formating

pephub/dependencies.py

@@ -19,11 +19,12 @@
 from pepdbagent import PEPDatabaseAgent
 from pepdbagent.const import DEFAULT_TAG
 from pepdbagent.exceptions import ProjectNotFoundError
+from pepdbagent.models import AnnotationModel, Namespace
 from qdrant_client import QdrantClient
 from qdrant_client.http.exceptions import ResponseHandlingException
 from sentence_transformers import SentenceTransformer
 
-from .routers.models import AnnotationModel, Namespace, ForkRequest
+from .routers.models import ForkRequest
 from .const import (
     DEFAULT_POSTGRES_HOST,
     DEFAULT_POSTGRES_PASSWORD,

pephub/helpers.py

@@ -1,7 +1,6 @@
-import json
 from datetime import date
 from typing import List, Union, Tuple
-from fastapi import Response, Depends, UploadFile
+from fastapi import Response, UploadFile
 from fastapi.exceptions import HTTPException
 from ubiquerg import VersionInHelpParser
 
@@ -54,7 +53,7 @@ def add_subparser(cmd, description):
             "--config",
             required=False,
             dest="config",
-            help=f"A path to the pepserver config file",
+            help="A path to the pepserver config file",
         )
 
     sps["serve"].add_argument(

pephub/main.py

@@ -27,7 +27,7 @@
 _LOGGER_PEPPY = logging.getLogger("peppy")
 coloredlogs.install(
     logger=_LOGGER_PEPPY,
-    level=logging.INFO,
+    level=logging.ERROR,
     datefmt="%b %d %Y %H:%M:%S",
     fmt="[%(levelname)s] [%(asctime)s] [PEPPY] %(message)s",
 )

pephub/middleware.py

@@ -4,7 +4,7 @@
 from fastapi.responses import FileResponse
 from starlette.middleware.base import BaseHTTPMiddleware
 from starlette.responses import Response
-from starlette.types import ASGIApp, Receive, Scope, Send
+from starlette.types import Send
 
 from .const import SPA_PATH
 

pephub/routers/api/v1/namespace.py

@@ -12,11 +12,10 @@
 from pepdbagent import PEPDatabaseAgent
 from pepdbagent.exceptions import ProjectUniqueNameError
 from pepdbagent.const import DEFAULT_LIMIT_INFO
-from pepdbagent.models import ListOfNamespaceInfo
+from pepdbagent.models import ListOfNamespaceInfo, Namespace
 from typing import Literal
 from typing_extensions import Annotated
 
-from ...models import Namespace
 from ....dependencies import (
     get_db,
     get_namespace_info,

pephub/routers/api/v1/project.py

@@ -14,7 +14,14 @@
     SUBSAMPLE_RAW_LIST_KEY,
 )
 
-from ...models import ProjectOptional, ProjectRawModel, AnnotationModel, ForkRequest
+from pepdbagent import PEPDatabaseAgent
+from pepdbagent.exceptions import ProjectUniqueNameError
+from pepdbagent.models import AnnotationModel
+
+from dotenv import load_dotenv
+
+
+from ...models import ProjectOptional, ProjectRawModel, ForkRequest
 from ....helpers import zip_conv_result, get_project_sample_names, zip_pep
 from ....dependencies import (
     get_db,
@@ -27,10 +34,6 @@
 )
 from ....const import SAMPLE_CONVERSION_FUNCTIONS, VALID_UPDATE_KEYS
 
-from pepdbagent import PEPDatabaseAgent
-from pepdbagent.exceptions import ProjectUniqueNameError
-
-from dotenv import load_dotenv
 
 load_dotenv()
 

pephub/routers/auth/base.py

@@ -5,7 +5,7 @@
 import time
 from typing import Union
 from fastapi import APIRouter, Request, Header, BackgroundTasks, Depends
-from fastapi.responses import RedirectResponse, Response
+from fastapi.responses import RedirectResponse
 from fastapi.exceptions import HTTPException
 from fastapi.templating import Jinja2Templates
 from dotenv import load_dotenv
@@ -136,7 +136,7 @@ def callback(
 
     if state.get("device"):
         DEVICE_CODES[state["device_code"]]["token"] = token
-        return f"/login/device/success"
+        return "/login/device/success"
 
     else:
         # create random auth code

pephub/routers/models.py

@@ -1,6 +1,6 @@
-from typing import Optional
-from pydantic import BaseModel
-from pepdbagent.models import *
+from typing import Optional, List
+from pydantic import BaseModel, Field, Extra
+from pepdbagent.models import UpdateItems
 from pepdbagent.const import DEFAULT_TAG
 
 from ..const import DEFAULT_PEP_SCHEMA

pephub/routers/profile.py

@@ -1,12 +1,13 @@
-from fastapi import APIRouter, Request
+from fastapi import APIRouter, Request, Depends
 from fastapi.templating import Jinja2Templates
 from fastapi.responses import RedirectResponse
 from platform import python_version
+from pepdbagent import PEPDatabaseAgent
 
 from .._version import __version__ as pephub_version
+from ..dependencies import get_db
 
-from ..dependencies import *
-from ..view_dependencies import *
+# from ..view_dependencies import *
 from ..const import BASE_TEMPLATES_PATH
 
 router = APIRouter(prefix="/profile", tags=["profile"])

pephub/routers/views/eido.py

@@ -1,18 +1,14 @@
 import jinja2
 import eido
-import peppy
 
 from fastapi import APIRouter, Request
-from fastapi.responses import RedirectResponse, HTMLResponse
+from fastapi.responses import HTMLResponse
 from starlette.templating import Jinja2Templates
 from peppy import __version__ as peppy_version
-from peppy.const import SAMPLE_RAW_DICT_KEY, CONFIG_KEY
 from platform import python_version
 from dotenv import load_dotenv
 
 from ..._version import __version__ as pephub_version
-from ...dependencies import *
-from ...view_dependencies import *
 from ...const import EIDO_TEMPLATES_PATH