Template and dependencies are updated

.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
 

.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, 3.8, 3.7, 3.6
 {
 	"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",
@@ -75,4 +71,4 @@
 		// 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": {}
 	}
-}
+}

.devcontainer/license_header.txt

@@ -1,4 +1,4 @@
-Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+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");

.github/workflows/check_config_docs.yaml

@@ -1,17 +1,24 @@
-name: Check if the config schema and the example are up to date.
+name: Check if the config schema and the example are up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check config schema and example
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check config docs
+        id: check-config-docs
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 

.github/workflows/check_pyproject.yaml

@@ -1,16 +1,23 @@
-name: Check if the config schema and the example are up to date.
+name: Check if pyproject.toml file is up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check pyproject file
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check pyproject.toml
+        id: check-pyproject
         run: |
           ./scripts/update_pyproject.py --check

.github/workflows/check_readme.yaml

@@ -1,16 +1,23 @@
-name: Check if the readme is up to date.
+name: Check if the README file is up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check README file
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - name: Check readme
+      - name: Check README
+        id: check-readme
         run: |
           ./scripts/update_readme.py --check

.github/workflows/check_template_files.yaml

@@ -4,14 +4,23 @@ on: push
 
 jobs:
   check-template-files:
+    name: Check template files
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        id: setup-python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.12'
+
       - name: Check template files
+        id: check-template-files
         run: |
           if [ "${{ github.event.repository.name }}" == "microservice-repository-template" ]
           then

.github/workflows/ci_release.yaml

@@ -6,7 +6,10 @@ on:
 
 jobs:
   push_to_docker_hub:
+    name: Push to Docker Hub
+
     runs-on: ubuntu-latest
+
     steps:
       - uses: ghga-de/gh-action-ci@v1
         with:

.github/workflows/ci_workflow_dispatch.yaml

@@ -11,6 +11,7 @@ on:
 
 jobs:
   fetch-tag:
+    name: Fetch Tag
     runs-on: ubuntu-latest
     if:  github.event_name == 'workflow_dispatch' || ( github.event.action != 'labeled' && contains(github.event.pull_request.labels.*.name, 'build') ) || ( github.event.action == 'labeled' && github.event.label.name == 'build' )
     steps:
@@ -20,6 +21,7 @@ jobs:
       latest_tag: ${{ steps.fetch-tag.outputs.latest_tag }}
 
   push_to_docker_hub:
+    name: Push to Docker Hub
     needs: fetch-tag
     runs-on: ubuntu-latest
     steps:

.github/workflows/pypi_publish.yaml

@@ -8,20 +8,19 @@ jobs:
   pypi-publish:
     name: Publish tagged release on PyPI
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: '3.12'
 
-      - name: Ensure package version and tag are equal
+      - name: Ensure package version and tag name are equal
         run: |
-
           PKG_VER="$(grep -oP '^version = "\K[^"]+' pyproject.toml)"
           TAG_VER="${GITHUB_REF##*/}"
-
           echo "Package version is $PKG_VER" >&2
           echo "Tag version is $TAG_VER" >&2
           if [ "$PKG_VER" != "$TAG_VER" ]; then
@@ -45,10 +44,10 @@ jobs:
           --outdir dist/
           .
 
-      - name: Install the newly built package with all extras
+      - name: Install the newly build package with all extras
         run: |
           TAR_PATH="$( realpath ./dist/*.tar.gz)"
-          python -m \
+          python3 -m \
             pip install \
             "${TAR_PATH}[all]"
 
@@ -58,9 +57,8 @@ jobs:
           pip install
           --no-deps -r ./lock/requirements-dev.txt
 
-      - name: Run pytest on freshly installed package
+      - name: Run pytest on freshly install package
         run: |
-          export GHGA_CONNECTOR_CONFIG_YAML=./.devcontainer/.dev_config.yaml
           pytest .
 
       - name: Publish distribution package to PyPI (test)

.github/workflows/static_code_analysis.yaml

@@ -4,24 +4,36 @@ on: push
 
 jobs:
   static-code-analysis:
-    runs-on: ubuntu-latest
     name: Static Code Analysis
+
+    runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - uses: pre-commit/[email protected]
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]
         env:
           SKIP: no-commit-to-branch
-      - name: ruff
+
+      - name: Run ruff
+        id: ruff
         run: |
           ruff check --output-format=github .
           ruff format --check .
-      - name: mypy
+
+      - name: Run mypy
+        id: mypy
         run: |
           mypy .
+
       - name: Check license header and file
+        id: license-checker
         run: |
-          ./scripts/license_checker.py
+          ./scripts/check_license.py

.github/workflows/tests.yaml

@@ -1,19 +1,24 @@
-name: Tests
+name: Run test suite and measure coverage
 
 on: push
 
 jobs:
   tests:
+    name: Run test suite
+
     runs-on: ubuntu-latest
-    name: Tests
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - id: pytest
+      - name: Run tests
+        id: pytest
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 
@@ -22,8 +27,8 @@ jobs:
             --cov-report=xml \
             tests
 
-      - id: coveralls
-        name: Upload coverage to coveralls
+      - name: Upload coverage to coveralls
+        id: coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

.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
@@ -48,18 +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: v0.3.3
-    hooks:
-      - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.4.8
     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: v1.10.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ 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");

.pyproject_generation/pyproject_custom.toml

@@ -1,12 +1,12 @@
 [project]
 name = "ghga_connector"
-version = "1.2.1"
+version = "1.3.0"
 description = "GHGA Connector - A CLI client application for interacting with the GHGA system."
 dependencies = [
-    "typer~=0.9.0",
+    "typer~=0.12",
     "crypt4gh>=1.6, <2",
     "ghga-service-commons[api, crypt]>=3.1.1, <4",
-    "hexkit[s3]>=2.1.1, <3",
+    "hexkit[s3]>=3, <4",
     "rich>=13.7.1, <14"
 ]