Upgrade schemapack to 2.0.0-alpha3 in 'schemapack' branch

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/vscode/devcontainers/python:3.9-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
 
 ENV PYTHONUNBUFFERED 1
 
@@ -7,23 +7,13 @@ ARG USER_UID=1000
 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
 
-# Copy install script
-COPY ./dev_install /bin
+# [Option] Install Node.js
+ARG INSTALL_NODE="true"
+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
 
-# Install secondary Python version
-USER vscode
-RUN <<EOF
-curl -sS https://pyenv.run | /bin/sh
-INIT_PYENV='
-export PYENV_ROOT="$HOME/.pyenv"
-[ -d "$PYENV_ROOT/bin" ] && export PATH="$PYENV_ROOT/bin:$PATH"
-eval "$(pyenv init -)"
-'
-echo "$INIT_PYENV" >> ~/.profile
-echo "$INIT_PYENV" >> ~/.bashrc
-. ~/.profile
-pyenv install --skip-existing 3.12
-pyenv global system 3.12
-EOF
+# Copy install and launcher script to bin:
+COPY ./dev_install /bin
+COPY ./dev_launcher /bin
 
 CMD ["sleep", "infinity"]

.devcontainer/dev_launcher

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+echo "The dev_launcher for this project is not implemented." >&2
+exit 1

.devcontainer/devcontainer.json

@@ -1,6 +1,5 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.177.0/containers/python-3-postgres
-// Update the VARIANT arg in docker-compose.yml to pick a Python version: 3, 3.12, 3.11, 3.10, 3.9
 {
 	"name": "${localWorkspaceFolderBasename}",
 	"dockerComposeFile": "docker-compose.yml",
@@ -23,7 +22,7 @@
 				"python.testing.unittestEnabled": false,
 				"python.testing.pytestEnabled": true,
 				"editor.codeActionsOnSave": {
-					"source.organizeImports": true
+					"source.organizeImports": "explicit"
 				},
 				"editor.formatOnSave": true,
 				"editor.renderWhitespace": "all",

.github/workflows/check_pyproject.yaml

@@ -15,9 +15,7 @@ jobs:
 
       - name: Common steps
         id: common
-        uses: ghga-de/gh-action-common@v5
-        with:
-          python-version: '3.12'
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check pyproject.toml
         id: check-pyproject

.github/workflows/static_code_analysis.yaml

@@ -15,7 +15,7 @@ jobs:
 
       - name: Common steps
         id: common
-        uses: ghga-de/gh-action-common@v5
+        uses: ghga-de/gh-action-common@v6
 
       - name: Run pre-commit
         uses: pre-commit/action@v3.0.1
@@ -36,4 +36,4 @@ jobs:
       - name: Check license header and file
         id: license-checker
         run: |
-          ./scripts/license_checker.py
+          ./scripts/check_license.py

.github/workflows/tests.yaml

@@ -1,52 +1,34 @@
-name: Tests
+name: Run test suite and measure coverage
 
 on: push
 
 jobs:
   tests:
-    name: Tests
+    name: Run test suite
 
     runs-on: ubuntu-latest
 
-    strategy:
-      matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-
     steps:
       - name: Checkout repository
         id: checkout
         uses: actions/checkout@v4
 
       - name: Common steps
         id: common
-        uses: ghga-de/gh-action-common@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install tox plugin
-        id: install-tox-gh-actions
-        run: |
-          pip install --disable-pip-version-check "tox-gh-actions>=3.2,<4"
+        uses: ghga-de/gh-action-common@v6
 
-      - name: Run tests with Python ${{ matrix.python-version }}
+      - name: Run tests
         id: pytest
-        if: ${{ matrix.python-version != '3.12' }}
-        run: |
-          export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
-
-          tox
-
-      - name: Run tests with Python ${{ matrix.python-version }} measuring coverage
-        id: pytest-coverage
-        if: ${{ matrix.python-version == '3.12' }}
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 
-          tox -- --cov="${{ steps.common.outputs.PACKAGE_NAME }}" --cov-report=xml
+          pytest \
+            --cov="${{ steps.common.outputs.PACKAGE_NAME }}" \
+            --cov-report=xml \
+            tests
 
