Merge branch 'release/v0.3.4'

.env.example

@@ -0,0 +1,30 @@
+MONGODB_URL="mongodb://localhost:27017"
+MONGODB_USER=None
+MONGODB_PASSWORD=None
+
+MONGODB_GLOBAL_DATABASE_URL=None
+MONGODB_GLOBAL_DATABASE_USER=None
+MONGODB_GLOBAL_DATABASE_PASSWORD=None
+
+EMAIL_VERIFICATION_REQUIRED=False
+
+MAIL_USERNAME="[email protected]"
+MAIL_PASSWORD=""
+MAIL_PORT=587
+MAIL_SMTP_SERVER=""
+MAIL_STARTTLS=True
+MAIL_SSL_TLS=False
+
+PASSWORD_RESET_URL=""
+EMAIL_VERIFY_URL=""
+SECRET="totally secret"
+
+REGISTRATION_ENABLED=True
+REGISTRATION_ADMIN_APPROVAL=False
+
+CREATE_INDEXES_WITH_PROJECT=True
+
+DEBUG=False
+PANDAHUB_SERVER_URL="0.0.0.0"
+PANDAHUB_SERVER_PORT=8002
+WORKERS=2

.github/workflows/github_test_action.yml

@@ -19,26 +19,27 @@ jobs:
           - 27017:27017
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4.7.0
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install -U pytest
-        pip install -r requirements.txt
-        pip install -r requirements_dev.txt
-        pip install .["all"]
+        python -m pip install .["all"]
     - name: List of installed packages
       run: |
         pip list
     - name: Test with pytest and Codecov
       run: |
-        pytest --cov=./ --cov-report=xml
+        python -m pip install pytest-cov pytest-xdist nbmake
+        python -m pytest -n=auto --cov=./ --cov-report=xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      if: ${{ github.ref == 'refs/heads/develop' || github.ref != 'refs/heads/master' }}
+      uses: codecov/codecov-action@v4
       with:
-        fail_ci_if_error: true
+        file: ./coverage.xml
         token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true

.github/workflows/release.yml

@@ -26,10 +26,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # Sets up python3
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       # Installs and upgrades pip, installs other dependencies and installs the package from setup.py
@@ -80,7 +80,7 @@ jobs:
         os:  [ ubuntu-latest, windows-latest ]
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -94,10 +94,10 @@ jobs:
       - name: Install pandahub from PyPI
         if: ${{ inputs.upload_server == 'pypi'}}
         run: |
-          pip install pandahub
+          python -m pip install pandahub
       - name: List all installed packages
         run: |
-          pip list
+          python -m pip list
       - name: Test with pytest
         run: |
-          pytest --pyargs pandahub.test
+          python -m pytest --pyargs pandahub.test

.travis.yml

@@ -2,7 +2,7 @@
 
 language: python
 python:
-  - 3.8
+  - 3.10
 
 # Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
 install: pip install -U tox-travis

CHANGELOG.md

@@ -1,8 +1,8 @@
 # Change Log
 
 ## [0.2.4]
-    - BREAKING drops index argument from create_variant() function
 
+    - BREAKING drops index argument from create_variant() function
 
 ## [0.2.3]- 2022-08-04
 

Dockerfile

@@ -1,8 +1,19 @@
-FROM python:3.9 as dev
+FROM python:3.10 as dev
+
 ENV PYTHONUNBUFFERED 1
-ENV PYTHONPATH /code/
-WORKDIR /code
-COPY ./requirements.txt .
-RUN pip install -r requirements.txt
-RUN pip install watchdog pyyaml
-CMD uvicorn --host "0.0.0.0" --port "8002" "pandahub.api.main:app" --reload
+ENV PYTHONPATH /code/pandahub
+
+ENV DEBUG False
+ENV PANDAHUB_SERVER_URL 0.0.0.0
+ENV PANDAHUB_SERVER_PORT 8002
+ENV WORKERS 2
+
+COPY ./ /code/pandahub/
+WORKDIR /code/pandahub
+
+RUN python -m pip install --upgrade pip
+RUN python -m pip install .["all"]
+RUN python -m pip install watchdog pyyaml
+
+# CMD uvicorn --host "0.0.0.0" --port "8002" "pandahub.api.main:app" --reload
+ENTRYPOINT ["python", "pandahub/api/main.py"]

