config load refactored

.devcontainer/dev_install

@@ -7,7 +7,7 @@ cd /workspace
 python -m pip install --upgrade pip
 
 # install or upgrade dependencies for development and testing
-pip install --no-deps -r requirements-dev.txt
+pip install --no-deps -r ./lock/requirements-dev.txt
 
 # install the package itself in edit mode:
 pip install --no-deps -e .

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 // 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
+// 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",
@@ -75,4 +75,4 @@
 		// 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

@@ -0,0 +1,27 @@
+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:
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v5
+        with:
+          python-version: '3.12'
+
+      - name: Check config docs
+        id: check-config-docs
+        run: |
+          export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
+
+          ./scripts/update_config_docs.py --check

.github/workflows/check_openapi_spec.yaml

@@ -0,0 +1,28 @@
+# This file is only needed if your repository uses FastAPI
+name: Check if OpenAPI spec is up to date
+
+on: push
+
+jobs:
+  static-code-analysis:
+    name: Check OpenAPI spec
+
+    runs-on: ubuntu-latest
+
+    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: '3.12'
+
+      - name: Check openapi.yaml
+        id: check-openapi-docs
+        run: |
+          export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
+
+          ./scripts/update_openapi_docs.py --check

.github/workflows/check_pyproject.yaml

@@ -0,0 +1,25 @@
+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:
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v5
+        with:
+          python-version: '3.12'
+
+      - name: Check pyproject.toml
+        id: check-pyproject
+        run: |
+          ./scripts/update_pyproject.py --check

.github/workflows/check_readme.yaml

@@ -1,16 +1,25 @@
-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@v3
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v5
+        with:
+          python-version: '3.12'
 
-      - 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

@@ -11,15 +11,17 @@ on:
 
 jobs:
   fetch-tag:
+    name: Fetch Tag
     runs-on: ubuntu-latest
-    if: ( github.event.action != 'labeled' && contains(github.event.pull_request.labels.*.name, 'build') ) || ( github.event.action == 'labeled' && github.event.label.name == 'build' )
+    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:
       - id: fetch-tag
         uses: ghga-de/gh-action-fetch-tag@v1
     outputs:
       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/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@v3
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v5
 
-      - 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

.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@v3
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v5
 
-      - 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

@@ -52,7 +52,7 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.3.7
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -61,7 +61,7 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.9.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/README.md

@@ -0,0 +1,29 @@
+<!--
+ 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.
+
+-->
+
+# Generating the pyproject.toml
+
+The pyproject.toml of the service is generated by combining static configuration
+captured in [`./pyproject_template.toml`](./pyproject_template.toml) and custom
+package metadata specified in [`./pyproject_custom.toml`](./pyproject_custom.toml).
+
+The `./pyproject_template.toml` is managed by the template, please do not edit manually.
+
+You may specify properties in the `./pyproject_custom.toml` which are already specified
+in the `./pyproject_template.toml`. In that case, the `./pyproject_custom.toml` takes
+priority.

.pyproject_generation/pyproject_custom.toml

@@ -0,0 +1,20 @@
+[project]
+# please adapt to package name
+name = "ghga_transpiler"
+version = "2.0.0"
+description = "GHGA-Transpiler - excel to JSON converter"
+dependencies = [
+    "openpyxl >= 3.1.2, == 3.*",
+    "defusedxml >= 0.7, == 0.*",
+    "pydantic >=2, <3",
+    "PyYAML ~= 6.0",
+    "semver == 3.*"
+]
+
+[project.urls]
+# please adapt to package name
+Repository = "https://github.com/ghga-de/ghga-transpiler"
+
+[project.scripts]
+# please adapt to package name
+ghga-transpiler = "ghga_transpiler.__main__:run"