diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 5bfe492..925db27 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -4,9 +4,9 @@ jobs: ruff: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v7 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v7 with: python-version: '3.13' - name: Install Poetry diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 5ada215..57868dc 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -15,9 +15,9 @@ jobs: id-token: write contents: read steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v7 with: python-version: '3.12' - name: Install Poetry diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index a21703b..341130b 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -19,9 +19,9 @@ jobs: ] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} - name: Install Poetry diff --git a/CHANGELOG.md b/CHANGELOG.md index 90836cd..b75eeb5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## v0.6.0 + +Internal changes: +- Updated GitHub Actions. +- Updated dev dependencies. + ## v0.5.0 New: diff --git a/docs/README.md b/docs/README.md index dd02f66..38c8d30 100644 --- a/docs/README.md +++ b/docs/README.md @@ -79,6 +79,7 @@ class Base(DeclarativeBase): class Person(cdm54.BasePersonCdm54, Base): pass + # Etc. for all other tables ``` This approach allows for the greatest customization possibilities. @@ -162,6 +163,7 @@ E.g. for the person table: ```python from omop_cdm.constants 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["selenium"] +minio = ["minio (>=7)"] +mongodb = ["pymongo (>=4)"] +mssql = ["pymssql (>=2)", "sqlalchemy"] +mysql = ["pymysql[rsa] (>=1)", "sqlalchemy"] +nats = ["nats-py (>=2)"] +neo4j = ["neo4j (>=6)"] +openfga = ["openfga-sdk"] +opensearch = ["opensearch-py (>=3) ; python_version < \"4.0\""] +oracle = ["oracledb (>=3)", "sqlalchemy"] +oracle-free = ["oracledb (>=3)", "sqlalchemy"] +qdrant = ["qdrant-client (>=1)"] +rabbitmq = ["pika (>=1)"] +redis = ["redis (>=7)"] +registry = ["bcrypt (>=5)"] +scylla = ["cassandra-driver (>=3) ; python_version < \"3.14\""] +selenium = ["selenium (>=4)"] sftp = ["cryptography"] test-module-import = ["httpx"] trino = ["trino"] -weaviate = ["weaviate-client (>=4.5.4,<5.0.0)"] +weaviate = ["weaviate-client (>=4)"] [[package]] name = "tomli" @@ -1197,26 +1218,23 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.35.3" +version = "21.7.4" description = "Virtual Python Environment builder" optional = false -python-versions 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b/pyproject.toml index 1636367..c140062 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "omop-cdm" -version = "0.5.0" +version = "0.6.0" description = "SQLAlchemy ORM of the OHDSI OMOP CDM" authors = [ {name = "Spayralbe", email = "stefan@thehyve.nl"}, @@ -34,15 +34,15 @@ dependencies = [ "Changelog" = "https://github.com/thehyve/omop-cdm/blob/main/CHANGELOG.md" [tool.poetry.group.dev.dependencies] -nox = "^2026.2.9" -ruff = "^0.15.9" -pre-commit = "^4.5.1" +nox = "^2026.8.10" +ruff = "^0.16.2" +pre-commit = "^4.6.2" [tool.poetry.group.test.dependencies] -pytest = "^8.4.1" -pytest-cov = "^6.2.1" -testcontainers = "^4.13.2" -psycopg2-binary = "^2.9.9" +pytest = "^9.1.1" +pytest-cov = "^7.1.0" +testcontainers = "^4.15.0" +psycopg2-binary = "^2.9.12" [build-system] requires = ["poetry-core>=2.0"] diff --git a/tests/conftest.py b/tests/conftest.py index 3307822..3afc035 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,7 +5,7 @@ from sqlalchemy import Connection, Engine, MetaData, create_engine, select from sqlalchemy.orm import Session from sqlalchemy.sql.ddl import CreateSchema, DropSchema -from testcontainers.postgres import PostgresContainer +from testcontainers.community.postgres import PostgresContainer POSTGRES_IMAGE = "postgres:16-alpine"