docker-compose.yml

@@ -1,15 +1,34 @@
-version: '3.7'
+version: '3'
+
+networks:
+  test:
+    external: false
+
 services:
-  pandahub:
-    image: dev/pandahub
-    build: .
+  db:
+    user: ${CURRENT_UID}
+    image: mongo:latest
+    container_name: mongodb
+    restart: always
+    networks:
+        - test
+    ports:
+        - "27017:27017"
+
+  pandahub_server:
+    user: ${CURRENT_UID}
+    container_name: pandahub
+    build:
+        context: .
+        dockerfile: Dockerfile
     environment:
         - SECRET=devonly!
         - MONGODB_URL=${MONGODB_URL:-mongodb://db:27017}
     ports:
         - "8002:8002"
-    volumes:
-        - ./pandahub:/code/pandahub
-
-
-
+#    volumes:
+#        - ./:/code/pandahub
+    networks:
+        - test
+    depends_on:
+        - db

pandahub/__init__.py

@@ -1,6 +1,6 @@
-__version__ = "0.2.8"
+import importlib.metadata
+
+__version__ = importlib.metadata.version("pandahub")
 
 from pandahub.lib.PandaHub import PandaHub, PandaHubError
 from pandahub.client.PandaHubClient import PandaHubClient
-
-

pandahub/api/dependencies.py

@@ -1,11 +1,11 @@
 from fastapi import Depends
 
 from pandahub import PandaHub
-from .internal.models import UserDB
+from .internal.db import User
 from .internal.users import fastapi_users
 
 current_active_user = fastapi_users.current_user(active=True)
 
 
-def pandahub(user: UserDB = Depends(current_active_user)):
+def pandahub(user: User = Depends(current_active_user)):
     return PandaHub(user_id=str(user.id))

pandahub/api/internal/db.py

@@ -1,49 +1,40 @@
 import asyncio
+import uuid
 
 import motor.motor_asyncio
-from fastapi_users.db import MongoDBUserDatabase
-from fastapi_users_db_mongodb.access_token import MongoDBAccessTokenDatabase
-
+from beanie import Document
+from fastapi_users.db import BeanieBaseUser, BeanieUserDatabase
+from fastapi_users_db_beanie.access_token import (
+    BeanieAccessTokenDatabase,
+    BeanieBaseAccessToken,
+)
+
+from pandahub.api.internal.settings import REGISTRATION_ADMIN_APPROVAL
 from pandahub.api.internal import settings
-from pandahub.api.internal.models import AccessToken, UserDB
+from pydantic import Field
 
 mongo_client_args = {"host": settings.MONGODB_URL, "uuidRepresentation": "standard", "connect": False}
 if settings.MONGODB_USER:
     mongo_client_args |= {"username": settings.MONGODB_USER, "password": settings.MONGODB_PASSWORD}
 
 client = motor.motor_asyncio.AsyncIOMotorClient(**mongo_client_args)
-
 client.get_io_loop = asyncio.get_event_loop
-
 db = client["user_management"]
-collection = db["users"]
-access_tokens_collection = db["access_tokens"]
 
+class User(BeanieBaseUser, Document):
+    id: uuid.UUID = Field(default_factory=uuid.uuid4)
+    is_active: bool = not REGISTRATION_ADMIN_APPROVAL
+    class Settings(BeanieBaseUser.Settings):
+        name = "users"
 
-async def get_user_db():
-    if settings.COSMOSDB_COMPAT:
-        yield MongoDBUserDatabaseCosmos(UserDB, collection)
-    else:
-        yield MongoDBUserDatabase(UserDB, collection)
 
