chore: setup ruff

.github/workflows/checks.yml

@@ -38,8 +38,8 @@ jobs:
         run: |
           pip install poetry
           poetry install --with=code_quality,docs,test,types
-      - name: Lint with flake8
-        run: poetry run flake8
+      - name: Lint with ruff
+        run: poetry run ruff check .
       - name: Run mypy
         run: poetry run mypy foca
       - name: Start MongoDB

Makefile

@@ -36,7 +36,7 @@ cv: clean-venv
 .PHONY: format-lint fl
 format-lint:
 	@echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n"
-	@poetry run flake8
+	@poetry run ruff format && poetry run ruff check --fix
 	@typos .
 
 fl: format-lint

docs/api/conf.py

@@ -22,9 +22,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'FOCA'
-copyright = '2022, ELIXIR Cloud & AAI'
-author = 'ELIXIR Cloud & AAI'
+project = "FOCA"
+copyright = "2022, ELIXIR Cloud & AAI"
+author = "ELIXIR Cloud & AAI"
 
 # The full version, including alpha/beta/rc tags
 release = __version__  # noqa: F821
@@ -36,28 +36,28 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.napoleon',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
 
 # Default doc to search for
-master_doc = 'index'
+master_doc = "index"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -67,18 +67,13 @@
 
 # -- Automation -------------------------------------------------------------
 
+
 # Auto-generate API doc
 def run_apidoc(_):
-    ignore_paths = [
-    ]
-    argv = [
-        "--force",
-        "--module-first",
-        "-o", "./modules",
-        "../../foca"
-    ] + ignore_paths
+    ignore_paths = []
+    argv = ["--force", "--module-first", "-o", "./modules", "../../foca"] + ignore_paths
     apidoc.main(argv)
 
 
 def setup(app):
-    app.connect('builder-inited', run_apidoc)
+    app.connect("builder-inited", run_apidoc)

examples/petstore-access-control/app.py

@@ -2,9 +2,7 @@
 
 from foca import Foca
 
-if __name__ == '__main__':
-    foca = Foca(
-        config_file="config.yaml"
-    )
+if __name__ == "__main__":
+    foca = Foca(config_file="config.yaml")
     app = foca.create_app()
     app.run()

examples/petstore-access-control/controllers.py

@@ -2,62 +2,60 @@
 
 import logging
 
-from flask import (current_app, make_response)
+from flask import current_app, make_response
 from pymongo.collection import Collection
 
 from exceptions import NotFound
-from foca.security.access_control.register_access_control import (
-    check_permissions
-)
+from foca.security.access_control.register_access_control import check_permissions
 
 logger = logging.getLogger(__name__)
 
 
 @check_permissions
 def findPets(limit=None, tags=None):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore-access-control']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore-access-control"]
+        .collections["pets"]
+        .client
     )
-    filter_dict = {} if tags is None else {'tag': {'$in': tags}}
+    filter_dict = {} if tags is None else {"tag": {"$in": tags}}
     if not limit:
         limit = 0
-    records = db_collection.find(
-        filter_dict,
-        {'_id': False}
-    ).sort([('$natural', -1)]).limit(limit)
+    records = (
+        db_collection.find(filter_dict, {"_id": False})
+        .sort([("$natural", -1)])
+        .limit(limit)
+    )
     return list(records)
 
 
 @check_permissions
 def addPet(pet):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore-access-control']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore-access-control"]
+        .collections["pets"]
+        .client
     )
     counter = 0
-    ctr = db_collection.find({}).sort([('$natural', -1)])
+    ctr = db_collection.find({}).sort([("$natural", -1)])
     if not db_collection.count_documents({}) == 0:
-        counter = ctr[0].get('id') + 1
-    record = {
-        "id": counter,
-        "name": pet['name'],
-        "tag": pet['tag']
-    }
+        counter = ctr[0].get("id") + 1
+    record = {"id": counter, "name": pet["name"], "tag": pet["tag"]}
     db_collection.insert_one(record)
-    del record['_id']
+    del record["_id"]
     return record
 
