update pre-commit versions (#592)

.pre-commit-config.yaml

@@ -1,19 +1,20 @@
 repos:
   - repo: https://github.com/pycqa/isort
-    rev: 5.7.0
+    rev: 5.12.0
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 3.8.4
+    rev: 6.0.0
     hooks:
       - id: flake8
         additional_dependencies:
           - flake8-use-fstring
   - repo: https://github.com/pre-commit/mirrors-mypy
+    # Note: updating to v1.0.0 a bit more work
     rev: v0.902
     hooks:
       - id: mypy

plugins/quetz_conda_suggest/quetz_conda_suggest/main.py

@@ -93,7 +93,7 @@ def generate_channel_suggest_map(db, channel_name, subdir):
             pass
         else:
             files_data = json.loads(each_package.binfiles.data)
-            for (k, v) in files_data.items():
+            for k, v in files_data.items():
                 channel_suggest_map[k] = v
 
     fname = f"{channel_name}.{subdir}.map"

plugins/quetz_content_trust/quetz_content_trust/api.py

@@ -119,7 +119,6 @@ def post_role(
             )
 
         def get_self_delegation(nullable: bool = False):
-
             query = (
                 db.query(db_models.RoleDelegation)
                 .filter(

plugins/quetz_content_trust/tests/conftest.py

@@ -202,7 +202,6 @@ def pkg_mgr_role_file(tmp_path, offline_keys, signing_key):
 def signed_package(
     client, channel, root_role_file, key_mgr_role_file, pkg_mgr_role_file
 ):
-
     client.post(
         f"/api/content-trust/{channel.name}/roles?type=root",
         files={"file": (root_role_file.name, open(root_role_file, 'rb'))},

plugins/quetz_dictauthenticator/quetz_dictauthenticator/__init__.py

@@ -3,12 +3,10 @@
 
 
 class DictionaryAuthenticator(SimpleAuthenticator):
-
     passwords: dict
     provider = "dict"
 
     def configure(self, config: Config):
-
         config.register(
             [
                 ConfigSection(

plugins/quetz_harvester/tests/conftest.py

@@ -28,7 +28,6 @@ def user_role():
 
 @pytest.fixture
 def user(db, user_role):
-
     new_user = User(id=uuid.uuid4().bytes, username="bartosz", role=user_role)
     profile = Profile(name="Bartosz", avatar_url="http:///avatar", user=new_user)
     db.add(profile)
@@ -69,7 +68,6 @@ def package_version(
     dao: Dao,
     config: Config,
 ):
-
     pkgstore = config.get_package_store()
     filename = Path(__file__).parent / "data" / "xtensor-io-0.10.3-hb585cf6_0.tar.bz2"
     with open(filename, "rb") as fid:
@@ -114,7 +112,6 @@ def package_role():
 
 @pytest.fixture
 def public_channel(dao: Dao, user, channel_role, channel_name, db):
-
     channel_data = Channel(name=channel_name, private=False)
     channel = dao.create_channel(channel_data, user.id, channel_role)
 
@@ -125,7 +122,6 @@ def public_channel(dao: Dao, user, channel_role, channel_name, db):
 
 @pytest.fixture
 def public_package(db, user, public_channel, dao, package_role, package_name):
-
     package_data = Package(name=package_name)
 
     package = dao.create_package(
@@ -153,7 +149,6 @@ def sqlite_in_memory():
 
 @pytest.fixture
 def api_key(db, user):
-
     key = ApiKey(
         key="apikey",
         time_created=date.today(),

plugins/quetz_harvester/tests/test_main.py

@@ -14,7 +14,6 @@
 def test_harvest_endpoint_and_job(
     api_key, auth_client, db, config, supervisor, package_version, app, channel_name
 ):
-
     response = auth_client.post(
         "/api/jobs", json={"items_spec": "*", "manifest": "quetz-harvester:harvest"}
     )

plugins/quetz_repodata_patching/quetz_repodata_patching/main.py

@@ -108,7 +108,6 @@ def _load_instructions(tar, path):
 @quetz.hookimpl(tryfirst=True)
 def post_package_indexing(tempdir: Path, channel_name, subdirs, files, packages):
     with get_db_manager() as db:
-
         query = (
             db.query(PackageVersion)
             .filter(
@@ -131,7 +130,6 @@ def post_package_indexing(tempdir: Path, channel_name, subdirs, files, packages)
             extract_ = extract_from_conda
 
         with extract_(fs) as tar:
-
             for subdir in subdirs:
                 packages[subdir] = {}
                 path = f"{subdir}/patch_instructions.json"

plugins/quetz_repodata_patching/tests/test_main.py

@@ -52,7 +52,6 @@ def package_file_name(package_name, package_format):
 
