microservice template is updated (#51)

* update template files

* revert for TypeError

* precommit fixes

* remvoe unused ignore

* Pin linkml dependencies

* Update test fixture to latest linkml version

* further update of template files

---------

Co-authored-by: Léon Kuchenbecker <leon.kuchenbecker@uni-tuebingen.de>

.coveragerc

@@ -0,0 +1,5 @@
+[paths]
+source =
+  src
+  /workspace/src
+  **/lib/python*/site-packages

.deprecated_files

@@ -9,8 +9,15 @@
 
 .github/workflows/check_mandatory_and_static_files.yaml
 .github/workflows/dev_cd.yaml
+.github/workflows/unit_and_int_tests.yaml
 
 scripts/check_mandatory_and_static_files.py
 scripts/update_static_files.py
 
 docs
+
+setup.py
+setup.cfg
+
+.pylintrc
+.flake8

.devcontainer/dev_install

@@ -6,11 +6,11 @@ cd /workspace
 # upgrade pip
 python -m pip install --upgrade pip
 
-# install with all extras in editable mode
-pip install -e .[all]
-
 # install or upgrade dependencies for development and testing
-pip install -r requirements-dev.txt
+pip install --no-deps -r requirements-dev.txt
+
+# install the package itself in edit mode:
+pip install --no-deps -e .
 
 # install pre-commit hooks to git
 pre-commit install

.github/workflows/cd.yaml

@@ -44,7 +44,7 @@ jobs:
         name: Verify package version vs tag version
         # package version must be same with tag version
         run: |
-          PKG_VER="$(python setup.py --version)"
+          PKG_VER="$(grep -oP 'version = \"\K[^\"]+' pyproject.toml)"
           echo "Package version is $PKG_VER" >&2
           echo "Tag version is ${{ steps.get_version_tag.outputs.version }}" >&2
           if [ "$PKG_VER" != "${{ steps.get_version_tag.outputs.version }}" ]; then

.github/workflows/check_config_docs.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v2
+        uses: ghga-de/gh-action-common@v3
 
       - name: Check config docs
         run: |

.github/workflows/check_readme.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v2
+        uses: ghga-de/gh-action-common@v3
 
       - name: Check readme
         run: |

.github/workflows/pypi_publish.yaml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Verify Package Version vs Tag Version
         run: |
-          PKG_VER="$(python setup.py -V)"
+          PKG_VER="$(grep -oP 'version = \"\K[^\"]+' pyproject.toml)"
           TAG_VER="${GITHUB_REF##*/}"
           echo "Package version is $PKG_VER" >&2
           echo "Tag version is $TAG_VER" >&2

.github/workflows/static_code_analysis.yaml

@@ -10,29 +10,19 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v2
+        uses: ghga-de/gh-action-common@v3
 
       - uses: pre-commit/action@v3.0.0
         env:
           SKIP: no-commit-to-branch
+      - name: ruff
+        uses: chartboost/ruff-action@v1
       - name: black
         run: |
           black --check .
-      - name: isort
-        run: |
-          isort --check --profile black .
       - name: mypy
         run: |
           mypy .
-      - name: pylint
-        run: |
-          pylint "${{ steps.common.outputs.MAIN_SRC_DIR }}"
-      - name: flake8
-        run: |
-          flake8 --config .flake8
-      - name: bandit
-        run: |
-          bandit -r "${{ steps.common.outputs.MAIN_SRC_DIR }}"
       - name: Check license header and file
         run: |
           ./scripts/license_checker.py

.github/workflows/unit_and_int_tests.yaml → .github/workflows/tests.yaml

@@ -1,24 +1,26 @@
-name: Unit and Integration Tests
+name: Tests
 
 on: push
 
 jobs:
-  unit_and_int_tests:
+  tests:
     runs-on: ubuntu-latest
-    name: Unit and Integration Tests
+    name: Tests
 
     steps:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v2
+        uses: ghga-de/gh-action-common@v3
 
-      - name: Run pytest
+      - id: pytest
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
+
           pytest \
-            --cov="${{ steps.common.outputs.MAIN_SRC_DIR }}" \
-            --cov-report=xml
+            --cov="${{ steps.common.outputs.PACKAGE_NAME }}" \
+            --cov-report=xml \
+            tests
 
       - id: coveralls
         name: Upload coverage to coveralls

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 prof/
 
 # Translations

.mandatory_files

@@ -19,10 +19,12 @@ Dockerfile
 config_schema.json
 example_config.yaml
 LICENSE
+pyproject.toml
 README.md
-setup.py
-setup.cfg
+requirements-dev.in
 requirements-dev.txt
+requirements.txt
 
 .description.md
 .design.md
+.pre-commit-config.yaml

.pre-commit-config.yaml

@@ -7,6 +7,20 @@ default_language_version:
 minimum_pre_commit_version: 3.0.0
 
 repos:
+  - repo: local
+    hooks:
+      - id: update-hook-revs
+        name: "ensure hooks are up to date"
+        language: python
+        additional_dependencies:
+          - "packaging"
+          - "typer"
+        fail_fast: true
+        always_run: true
+        entry: ./scripts/update_hook_revs.py
+        files: '\.pre-commit-config.yaml'
+        args: [--check]
+        pass_filenames: false
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -15,7 +29,6 @@ repos:
         exclude: '.*\.json|example_config.yaml'
       - id: check-yaml
       - id: check-added-large-files
-        exclude: tests/fixtures/load/example_models/embedded_public_model.yaml
       - id: check-ast
       - id: check-json
         exclude: devcontainer.json
@@ -37,33 +50,17 @@ repos:
       - id: debug-statements
       - id: debug-statements
       - id: debug-statements
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.292
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.9.1
     hooks:
       - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: [--profile, black]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.0
+    rev: v1.5.1
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]
-  - repo: https://github.com/PyCQA/pylint
-    rev: v2.16.4
-    hooks:
-      - id: pylint
-        args: [--disable=E0401]
-        exclude: tests|.devcontainer
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        args: [--config, .flake8]
-  - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.4
-    hooks:
-      - id: bandit
-        exclude: tests|.devcontainer|scripts