 
 @check_permissions
 def findPetById(id):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore-access-control']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore-access-control"]
+        .collections["pets"]
+        .client
     )
     record = db_collection.find_one(
         {"id": id},
-        {'_id': False},
+        {"_id": False},
     )
     if record is None:
         raise NotFound
@@ -67,17 +65,18 @@ def findPetById(id):
 @check_permissions
 def deletePet(id):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore-access-control']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore-access-control"]
+        .collections["pets"]
+        .client
     )
     record = db_collection.find_one(
         {"id": id},
-        {'_id': False},
+        {"_id": False},
     )
     if record is None:
         raise NotFound
     db_collection.delete_one(
         {"id": id},
     )
-    response = make_response('', 204)
+    response = make_response("", 204)
     return response

examples/petstore-access-control/exceptions.py

@@ -45,9 +45,7 @@
         "code": 401,
     },
     Forbidden: {
-        "message": (
-            "Sorry, but you don't have permission to play with the pets."
-        ),
+        "message": ("Sorry, but you don't have permission to play with the pets."),
         "code": 403,
     },
     NotFound: {

examples/petstore/app.py

@@ -2,9 +2,7 @@
 
 from foca import Foca
 
-if __name__ == '__main__':
-    foca = Foca(
-        config_file="config.yaml"
-    )
+if __name__ == "__main__":
+    foca = Foca(config_file="config.yaml")
     app = foca.create_app()
     app.run()

examples/petstore/controllers.py

@@ -2,7 +2,7 @@
 
 import logging
 
-from flask import (current_app, make_response)
+from flask import current_app, make_response
 from pymongo.collection import Collection
 
 from exceptions import NotFound
@@ -12,46 +12,40 @@
 
 def findPets(limit=None, tags=None):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore"].collections["pets"].client
     )
-    filter_dict = {} if tags is None else {'tag': {'$in': tags}}
+    filter_dict = {} if tags is None else {"tag": {"$in": tags}}
     if not limit:
         limit = 0
-    records = db_collection.find(
-        filter_dict,
-        {'_id': False}
-    ).sort([('$natural', -1)]).limit(limit)
+    records = (
+        db_collection.find(filter_dict, {"_id": False})
+        .sort([("$natural", -1)])
+        .limit(limit)
+    )
     return list(records)
 
 
 def addPet(pet):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore"].collections["pets"].client
     )
     counter = 0
-    ctr = db_collection.find({}).sort([('$natural', -1)])
+    ctr = db_collection.find({}).sort([("$natural", -1)])
     if not db_collection.count_documents({}) == 0:
-        counter = ctr[0].get('id') + 1
-    record = {
-        "id": counter,
-        "name": pet['name'],
-        "tag": pet['tag']
-    }
+        counter = ctr[0].get("id") + 1
+    record = {"id": counter, "name": pet["name"], "tag": pet["tag"]}
     db_collection.insert_one(record)
-    del record['_id']
+    del record["_id"]
     return record
 
 
 def findPetById(id):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore"].collections["pets"].client
     )
     record = db_collection.find_one(
         {"id": id},
-        {'_id': False},
+        {"_id": False},
     )
     if record is None:
         raise NotFound
@@ -60,17 +54,16 @@ def findPetById(id):
 
 def deletePet(id):
     db_collection: Collection = (
-        current_app.config.foca.db.dbs['petstore']
-        .collections['pets'].client
+        current_app.config.foca.db.dbs["petstore"].collections["pets"].client
     )
     record = db_collection.find_one(
         {"id": id},
-        {'_id': False},
+        {"_id": False},
     )
     if record is None:
         raise NotFound
     db_collection.delete_one(
         {"id": id},
     )
-    response = make_response('', 204)
+    response = make_response("", 204)
     return response