template update

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
 
 ENV PYTHONUNBUFFERED 1
 
@@ -8,7 +8,7 @@ ARG USER_GID=$USER_UID
 RUN if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then groupmod --gid $USER_GID vscode && usermod --uid $USER_UID --gid $USER_GID vscode; fi
 
 # [Option] Install Node.js
-ARG INSTALL_NODE="true"
+ARG INSTALL_NODE="false"
 ARG NODE_VERSION="lts/*"
 RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
 

.pre-commit-config.yaml

@@ -48,12 +48,12 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.4
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.13.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/pyproject_template.toml

@@ -40,6 +40,7 @@ fixable = [
     "UP", # e.g. List -> list
     "I", # sort imports
     "D", # pydocstyle
+    "RUF022", # sort items in __all__
 ]
 ignore = [
     "E111", # indentation with invalid multiple (for formatter)
@@ -59,6 +60,7 @@ ignore = [
     "D206", # indent-with-spaces (for formatter)
     "D300", # triple-single-quotes (for formatter)
     "UP040", # type statement (not yet supported by mypy)
+    "PLC0206", # Extracting value from dictionary without calling `.items()`
 ]
 select = [
     "C90", # McCabe Complexity

.template/mandatory_files.txt

@@ -23,6 +23,7 @@ lock/requirements-dev.txt
 lock/requirements.txt
 
 Dockerfile
+Dockerfile.debian
 config_schema.json
 example_config.yaml
 LICENSE

.template/mandatory_files_ignore.txt

@@ -3,10 +3,6 @@
 
 .devcontainer/docker-compose.yml
 
-.github/workflows/cd.yaml
-.github/workflows/dev_cd.yaml
-.github/workflows/check_openapi_spec.yaml
-
 scripts/script_utils/fastapi_app_location.py
 
 Dockerfile

Dockerfile.debian

@@ -0,0 +1,48 @@
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+## creating building container
+FROM python:3.12-slim-bookworm AS builder
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+RUN pip install build
+# copy code
+COPY . /service
+WORKDIR /service
+# build wheel
+RUN python -m build
+
+# creating running container
+FROM python:3.12-slim-bookworm
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+# copy and install requirements and wheel
+WORKDIR /service
+COPY --from=builder /service/lock/requirements.txt /service
+RUN pip install --no-deps -r requirements.txt
+RUN rm requirements.txt
+COPY --from=builder /service/dist/ /service
+RUN pip install --no-deps *.whl
+RUN rm *.whl
+# create new user and execute as that user
+RUN useradd --create-home appuser
+WORKDIR /home/appuser
+USER appuser
+# set environment
+ENV PYTHONUNBUFFERED=1
+# Please adapt to package name:
+ENTRYPOINT ["my-microservice"]

lock/requirements-dev-template.in

@@ -1,7 +1,7 @@
 # common requirements for development and testing of services
 
 pytest>=8.2
-pytest-asyncio>=0.23.6
+pytest-asyncio>=0.23.7
 pytest-cov>=5
 snakeviz>=2.2
 logot>=1.3
@@ -29,4 +29,4 @@ setuptools>=69.5
 # required since switch to pyproject.toml and pip-tools
 tomli_w>=1.0
 
-uv>=0.1.39
+uv>=0.2.13

pyproject.toml

@@ -68,6 +68,7 @@ fixable = [
     "UP",
     "I",
     "D",
+    "RUF022",
 ]
 ignore = [
     "E111",
@@ -87,6 +88,7 @@ ignore = [
     "D206",
     "D300",
     "UP040",
+    "PLC0206",
 ]
 select = [
     "C90",