chore(tooling): adopt pyproject, ruff, and update CI

- Consolidate packaging and tooling into pyproject.toml and standardise linting and formatting with ruff.
- Move metadata and deps into pyproject.toml; compile requirements.txt (runtime) and requirements-dev.txt (runtime + dev: pytest, pytest-mock, moto, ruff) from it via pip-tools; retire requirements.in.
- Move pytest config into [tool.pytest.ini_options] and remove pytest.ini.
- Add [tool.ruff] config; apply ruff check --fix and ruff format across code.
- CI: unit_tests installs requirements-dev.txt; add a lint workflow running ruff check and ruff format --check on PRs to develop.

Closes #183, #173

Author: alexhambley

.github/workflows/lint.yml

@@ -0,0 +1,29 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Lint
+        run: ruff check .
+
+      - name: Format check
+        run: ruff format --check .

.github/workflows/unit_tests.yml

@@ -20,8 +20,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install pytest pytest-mock "moto[s3]"
+          pip install -r requirements-dev.txt
 
       - name: Run tests (excluding integration tests)
         run: |

app/__init__.py

@@ -3,23 +3,23 @@
 import logging
 
 from apiflask import APIFlask
+from flask import jsonify, request
 
 from app.crates.ids import InvalidCrateId
-from app.crates.resolver import CrateNotFound, AmbiguousCrate
+from app.crates.resolver import AmbiguousCrate, CrateNotFound
 from app.health import health_bp
-from app.ro_crates.routes import v1_post_bp, v1_minio_post_bp, v1_minio_get_bp
+from app.ro_crates.routes import v1_minio_get_bp, v1_minio_post_bp, v1_post_bp
 from app.services.logging_service import (
+    get_request_id,
     new_request_id,
     set_request_id,
-    get_request_id,
 )
 from app.storage.errors import StorageError
 from app.utils.config import (
-    Settings,
     InvalidAPIUsage,
+    Settings,
     make_celery,
 )
-from flask import jsonify, request
 
 logger = logging.getLogger(__name__)
 

app/celery_worker.py

@@ -6,5 +6,4 @@
 
 from celery import Celery
 
-
 celery = Celery()

app/crates/resolver.py

@@ -10,7 +10,7 @@
 from dataclasses import dataclass
 
 from app.crates.ids import validate_crate_id
-from app.crates.layout import crate_zip_key, crate_dir_prefix, crate_metadata_key
+from app.crates.layout import crate_dir_prefix, crate_metadata_key, crate_zip_key
 from app.storage.base import StorageBackend
 from app.storage.errors import ObjectNotFound
 

app/ro_crates/routes/__init__.py

@@ -1,7 +1,7 @@
 """Defines main Blueprint and registers sub-Blueprints for organising related routes."""
 
-from app.ro_crates.routes.post_routes import post_routes_bp, minio_post_routes_bp
 from app.ro_crates.routes.get_routes import get_routes_bp
+from app.ro_crates.routes.post_routes import minio_post_routes_bp, post_routes_bp
 
 # Always registered:
 v1_post_bp = post_routes_bp

app/ro_crates/routes/post_routes.py

@@ -79,6 +79,4 @@ def validate_ro_crate_metadata(json_data) -> tuple[Response, int]:
 
     profiles_path = current_app.config["PROFILES_PATH"]
 
-    return run_metadata_validation(
-        crate_json, profile_name, profiles_path=profiles_path
-    )
+    return run_metadata_validation(crate_json, profile_name, profiles_path=profiles_path)

app/services/logging_service.py

@@ -3,7 +3,6 @@
 import json
 import logging
 import uuid
-
 from contextvars import ContextVar
 from typing import Iterable, Optional
 

app/services/validation_service.py

@@ -3,7 +3,7 @@
 import json
 import logging
 
-from flask import jsonify, Response, current_app
+from flask import Response, current_app, jsonify
 
 from app.crates.ids import validate_crate_id
 from app.crates.layout import result_key
@@ -76,9 +76,7 @@ def run_metadata_validation(
     if not metadata:
         return jsonify({"error": "Required parameter crate_json is empty"}), 422
 
-    outcome = validate_metadata(
-        metadata, profile_name=profile_name, profiles_path=profiles_path
-    )
+    outcome = validate_metadata(metadata, profile_name=profile_name, profiles_path=profiles_path)
     status_code = 422 if outcome.status is ValidationStatus.ERROR else 200
     return jsonify(outcome.to_dict()), status_code
 

app/storage/__init__.py

@@ -5,7 +5,7 @@
 are interchangeable.
 """
 
-from app.storage.base import StorageBackend, ObjectStat
-from app.storage.errors import StorageError, ObjectNotFound
+from app.storage.base import ObjectStat, StorageBackend
+from app.storage.errors import ObjectNotFound, StorageError
 
 __all__ = ["StorageBackend", "ObjectStat", "StorageError", "ObjectNotFound"]