Update hexkit and other dependencies (#24)

.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-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
 

.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",
@@ -20,13 +19,10 @@
 				"python.languageServer": "Pylance",
 				"python.analysis.typeCheckingMode": "basic",
 				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest",
-				"python.testing.pytestArgs": [
-					"--profile"
-				],
 				"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_config_docs.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 config docs
         id: check-config-docs

.github/workflows/check_openapi_spec.yaml

@@ -16,9 +16,7 @@ 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 openapi.yaml
         id: check-openapi-docs

.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/check_readme.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 README
         id: check-readme

.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/[email protected]
@@ -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

@@ -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 tests
         id: pytest

.pre-commit-config.yaml

@@ -1,10 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 
-default_language_version:
-  python: python3.9
-
-minimum_pre_commit_version: 3.0.0
+minimum_pre_commit_version: 3.7.0
 
 repos:
   - repo: local
@@ -48,13 +45,13 @@ 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: v0.5.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.10.1
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/pyproject_custom.toml

@@ -1,11 +1,11 @@
 [project]
 name = "wps"
-version = "2.0.2"
+version = "2.0.3"
 description = "Work Package Service"
 dependencies = [
-    "ghga-event-schemas~=3.1.0",
-    "ghga-service-commons[api,auth,crypt]>=3.1.3",
-    "hexkit[akafka,mongodb]>=3.0.0",
+    "ghga-event-schemas~=3.3.1",
+    "ghga-service-commons[api,auth,crypt]>=3.1.5",
+    "hexkit[akafka,mongodb]>=3.3.0",
     "httpx>=0.27",
     "typer>=0.12",
 ]

.pyproject_generation/pyproject_template.toml

@@ -7,14 +7,12 @@ readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "[email protected]" },
 ]
-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/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

Dockerfile

@@ -14,7 +14,7 @@
 # limitations under the License.
 
 ## creating building container
-FROM python:3.10.9-slim-bullseye AS builder
+FROM python:3.12-slim-bookworm AS builder
 # update and install dependencies
 RUN apt update
 RUN apt upgrade -y
@@ -26,7 +26,7 @@ WORKDIR /service
 RUN python -m build
 
 # creating running container
-FROM python:3.10.9-slim-bullseye
+FROM python:3.12-slim-bookworm
 # update and install dependencies
 RUN apt update
 RUN apt upgrade -y

README.md

@@ -52,21 +52,21 @@ We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/work-package-service):
 ```bash
-docker pull ghga/work-package-service:2.0.2
+docker pull ghga/work-package-service:2.0.3
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/work-package-service:2.0.2 .
+docker build -t ghga/work-package-service:2.0.3 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/work-package-service:2.0.2 --help
+docker run -p 8080:8080 ghga/work-package-service:2.0.3 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
@@ -118,6 +118,8 @@ The service requires the following configuration parameters:
   ```
 
 
+- **`log_traceback`** *(boolean)*: Whether to include exception tracebacks in log messages. Default: `true`.
+
 - **`datasets_collection`** *(string)*: The name of the database collection for datasets. Default: `"datasets"`.
 
 - **`work_packages_collection`** *(string)*: The name of the database collection for work packages. Default: `"workPackages"`.

config_schema.json

@@ -46,6 +46,12 @@
       ],
       "title": "Log Format"
     },
+    "log_traceback": {
+      "default": true,
+      "description": "Whether to include exception tracebacks in log messages.",
+      "title": "Log Traceback",
+      "type": "boolean"
+    },
     "datasets_collection": {
       "default": "datasets",
       "description": "The name of the database collection for datasets",

example_config.yaml

@@ -33,6 +33,7 @@ kafka_ssl_keyfile: ''
 kafka_ssl_password: ''
 log_format: null
 log_level: INFO
+log_traceback: true
 openapi_url: /openapi.json
 port: 8080
 service_instance_id: wps_1

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>=0.23.7
 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>=0.2.13