 @pytest.fixture
 def channel(dao: "quetz.dao.Dao", channel_name, user):
-
     channel_data = Channel(name=channel_name, private=False)
     channel = dao.create_channel(channel_data, user.id, "owner")
     return channel
@@ -137,7 +136,6 @@ def patched_package_name(package_file_name):
 
 @pytest.fixture
 def patch_content(patched_package_name, revoke_instructions, remove_instructions):
-
     d = {}
 
     package_file_name = patched_package_name
@@ -167,7 +165,6 @@ def patches_subdir():
 
 @pytest.fixture
 def repodata_archive(repodata_file_name, patch_content, archive_format, patches_subdir):
-
     from io import BytesIO
 
     patch_instructions = json.dumps(patch_content).encode('ascii')
@@ -221,7 +218,6 @@ def package_repodata_patches(
     repodata_archive,
     archive_format,
 ):
-
     package_name = repodata_name
     package_data = Package(name=package_name)
 

plugins/quetz_repodata_zchunk/tests/test_main.py

@@ -46,7 +46,6 @@ def package_file_name(package_name, package_format):
 
 @pytest.fixture
 def channel(dao: "quetz.dao.Dao", channel_name, user):
-
     channel_data = Channel(name=channel_name, private=False)
     channel = dao.create_channel(channel_data, user.id, "owner")
     return channel
@@ -132,7 +131,6 @@ def test_repodata_zchunk(
     assert "repodata.json.zck" in content
 
     for fname in ("repodata.json", "repodata.json.zck"):
-
         repodata_path = os.path.join(
             pkgstore.channels_dir, channel_name, "noarch", fname
         )

plugins/quetz_runexports/quetz_runexports/api.py

@@ -20,7 +20,6 @@ def get_run_exports(
     filename: str,
     db: Session = Depends(get_db),
 ):
-
     package_version = (
         db.query(PackageVersion)
         .filter(PackageVersion.channel_name == channel_name)

plugins/quetz_runexports/quetz_runexports/main.py

@@ -17,7 +17,6 @@ def post_add_package_version(version, condainfo):
     run_exports = json.dumps(condainfo.run_exports)
 
     with get_db_manager() as db:
-
         if not version.runexports:
             metadata = db_models.PackageVersionMetadata(
                 version_id=version.id, data=run_exports

plugins/quetz_runexports/tests/conftest.py

@@ -26,7 +26,6 @@ def user(db):
 
 @fixture
 def channel(dao, user, db):
-
     channel_data = rest_models.Channel(
         name="test-mirror-channel",
         private=False,
@@ -87,7 +86,6 @@ def package_version(user, channel, db, dao, package):
 
 @fixture
 def package_runexports(package_version, db):
-
     meta = db_models.PackageVersionMetadata(
         version_id=package_version.id,
         data=json.dumps({"weak": ["somepackage > 3.0"]}),

plugins/quetz_transmutation/tests/conftest.py

@@ -28,7 +28,6 @@ def user_role():
 
 @pytest.fixture
 def user(db, user_role):
-
     new_user = User(id=uuid.uuid4().bytes, username="bartosz", role=user_role)
     profile = Profile(name="Bartosz", avatar_url="http:///avatar", user=new_user)
     db.add(profile)
@@ -43,7 +42,6 @@ def user(db, user_role):
 
 @pytest.fixture
 def api_key(db, user):
-
     key = ApiKey(
         key="apikey",
         time_created=date.today(),
@@ -84,7 +82,6 @@ def package_version(
     dao: Dao,
     config: Config,
 ):
-
     pkgstore = config.get_package_store()
     filename = Path("test-package-0.1-0.tar.bz2")
     with open(filename, "rb") as fid:
@@ -129,7 +126,6 @@ def package_role():
 
 @pytest.fixture
 def public_channel(dao: Dao, user, channel_role, channel_name, db):
-
     channel_data = Channel(name=channel_name, private=False)
     channel = dao.create_channel(channel_data, user.id, channel_role)
 
@@ -140,7 +136,6 @@ def public_channel(dao: Dao, user, channel_role, channel_name, db):
 
