Bump cookiecutter template to af56c8

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/robert-koch-institut/mex-template",
-  "commit": "fca460e90134ef8c10f54d491aa80891509b1b6c",
+  "commit": "af56c8fa17144906e94518391acc9795d5f2dc89",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/cookiecutter.yml

@@ -52,16 +52,7 @@ jobs:
           SIGNING_PUB: ${{ secrets.SIGNING_PUB }}
         run: |
           eval "$(ssh-agent -s)"
-          install --directory ~/.ssh --mode 700
-          base64 -d <<< '${{ secrets.SIGNING_KEY }}' > ~/.ssh/mex
-          base64 -d <<< '${{ secrets.SIGNING_PUB }}' > ~/.ssh/mex.pub
-          chmod 600 ~/.ssh/*
-          ssh-add ~/.ssh/mex
-          git config --local user.email ${{ vars.MEX_BOT_EMAIL }}
-          git config --local user.name ${{ vars.MEX_BOT_USER }}
-          git config --local gpg.format ssh
-          git config --local user.signingkey ~/.ssh/mex.pub
-          git config --local commit.gpgsign true
+          pdm setup-commit-signing
 
       - name: Update template
         env:

.github/workflows/release.yml

@@ -63,16 +63,7 @@ jobs:
           SIGNING_PUB: ${{ secrets.SIGNING_PUB }}
         run: |
           eval "$(ssh-agent -s)"
-          install --directory ~/.ssh --mode 700
-          base64 -d <<< '${{ secrets.SIGNING_KEY }}' > ~/.ssh/mex
-          base64 -d <<< '${{ secrets.SIGNING_PUB }}' > ~/.ssh/mex.pub
-          chmod 600 ~/.ssh/*
-          ssh-add ~/.ssh/mex
-          git config --local user.email ${{ vars.MEX_BOT_EMAIL }}
-          git config --local user.name ${{ vars.MEX_BOT_USER }}
-          git config --local gpg.format ssh
-          git config --local user.signingkey ~/.ssh/mex.pub
-          git config --local commit.gpgsign true
+          pdm setup-commit-signing
 
       - name: Release new version
         id: release

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
   python: python3.11
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.5
+    rev: v0.7.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -9,7 +9,7 @@ Backend server for the RKI metadata exchange.
 [![open-code](https://github.com/robert-koch-institut/mex-backend/actions/workflows/open-code.yml/badge.svg)](https://gitlab.opencode.de/robert-koch-institut/mex/mex-backend)
 [![testing](https://github.com/robert-koch-institut/mex-backend/actions/workflows/testing.yml/badge.svg)](https://github.com/robert-koch-institut/mex-backend/actions/workflows/testing.yml)
 
-## project
+## Project
 
 The Metadata Exchange (MEx) project is committed to improve the retrieval of RKI
 research data and projects. How? By focusing on metadata: instead of providing the
@@ -39,27 +39,28 @@ data Findable, Accessible, Interoperable and Reusable.
 **Contact** \
 For more information, please feel free to email us at [[email protected]](mailto:[email protected]).
 
-### Publisher of this document
+### Publisher
+
 **Robert Koch-Institut** \
 Nordufer 20 \
 13353 Berlin \
 Germany
 
-## package
+## Package
 
 The `mex-backend` package is a multi-purpose backend application with an HTTP-API. It
 provides endpoints to ingest data from ETL-pipelines, for a metadata editor application,
 and for publishing pipelines to extract standardized data for use in upstream frontend
 applications.
 
-## license
+## License
 
 This package is licensed under the [MIT license](/LICENSE). All other software
 components of the MEx project are open-sourced under the same license as well.
 
-## development
+## Development
 
-### installation
+### Installation
 
 - on unix, consider using pyenv https://github.com/pyenv/pyenv
   - get pyenv `curl https://pyenv.run | bash`
@@ -72,32 +73,32 @@ components of the MEx project are open-sourced under the same license as well.
   - switch version `pyenv global 3.11`
   - run `.\mex.bat install`
 
-### linting and testing
+### Linting and testing
 
 - run all linters with `pdm lint`
 - run only unit tests with `pdm unit`
 - run unit and integration tests with `pdm test`
 
-### updating dependencies
+### 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 update-all`
 - update github actions in `.github/workflows/*.yml` manually
 
-### creating release
+### Creating release
 
 - run `pdm release RULE` to release a new version where RULE determines which part of
   the version to update and is one of `major`, `minor`, `patch`.
 
-### container workflow
+### Container workflow
 
 - build image with `make image`
 - run directly using docker `make run`
 - start with docker compose `make start`
 
-## commands
+## Commands
 
 - run `pdm run {command} --help` to print instructions
 - run `pdm run {command} --debug` for interactive debugging

pyproject.toml

@@ -8,25 +8,25 @@ license = { file = "LICENSE" }
 urls = { Repository = "https://github.com/robert-koch-institut/mex-backend" }
 requires-python = ">=3.11,<3.13"
 dependencies = [
-    "fastapi>=0.115.4,<1",
-    "httpx>=0.27.2,<1",
-    "jinja2>=3.1.4,<4",
+    "fastapi>=0.115,<1",
+    "httpx>=0.27,<1",
+    "jinja2>=3,<4",
     "mex-common @ git+https://github.com/robert-koch-institut/[email protected]",
-    "neo4j>=5.24.0,<6",
-    "pydantic>=2.9.1,<3",
-    "starlette>=0.41.2,<1",
-    "uvicorn[standard]>=0.30.6,<1",
+    "neo4j>=5,<6",
+    "pydantic>=2,<3",
+    "starlette>=0.41,<1",
+    "uvicorn[standard]>=0.30,<1",
 ]
 optional-dependencies.dev = [
     "black>=24,<25",
-    "ipdb>=0.13.13,<1",
-    "mypy>=1.11.2,<2",
+    "ipdb>=0.13,<1",
+    "mypy>=1,<2",
     "pytest-cov>=6,<7",
-    "pytest-random-order>=1.1.1,<2",
-    "pytest>=8.3.3,<9",
-    "ruff>=0.6.5,<1",
-    "sphinx>=8.0.2,<9",
-    "types-pytz>=2024.1.0,<2025",
+    "pytest-random-order>=1,<2",
+    "pytest>=8,<9",
+    "ruff>=0.6,<1",
+    "sphinx>=8,<9",
+    "types-pytz>=2024,<2024.2",
 ]
 