       - name: Upload coverage to coveralls
         id: coveralls
-        if: ${{ matrix.python-version == '3.12' }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

.pre-commit-config.yaml

@@ -45,7 +45,7 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.1
+    rev: v0.4.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.pyproject_generation/pyproject_custom.toml

@@ -4,7 +4,7 @@ name = "metldata"
 version = "1.0.0"
 description = "metldata - A framework for handling metadata based on ETL, CQRS, and event sourcing."
 dependencies = [
-    "schemapack<=1.0.0, <2.0.0"
+    "schemapack == 2.0.0-alpha.3"
 ]
 
 [project.urls]

.pyproject_generation/pyproject_template.toml

@@ -7,14 +7,12 @@ readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 license = { text = "Apache 2.0" }
 classifiers = [
     "Development Status :: 1 - Planning",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: Apache Software License",
     "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
@@ -35,7 +33,7 @@ exclude = [
 ]
 line-length = 88
 src = ["src", "tests", "examples", "scripts"]
-target-version = "py39"
+target-version = "py312"
 
 [tool.ruff.lint]
 fixable = [
@@ -60,6 +58,7 @@ ignore = [
     "D107", # missing docstring in __init__
     "D206", # indent-with-spaces (for formatter)
     "D300", # triple-single-quotes (for formatter)
+    "UP040", # type statement (not yet supported by mypy)
 ]
 select = [
     "C90", # McCabe Complexity
@@ -105,7 +104,7 @@ asyncio_mode = "strict"
 
 [tool.coverage.paths]
 source = [
-  "src",
-  "/workspace/src",
-  "**/lib/python*/site-packages",
+    "src",
+    "/workspace/src",
+    "**/lib/python*/site-packages",
 ]

.template/deprecated_files.txt

@@ -13,6 +13,7 @@
 .github/workflows/cd.yaml
 
 scripts/check_mandatory_and_static_files.py
+scripts/license_checker.py
 scripts/update_static_files.py
 
 docs

.template/mandatory_files_ignore.txt

@@ -1,7 +1,6 @@
 # Optional list of files which are actually mandatory in the template
 # but are allowed to be removed in the current repository
 
-.devcontainer/dev_launcher
 
 .github/workflows/cd.yaml
 .github/workflows/dev_cd.yaml

.template/static_files.txt

@@ -15,10 +15,12 @@
 
 scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
+scripts/script_utils/deps.py
+scripts/script_utils/lock_deps.py
 
 scripts/__init__.py
 scripts/update_all.py
-scripts/license_checker.py
+scripts/check_license.py
 scripts/get_package_name.py
 scripts/update_config_docs.py
 scripts/update_template_files.py

.template/static_files_ignore.txt

@@ -5,7 +5,6 @@
 .github/workflows/check_openapi_spec.yaml
 .github/workflows/check_readme.yaml
 .github/workflows/cd.yaml
-.github/workflows/tests.yaml
 .github/workflows/ci_release.yaml
 .github/workflows/ci_workflow_dispatch.yaml
 
@@ -16,7 +15,5 @@ scripts/update_all.py
 
 example_data/README.md
 
-.devcontainer/Dockerfile
-.devcontainer/dev_install
 .readme_generation/README.md
 .readme_generation/readme_template.md

lock/requirements-dev-template.in

@@ -1,17 +1,17 @@
 # common requirements for development and testing of services
 
-pytest>=8.1
-pytest-asyncio>=0.23
+pytest>=8.2
+pytest-asyncio>=0.23.6
 pytest-cov>=5
 snakeviz>=2.2
 logot>=1.3
 
 pre-commit>=3.7
 
-mypy>=1.9
+mypy>=1.10
 mypy-extensions>=1.0
 
-ruff>=0.3
+ruff>=0.4
 
 click>=8.1
 typer>=0.12
@@ -27,7 +27,6 @@ jsonschema2md>=1.1
 setuptools>=69.5
 
 # required since switch to pyproject.toml and pip-tools
-tomli>=2.0.1
 tomli_w>=1.0
 
-uv>=0.1.31
+uv>=0.1.39