feature/mx-1446 harmonize template (#13)

# PR Context

- reduces diffs in dependant repositories

# Added
- add badges for open-code and cookiecutter
 
# Changes
- add tests and ruff cache to dockerignore
- use `WORKFLOW_TOKEN` in cookiecutter job for consistency
- switch json linting to 4-spaces and utf-8
- clean up and expand pdm scripts
- improve and simplify mex.bat and makefile
- update pdm, ruff and pre-commit

---------

Signed-off-by: Nicolas Drebenstedt <[email protected]>

.gitignore

@@ -101,6 +101,10 @@ dmypy.json
 # ruff
 .ruff_cache
 
+# cruft
+.cruft-pr-body
+*.rej
+
 # PyCharm
 .idea/
 .idea_modules/

CHANGELOG.md

@@ -10,12 +10,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - add review assignment to mex-template itself
+- add code of conduct file to mex-template itself
+- add badges for open-code and cookiecutter
 
 ### Changes
 
 - improve prompt for project name
 - switch from poetry to pdm
-- switch order of black and ruff linter, as ruff often complains about issues, that are automatically fixed by black
+- switch order of black and ruff linter, as ruff often complains about issues,
+  that are automatically fixed by black
+- add tests and ruff cache to dockerignore
+- use `WORKFLOW_TOKEN` in cookiecutter job for consistency
+- switch json linting to 4-spaces and utf-8
+- clean up and expand pdm scripts
+- improve and simplify mex.bat and makefile
+- update pdm, ruff and pre-commit
 
 ### Deprecated
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and
+maintainers pledge to make participation in our project and our community a
+harassment-free experience for everyone, regardless of age, body size, disability,
+ethnicity, sex characteristics, gender identity and expression, level of experience,
+education, socio-economic status, nationality, personal appearance, race, religion,
+or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project team members are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in response to
+any instances of unacceptable behavior.
+
+Project team members have the right and responsibility to remove, edit, or reject
+comments, commits, code, and other contributions that are not aligned to this
+Code of Conduct, or to ban temporarily or permanently any contributor for other
+behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and it also applies when an
+individual is representing the project or its community in public spaces. Examples of
+representing a project or community include using an official project e-mail address,
+appearing as a project maintainer, or acting as an appointed representative at an online
+or offline event. Representation of a project may be further defined and clarified by
+the project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
+contacting the project team at [email protected]. All complaints will be reviewed and
+investigated and will result in a response that is deemed necessary and appropriate to
+the circumstances. The project team is obligated to maintain confidentiality with regard
+to the reporter of an incident. Further details of specific enforcement policies may be
+posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may
+face temporary or permanent repercussions as determined by project, departmental
+or organizational leadership roles.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

README.md

@@ -2,6 +2,8 @@
 
 Cookiecutter template for MEx python projects.
 
+[![open-code](https://github.com/robert-koch-institut/mex-template/actions/workflows/open-code.yml/badge.svg)](https://gitlab.opencode.de/robert-koch-institut/mex/mex-template)
+
 ## project
 
 The Metadata Exchange (MEx) project is committed to improve the retrieval of RKI

mex-{{ cookiecutter.project_name }}/.dockerignore

@@ -35,6 +35,7 @@ pip-log.txt
 pip-delete-this-directory.txt
 
 # Unit test / coverage reports
+tests/
 htmlcov/
 .tox/
 .nox/
@@ -96,6 +97,9 @@ venv.bak/
 .dmypy.json
 dmypy.json
 
+# ruff
+.ruff_cache
+
 # PyCharm
 .idea/
 .idea_modules/

mex-{{ cookiecutter.project_name }}/.github/workflows/cookiecutter.yml

@@ -63,7 +63,7 @@ jobs:
 
