabulary",
 ]

src/omop_cdm/regular/cdm54/__init__.py

@@ -63,41 +63,41 @@
 
 __all__ = [
     "Base",
-    "Person",
-    "Death",
-    "Note",
-    "Measurement",
-    "NoteNlp",
-    "Observation",
-    "Specimen",
-    "VisitDetail",
-    "ConditionOccurrence",
-    "DeviceExposure",
-    "DrugExposure",
-    "FactRelationship",
-    "ObservationPeriod",
-    "ProcedureOccurrence",
-    "VisitOccurrence",
     "CareSite",
-    "Location",
-    "Provider",
-    "Cost",
-    "PayerPlanPeriod",
-    "DoseEra",
-    "DrugEra",
-    "ConditionEra",
-    "Episode",
-    "EpisodeEvent",
-    "Metadata",
     "CdmSource",
-    "Vocabulary",
-    "SourceToConceptMap",
     "Concept",
     "ConceptAncestor",
     "ConceptClass",
     "ConceptRelationship",
     "ConceptSynonym",
+    "ConditionEra",
+    "ConditionOccurrence",
+    "Cost",
+    "Death",
+    "DeviceExposure",
     "Domain",
+    "DoseEra",
+    "DrugEra",
+    "DrugExposure",
     "DrugStrength",
+    "Episode",
+    "EpisodeEvent",
+    "FactRelationship",
+    "Location",
+    "Measurement",
+    "Metadata",
+    "Note",
+    "NoteNlp",
+    "Observation",
+    "ObservationPeriod",
+    "PayerPlanPeriod",
+    "Person",
+    "ProcedureOccurrence",
+    "Provider",
     "Relationship",
+    "SourceToConceptMap",
+    "Specimen",
+    "VisitDetail",
+    "VisitOccurrence",
+    "Vocabulary",
 ]

src/omop_cdm/regular/cdm54/tables.py

@@ -2,7 +2,7 @@
 
 import datetime
 import decimal
-from typing import List, Optional
+from typing import Optional
 
 from sqlalchemy import BigInteger, Date, DateTime, ForeignKey, Integer, MetaData, Numeric, String, Text
 from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
@@ -347,35 +347,35 @@ class Person(Base):
     race_concept: Mapped["Concept"] = relationship("Concept", foreign_keys="Person.race_concept_id")
     race_source_concept: Mapped["Concept"] = relationship("Concept", foreign_keys="Person.race_source_concept_id")
 
-    observation_periods: Mapped[List["ObservationPeriod"]] = relationship(
+    observation_periods: Mapped[list["ObservationPeriod"]] = relationship(
         back_populates="person", cascade="all, delete-orphan"
     )
-    visit_occurrences: Mapped[List["VisitOccurrence"]] = relationship(
+    visit_occurrences: Mapped[list["VisitOccurrence"]] = relationship(
         back_populates="person", cascade="all, delete-orphan"
     )
-    visit_details: Mapped[List["VisitDetail"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    condition_occurrences: Mapped[List["ConditionOccurrence"]] = relationship(
+    visit_details: Mapped[list["VisitDetail"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    condition_occurrences: Mapped[list["ConditionOccurrence"]] = relationship(
         back_populates="person", cascade="all, delete-orphan"
     )
-    drug_exposures: Mapped[List["DrugExposure"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    procedure_occurrences: Mapped[List["ProcedureOccurrence"]] = relationship(
+    drug_exposures: Mapped[list["DrugExposure"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    procedure_occurrences: Mapped[list["ProcedureOccurrence"]] = relationship(
         back_populates="person", cascade="all, delete-orphan"
     )
-    device_exposures: Mapped[List["DeviceExposure"]] = relationship(
+    device_exposures: Mapped[list["DeviceExposure"]] = relationship(
         back_populates="person", cascade="all, delete-orphan"
     )
-    measurements: Mapped[List["Measurement"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    observations: Mapped[List["Observation"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    measurements: Mapped[list["Measurement"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    observations: Mapped[list["Observation"]] = relationship(back_populates="person", cascade="all, delete-orphan")
     death: Mapped["Death"] = relationship(back_populates="person", cascade="all, delete-orphan")
-    notes: Mapped[List["Note"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    specimens: Mapped[List["Specimen"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    payer_plan_periods: Mapped[List["PayerPlanPeriod"]] = relationship(
+    notes: Mapped[list["Note"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    specimens: Mapped[list["Specimen"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    payer_plan_periods: Mapped[list["PayerPlanPeriod"]] = relationship(
         back_populates="person", cascade="all, delete-orphan"
     )
-    drug_eras: Mapped[List["DrugEra"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    dose_eras: Mapped[List["DoseEra"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    condition_eras: Mapped[List["ConditionEra"]] = relationship(back_populates="person", cascade="all, delete-orphan")
-    episodes: Mapped[List["Episode"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    drug_eras: Mapped[list["DrugEra"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    dose_eras: Mapped[list["DoseEra"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    condition_eras: Mapped[list["ConditionEra"]] = relationship(back_populates="person", cascade="all, delete-orphan")
+    episodes: Mapped[list["Episode"]] = relationship(back_populates="person", cascade="all, delete-orphan")
 
 
 class ObservationPeriod(Base):