+class AccessToken(BeanieBaseAccessToken, Document):
+    user_id: uuid.UUID = Field(default_factory=uuid.uuid4)
+    class Settings(BeanieBaseAccessToken.Settings):
+        name = "access_tokens"
+
+async def get_user_db():
+    yield BeanieUserDatabase(User)
 
 async def get_access_token_db():
-    yield MongoDBAccessTokenDatabase(AccessToken, access_tokens_collection)
-
-class MongoDBUserDatabaseCosmos(MongoDBUserDatabase):
-    from typing import Optional
-    from fastapi_users.models import UD
-    async def get_by_email(self, email: str) -> Optional[UD]:
-        await self._initialize()
-
-        user = await self.collection.find_one(
-            {"email": email}
-        )
-        return self.user_db_model(**user) if user else None
-
-    async def _initialize(self):
-        if not self.initialized:
-            if "email_1" not in await self.collection.index_information():
-                await self.collection.create_index("id", unique=True)
-                await self.collection.create_index("email", unique=True)
-        self.initialized = True
+    yield BeanieAccessTokenDatabase(AccessToken)

pandahub/api/internal/schemas.py

@@ -0,0 +1,16 @@
+import uuid
+
+from fastapi_users import schemas
+from pandahub.api.internal.settings import REGISTRATION_ADMIN_APPROVAL
+
+
+class UserRead(schemas.BaseUser[uuid.UUID]):
+    pass
+
+
+class UserCreate(schemas.BaseUserCreate):
+    is_active: bool = not REGISTRATION_ADMIN_APPROVAL
+
+
+class UserUpdate(schemas.BaseUserUpdate):
+    pass

pandahub/api/internal/settings.py

@@ -31,14 +31,14 @@ def get_secret(key, default=None):
 if not MONGODB_GLOBAL_DATABASE_URL:
     MONGODB_GLOBAL_DATABASE_URL = os.getenv("MONGODB_URL_GLOBAL_DATABASE") or None
 
-EMAIL_VERIFICATION_REQUIRED = settings_bool("EMAIL_VERIFICATION_REQUIRED")
+EMAIL_VERIFICATION_REQUIRED = settings_bool("EMAIL_VERIFICATION_REQUIRED", default=False)
 
 MAIL_USERNAME = os.getenv("MAIL_USERNAME") or "[email protected]"
 MAIL_PASSWORD = os.getenv("MAIL_PASSWORD") or ""
 MAIL_PORT = os.getenv("MAIL_PORT") or 587
 MAIL_SMTP_SERVER = os.getenv("MAIL_SMTP_SERVER") or ""
-MAIL_TLS = os.getenv("MAIL_TLS") or True
-MAIL_SSL = os.getenv("MAIL_SSL") or False
+MAIL_STARTTLS = settings_bool("MAIL_STARTTLS", default=True)
+MAIL_SSL_TLS = settings_bool("MAIL_SSL_TLS", default=False)
 
 PASSWORD_RESET_URL = os.getenv("PASSWORD_RESET_URL") or ""
 EMAIL_VERIFY_URL = os.getenv("EMAIL_VERIFY_URL") or ""
@@ -47,5 +47,9 @@ def get_secret(key, default=None):
 REGISTRATION_ENABLED = settings_bool("REGISTRATION_ENABLED", default=True)
 REGISTRATION_ADMIN_APPROVAL = settings_bool("REGISTRATION_ADMIN_APPROVAL", default=False)
 
-DATATYPES_MODULE = os.getenv("DATATYPES_MODULE") or "pandahub.lib.datatypes"
-COSMOSDB_COMPAT = settings_bool("COSMOSDB_COMPAT", default=False)
+CREATE_INDEXES_WITH_PROJECT = settings_bool("CREATE_INDEXES_WITH_PROJECT", default=True)
+
+DEBUG = settings_bool("DEBUG", default=False)
+PANDAHUB_SERVER_URL = os.getenv("PANDAHUB_SERVER_URL", "0.0.0.0")
+PANDAHUB_SERVER_PORT = int(os.getenv('PANDAHUB_SERVER_PORT', 8002))
+WORKERS = int(os.getenv('WORKER', 2))

pandahub/api/internal/toolbox.py

@@ -8,8 +8,8 @@
     MAIL_FROM=settings.MAIL_USERNAME,
     MAIL_PORT=settings.MAIL_PORT,
     MAIL_SERVER=settings.MAIL_SMTP_SERVER,
-    MAIL_TLS=settings.MAIL_TLS,
-    MAIL_SSL=settings.MAIL_SSL
+    MAIL_SSL_TLS=settings.MAIL_SSL_TLS,
+    MAIL_STARTTLS=settings.MAIL_STARTTLS,
 )
 
 fast_mail = FastMail(email_conf)