       - name: Update template
         env:
-          {% raw %}GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}{% endraw %}
+          {% raw %}GH_TOKEN: ${{ secrets.WORKFLOW_TOKEN }}{% endraw %}
         run: |
           {% raw -%}
           if cruft check; then

mex-{{ cookiecutter.project_name }}/.github/workflows/cve-scan.yml

@@ -57,7 +57,7 @@ jobs:
       - name: Export dependencies
         run: |
           mkdir --parents pdm
-          pdm export -G :all -f requirements > pdm/requirements.txt
+          pdm export-all > pdm/requirements.txt
 
       - name: Run trivy
         uses: aquasecurity/trivy-action@master

mex-{{ cookiecutter.project_name }}/.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.3.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -16,26 +16,27 @@ repos:
     hooks:
       - id: pretty-format-json
         name: json
-        args: [--autofix]
+        args: [--autofix, --indent=4, --no-ensure-ascii]
         exclude: .cruft.json
       - id: check-yaml
         name: yaml
+        exclude: templates\/[a-z_-]+.yaml
       - id: end-of-file-fixer
         name: eof
       - id: trailing-whitespace
         name: whitespaces
       - id: fix-byte-order-marker
         name: byte-order
   - repo: https://github.com/pdm-project/pdm
-    rev: 2.12.4
+    rev: 2.13.2
     hooks:
       - id: pdm-lock-check
         name: pdm
   - repo: local
     hooks:
     - id: mypy
       name: mypy
-      entry: pdm run dmypy run --timeout 7200 -- mex
+      entry: pdm mypy-daemon
       files: ^mex/
       language: system
       pass_filenames: false

mex-{{ cookiecutter.project_name }}/Makefile

@@ -1,13 +1,14 @@
-.PHONY: all test setup hooks install linter pytest wheel container run start docs
+.PHONY: all test setup hooks install linter pytest wheel image run start docs
 all: install test
 test: linter pytest
 
 LATEST = $(shell git describe --tags $(shell git rev-list --tags --max-count=1))
+PWD = $(shell pwd)
 
 setup:
 	# install meta requirements system-wide
 	@ echo installing requirements; \
-	python -m pip --quiet --disable-pip-version-check install --force-reinstall -r requirements.txt; \
+	pip --disable-pip-version-check install --force-reinstall -r requirements.txt; \
 
 hooks:
 	# install pre-commit hooks when not in CI
@@ -18,48 +19,47 @@ hooks:
 install: setup hooks
 	# install packages from lock file in local virtual environment
 	@ echo installing package; \
-	pdm sync --clean --group dev; \
+	pdm install-all; \
 
 linter:
 	# run the linter hooks from pre-commit on all files
 	@ echo linting all files; \
-	pre-commit run --all-files; \
+	pdm lint; \
 
 pytest:
 	# run the pytest test suite with all unit tests
 	@ echo running unit tests; \
-	pdm run pytest -m "not integration"; \
+	pdm unit; \
 
 wheel:
 	# build the python package
 	@ echo building wheel; \
-	pdm build --no-sdist; \
+	pdm wheel; \
 
-container:
+image:
 	# build the docker image
 	@ echo building docker image mex-{{ cookiecutter.project_name }}:${LATEST}; \
 	export DOCKER_BUILDKIT=1; \
 	docker build \
 		--tag rki/mex-{{ cookiecutter.project_name }}:${LATEST} \
 		--tag rki/mex-{{ cookiecutter.project_name }}:latest .; \
 
-run: container
+run: image
 	# run the service as a docker container
 	@ echo running docker container mex-{{ cookiecutter.project_name }}:${LATEST}; \
 	docker run \
 		--env MEX_{{ cookiecutter.project_name|upper }}_HOST=0.0.0.0 \
 		--publish 8081:8081 \
 		rki/mex-{{ cookiecutter.project_name }}:${LATEST}; \
 