 @pytest.fixture
 def public_package(db, user, public_channel, dao, package_role, package_name):
-
     package_data = Package(name=package_name)
 
     package = dao.create_package(

plugins/quetz_transmutation/tests/test_main.py

@@ -17,7 +17,6 @@
 async def test_transmutation_endpoint(
     api_key, db, config, supervisor, package_version, app, channel_name
 ):
-
     # we need to use asynchronous http client because the test is async
     async with AsyncClient(app=app, base_url="http://test") as ac:
         response = await ac.post(
@@ -76,7 +75,6 @@ async def test_transmutation_endpoint(
 def test_package_specs(
     auth_client, db, config, supervisor, package_version, spec, n_tasks
 ):
-
     response = auth_client.post(
         "/api/jobs",
         json={"items_spec": spec, "manifest": "quetz-transmutation:transmutation"},
@@ -123,7 +121,6 @@ def test_package_specs(
     ],
 )
 def test_permissions(auth_client, db, expected_status):
-
     response = auth_client.post(
         "/api/jobs",
         json={"items_spec": "*", "manifest": "quetz-transmutation:transmutation"},

quetz/authentication/auth_dao.py

@@ -23,7 +23,6 @@ def create_user_with_identity(
     default_role: Optional[str],
     default_channels: Optional[List[str]],
 ) -> User:
-
     username = profile["login"]
     user = dao.create_user_with_profile(
         username=username,
@@ -37,15 +36,12 @@ def create_user_with_identity(
     )
 
     if default_channels is not None:
-
         for channel_name in default_channels:
-
             i = 0
 
             while (
                 dao.db.query(Channel).filter(Channel.name == channel_name).one_or_none()
             ):
-
                 channel_name = f"{username}-{i}"
 
                 i += 1
@@ -79,7 +75,6 @@ def user_profile_changed(user, identity, profile: 'base.UserProfile'):
 def update_user_from_profile(
     db: Session, user, identity, profile: 'base.UserProfile'
 ) -> User:
-
     identity.username = profile['login']
     user.profile.name = profile['name']
     user.profile.avatar_url = profile['avatar_url']
@@ -128,13 +123,14 @@ def get_user_by_identity(
     default_role: Optional[str] = None,
     default_channels: Optional[List[str]] = None,
 ) -> User:
-
     db = dao.db
 
     try:
         user, identity = db.query(User, Identity).join(Identity).filter(
             Identity.provider == provider
-        ).filter(Identity.identity_id == str(profile['id']),).one_or_none() or (
+        ).filter(
+            Identity.identity_id == str(profile['id']),
+        ).one_or_none() or (
             None,
             None,
         )

quetz/authentication/base.py

@@ -20,14 +20,12 @@
 
 
 class Email(TypedDict):
-
     email: str
     verified: Boolean
     primary: Boolean
 
 
 class UserProfile(TypedDict):
-
     id: str
     name: str
     avatar_url: str
@@ -66,7 +64,6 @@ class BaseAuthenticationHandlers:
     authorize_methods: List[str]
 
     def __init__(self, authenticator, app=None):
-
         self.authenticator = authenticator
 
         # dependency_overrides_provider kwarg is needed for unit test
@@ -253,7 +250,6 @@ async def authenticate(
 
 
 class FormHandlers(BaseAuthenticationHandlers):
-
     authorize_methods = ["POST"]
 
     async def login(self, request: Request):

quetz/authentication/jupyterhub.py

@@ -11,7 +11,6 @@
 
 
 class JupyterConfigEntry:
-
     config_section = "jupyterhubauthenticator"
     registered_entries: List[ConfigEntry] = []
     config = None
@@ -160,7 +159,6 @@ async def validate_token(self, token):
         return resp.status_code == 200
 
     def configure(self, config: Config):
-
         self.is_enabled = JupyterConfigEntry.register(config)
 
         super().configure(config)

quetz/authentication/oauth2.py

@@ -19,7 +19,6 @@ class OAuthHandlers(BaseAuthenticationHandlers):
     authorize_methods = ["GET"]
 
     def __init__(self, authenticator, app=None):
-
         super().__init__(authenticator, app)
 
         self.router.add_api_route("/revoke", self.revoke, methods=["GET"])
@@ -101,7 +100,6 @@ async def authenticate(self, request, data=None, dao=None, config=None):
         return {"username": username, "profile": profile, "auth_state": auth_state}
 
     def register(self, client_kwargs=None):
-
         if client_kwargs is None:
             client_kwargs = {}
 

quetz/authentication/pam.py

@@ -94,7 +94,6 @@ def _get_user_group_ids(self, username):
             return os.getgrouplist(username, user_gid)
 
         def configure(self, config: Config):
-
             config_options = self._make_config()
             config.register(config_options)
 
@@ -113,7 +112,6 @@ def configure(self, config: Config):
             super().configure(config)
 
         async def user_role(self, request: Request, profile: UserProfile):
-
             mappings = [
                 (ServerRole.OWNER, self.admin_groups),
                 (ServerRole.MAINTAINER, self.maintainer_groups),