Update template files

Author: TheByronHimes

.devcontainer/Dockerfile

@@ -1,6 +1,6 @@
-FROM mcr.microsoft.com/vscode/devcontainers/python:3.9-bullseye
+FROM mcr.microsoft.com/devcontainers/python:2.0.2-3.13-trixie
 
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONUNBUFFERED=1
 
 # Update args in docker-compose.yaml to set the UID/GID of the "vscode" user.
 ARG USER_UID=1000

.devcontainer/devcontainer.json

@@ -70,6 +70,6 @@
 	},
 	"features": {
 		// details can be found here: https://github.com/devcontainers/features/tree/main/src/docker-outside-of-docker
-		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {"moby": false}
 	}
 }

.github/workflows/check_config_docs.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check config docs
         id: check-config-docs

.github/workflows/check_pyproject.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check pyproject.toml
         id: check-pyproject

.github/workflows/check_readme.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check README
         id: check-readme

.github/workflows/check_template_files.yaml

@@ -11,13 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         id: setup-python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Check template files
         id: check-template-files

.github/workflows/static_code_analysis.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Run pre-commit
         uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
         args: [--check]
         pass_filenames: false
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -45,13 +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: v0.11.13
+    rev: v0.13.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.18.2
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/pyproject_template.toml

@@ -7,7 +7,7 @@ readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "[email protected]" },
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "Apache 2.0" }
 classifiers = [
     "Development Status :: 5 - Production/Stable",

.readme_generation/readme_template.md

@@ -51,7 +51,7 @@ $config_description
 ### Usage:
 
 A template YAML for configuring the service can be found at
-[`./example-config.yaml`](./example-config.yaml).
+[`./example_config.yaml`](./example_config.yaml).
 Please adapt it, rename it to `.$shortname.yaml`, and place it in one of the following locations:
 - in the current working directory where you execute the service (on Linux: `./.$shortname.yaml`)
 - in your home directory (on Linux: `~/.$shortname.yaml`)
@@ -60,7 +60,7 @@ The config yaml will be automatically parsed by the service.
 
 **Important: If you are using containers, the locations refer to paths within the container.**
 
-All parameters mentioned in the [`./example-config.yaml`](./example-config.yaml)
+All parameters mentioned in the [`./example_config.yaml`](./example_config.yaml)
 could also be set using environment variables or file secrets.
 
 For naming the environment variables, just prefix the parameter name with `${shortname}_`,
@@ -100,7 +100,7 @@ It installs the service with all development dependencies, and it installs pre-c
 
 The installation is performed automatically when you build the devcontainer. However,
 if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the
-[`./requirements-dev.txt`](./requirements-dev.txt), please run it again.
+[`lock/requirements-dev.txt`](./lock/requirements-dev.txt), please run it again.
 
 ## License
 
@@ -109,5 +109,5 @@ This repository is free to use and modify according to the
 
 ## README Generation
 
-This README file is auto-generated, please see [`readme_generation.md`](./readme_generation.md)
+This README file is auto-generated, please see [.readme_generation/README.md](./.readme_generation/README.md)
 for details.