-start: container
-	# start the service using docker-compose
-	@ echo running docker-compose with mex-{{ cookiecutter.project_name }}:${LATEST}; \
+start: image
+	# start the service using docker compose
+	@ echo start mex-{{ cookiecutter.project_name }}:${LATEST} with compose; \
 	export DOCKER_BUILDKIT=1; \
 	export COMPOSE_DOCKER_CLI_BUILD=1; \
-	docker-compose up; \
+	docker compose up --remove-orphans; \
 
 docs:
 	# use sphinx to auto-generate html docs from code
-	@ echo generating api docs; \
-	pdm run sphinx-apidoc -f -o docs/source mex; \
-	pdm run sphinx-build -aE -b dirhtml docs docs/dist; \
+	@ echo generating docs; \
+	pdm doc; \

mex-{{ cookiecutter.project_name }}/README.md

@@ -2,10 +2,12 @@
 
 {{ cookiecutter.short_summary }}
 
-[![testing](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/testing.yml/badge.svg)](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/testing.yml)
-[![linting](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/linting.yml)
+[![cookiecutter](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/cookiecutter.yml/badge.svg)](https://github.com/robert-koch-institut/mex-template)
 [![cve-scan](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/cve-scan.yml/badge.svg)](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/cve-scan.yml)
 [![documentation](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/documentation.yml/badge.svg)](https://robert-koch-institut.github.io/mex-{{ cookiecutter.project_name }})
+[![linting](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/linting.yml)
+[![open-code](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/open-code.yml/badge.svg)](https://gitlab.opencode.de/robert-koch-institut/mex/mex-{{ cookiecutter.project_name }})
+[![testing](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/testing.yml/badge.svg)](https://github.com/robert-koch-institut/mex-{{ cookiecutter.project_name }}/actions/workflows/testing.yml)
 
 ## project
 
@@ -60,19 +62,16 @@ components of the MEx project are open-sourced under the same license as well.
 
 ### linting and testing
 
-- on unix run `make test`
-- on windows run `.\mex.bat test`
-- or run manually
-  - linter checks via `pre-commit run --all-files`
-  - all tests via `pdm run pytest`
-  - just unit tests via `pdm run pytest -m "not integration"`
+- run all linters with `pdm lint`
+- run only unit tests with `pdm unit`
+- run unit and integration tests with `pdm test`
 
 ### updating dependencies
 
 - update boilerplate files with `cruft update`
 - update global requirements in `requirements.txt` manually
 - update git hooks with `pre-commit autoupdate`
-- update package dependencies using `pdm autoupdate`
+- update package dependencies using `pdm update-all`
 - update github actions in `.github/workflows/*.yml` manually
 
 ### creating release
@@ -84,9 +83,9 @@ components of the MEx project are open-sourced under the same license as well.
 
 ### container workflow
 
-- build container with `make container`
+- build image with `make image`
 - run directly using docker `make run`
-- start with docker-compose `make start`
+- start with docker compose `make start`
 
 ## commands
 

mex-{{ cookiecutter.project_name }}/mex.bat

@@ -11,7 +11,8 @@ exit /b 1
 
 :install
 @REM install meta requirements system-wide
-Python -m pip --quiet --disable-pip-version-check install --force-reinstall -r requirements.txt
+echo installing requirements
+pip --disable-pip-version-check install --force-reinstall -r requirements.txt
 if %errorlevel% neq 0 exit /b %errorlevel%
 
 @REM install pre-commit hooks when not in CI
@@ -22,26 +23,24 @@ if "%CI%"=="" (
 
 @REM install packages from lock file in local virtual environment
 echo installing package
-pdm sync --clean --group dev
+pdm install-all
 exit /b %errorlevel%
 
 
 :test
 @REM run the linter hooks from pre-commit on all files
 echo linting all files
-pre-commit run --all-files
+pdm lint
 if %errorlevel% neq 0 exit /b %errorlevel%
 
 @REM run the pytest test suite with unit and integration tests
 echo running all tests
-pdm run pytest
+pdm test
 exit /b %errorlevel%
 
 
 :docs
 @REM use sphinx to auto-generate html docs from code
-echo generating api docs
-pdm run sphinx-apidoc -f -o docs\source mex
-if %errorlevel% neq 0 exit /b %errorlevel%
-pdm run sphinx-build -aE -b dirhtml docs docs\dist
+echo generating docs
+pdm doc
 exit /b %errorlevel%