 [project.scripts]
@@ -90,51 +90,57 @@ docstring-code-format = true
 
 [tool.ruff.lint]
 ignore = [
-    "D100",   # Allow missing module docstring for brevity
-    "D104",   # Allow missing package docstring for brevity
-    "D106",   # Allow missing nested class docstring (eg pydantic Config)
-    "D203",   # Disallow blank line before class docstring (inverse of D211)
-    "D213",   # Disallow multi-line docstring starting at second line (inverse of D212)
-    "D406",   # Allow section name ending with newline (google style compat)
-    "D407",   # Allow missing dashed underline after section (google style compat)
-    "D413",   # Allow missing blank line after last section (google style compat)
-    "N805",   # Allow first argument of a method to be non-self (pydantic compat)
-    "N815",   # Allow mixedCase variables in class scope (model compat)
-    "RUF012", # Allow mutable class attributes (pydantic compat)
-]
-select = [
-    "A",    # Flake8 builtin shaddow
-    "B",    # BugBear bug and issue finder
-    "C90",  # McCabe complexity checker
-    "D",    # Python docstring style checker
-    "E",    # Python code style errors
-    "ERA",  # Commented-out code detector
-    "F",    # Pyflakes passive python checker
-    "I",    # Isort import utility
-    "N",    # Pep8 naming conventions
-    "PERF", # Lint performance anti-patterns
-    "RET",  # Flake8 return statement checker
-    "RUF",  # Ruff-specific rules
-    "S",    # Bandit automated security testing
-    "T10",  # Flake8 debug statement checker
-    "T20",  # Flake8 print statement checker
-    "UP",   # PyUpgrade syntax recommender
-    "W",    # Python code style warnings
+    "AIR",     # Disable airflow specific rules (we are not using airflow)
+    "ANN",     # Disable all annotations checks (handled by mypy)
+    "COM",     # Disable flake8-commas checks (let ruff format handle that)
+    "CPY",     # Disable copyright notice checks (we have LICENSE files)
+    "D100",    # Allow missing module docstring (for brevity and speed)
+    "D104",    # Allow missing package docstring (for brevity and speed)
+    "D203",    # Disallow blank line before class docstring (inverse of D211)
+    "D213",    # Disallow multi-line docstring starting at second line (inverse of D212)
+    "D406",    # Allow section name ending with newline (google style compat)
+    "D407",    # Allow missing dashed underline after section (google style compat)
+    "D413",    # Allow missing blank line after last section (google style compat)
+    "DJ",      # Disable django specific checks (we are not using django)
+    "FBT",     # Disable boolean type hint checks (for more flexibility)
+    "FIX",     # Allow committing with open TODOs (don't punish committers)
+    "ISC001",  # Disable checks for implicitly concatenated strings (formatter compat)
+    "N805",    # Allow first argument of a method to be non-self (pydantic compat)
+    "N815",    # Allow mixedCase variables in class scope (model compat)
+    "PTH123",  # Allow using builtin open method (simpler than pathlib)
+    "RUF012",  # Allow mutable class attributes (pydantic compat)
+    "SIM108",  # Allow explicit if-else instead of ternary (easier to read)
+    "TD003",   # Allow TODOs without ticket link (don't punish TODO writers)
+    "TRY003",  # Allow long exception message at the raise site (for pydantic)
 ]
+select = ["ALL"]
 
 [tool.ruff.lint.per-file-ignores]
-"tests/**" = [
-    "D101", # Allow missing docstring in public class for tests
-    "D102", # Allow missing docstring in public method for tests
-    "D103", # Allow missing docstring in public function for tests
-    "D107", # Allow missing docstring in `__init__` for tests
-    "E501", # Allow line too long in tests
-    "N807", # Allow mocking `__init__` for tests
-    "S101", # Allow use of `assert` in tests
+"docs/**" = [
+    "INP001",   # Docs folder does not need to be a package
 ]
-"**/main.py" = [
-    "N803", # Allow dromedaryCase query parameters
+"scripts/**" = [
+    "INP001",   # Scripts folder does not need to be a package
 ]
+"tests/**" = [
+    "ARG005",   # Allow unused lambda arguments for mocking
+    "D101",     # Allow missing docstring in public class
+    "D102",     # Allow missing docstring in public method
+    "D103",     # Allow missing docstring in public function
+    "D107",     # Allow missing docstring in `__init__`
+    "E501",     # Allow longer lines with test data
+    "ISC",      # Allow implicitly concatenated strings
+    "N807",     # Allow mocking `__init__`
+    "PLR0915",  # Allow functions with many statements
+    "PLR2004",  # Allow comparing with static values
+    "PT004",    # Allow public fixtures without returns
+    "PT013",    # Allow more flexible pytest imports
+    "S101",     # Allow use of `assert` in tests
+    "SLF",      # Allow private member access
+]
+
+[tool.ruff.lint.flake8-import-conventions.extend-aliases]
+"reflex" = "rx"
 
 [tool.ruff.lint.isort]
 known-first-party = ["mex", "tests"]