Merge pull request #2 from alneberg/github_actions

GitHub actions, config singleton and pre-commit

.devcontainer/devcontainer.json

@@ -1,33 +1,30 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
 {
-    "name": "spectacles",
-    "build": {
-        // Sets the run context to one level up instead of the .devcontainer folder.
-        "context": "..",
-        // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-        "dockerfile": "../Dockerfile",
-        "target": "base"
-    },
-    "features": {},
-    "customizations": {
-        "vscode": {
-            "extensions": [
-                "ms-python.python",
-                "charliermarsh.ruff"
-            ]
-        }
-    },
-    // Features to add to the dev container. More info: https://containers.dev/features.
-    // "features": {},
-    // Use 'forwardPorts' to make a list of ports inside the container available locally.
-    // "forwardPorts": [],
-    //"postCreateCommand": "cd ../flowcell_parser/ && pip3 install -e . && cd ../TACA && pip3 install -e .",
-    // Configure tool-specific properties.
-    // "customizations": {},
-    // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
-    // "remoteUser": "devcontainer"
-    //"mounts": [
-    //    "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached"
-    //]
-}
+  "name": "spectacles",
+  "build": {
+    // Sets the run context to one level up instead of the .devcontainer folder.
+    "context": "..",
+    // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+    "dockerfile": "../Dockerfile",
+    "target": "development"
+  },
+  "features": {},
+  "customizations": {
+    "vscode": {
+      "extensions": ["ms-python.python", "charliermarsh.ruff"]
+    }
+  }
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  // "features": {},
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+  //"postCreateCommand": "cd ../flowcell_parser/ && pip3 install -e . && cd ../TACA && pip3 install -e .",
+  // Configure tool-specific properties.
+  // "customizations": {},
+  // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+  // "remoteUser": "devcontainer"
+  //"mounts": [
+  //    "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached"
+  //]
+}

.github/workflows/lint-code.yml

@@ -0,0 +1,83 @@
+name: Lint code
+on: [push, pull_request]
+
+jobs:
+  # Use ruff to check for code style violations
+  ruff-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check for style violations
+        # Configured in pyproject.toml
+        run: ruff check .
+
+  # Use ruff to check code formatting
+  ruff-format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check code formatting
+        run: ruff format --check .
+
+  # Use mypy for static type checking
+  mypy-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Run image
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: 1.7.1
+      - name: Setup a local virtual environment (if no poetry.toml file)
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry config virtualenvs.in-project true --local
+      - uses: actions/cache@v3
+        name: Define a cache for the virtual environment based on the dependencies lock file
+        with:
+          path: ./.venv
+          key: venv-${{ hashFiles('poetry.lock') }}
+      - name: Install the project dependencies
+        run: poetry install
+      - name: Run mypy
+        run: poetry run mypy **/*.py
+
+  # Use Prettier to check various file formats
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+# .pre-commit-config.yaml
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.8.0"
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-PyYAML]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v4.0.0-alpha.8"
+    hooks:
+      - id: prettier
+  - repo: https://github.com/floatingpurr/sync_with_poetry
+    rev: "" # the revision or tag to clone at
+    hooks:
+      - id: sync_with_poetry
+        args: [] # optional args

Dockerfile

@@ -12,12 +12,18 @@ RUN pip install --no-cache-dir poetry
 
 # Use Poetry to install dependencies
 RUN poetry config virtualenvs.create false \
-    && poetry install --no-interaction --no-ansi
+    && poetry install --no-interaction --no-ansi --without=dev
 
 # Make port 8000 available to the world outside this container
 EXPOSE 8000
 
+FROM base AS development
+
+# Use Poetry to install dependencies
+RUN poetry config virtualenvs.create false \
+    && poetry install --with=dev --no-interaction --no-ansi
+
 FROM base AS main
 # Not meant for production.
 # Run app.py when the container launches
-CMD ["poetry", "run", "uvicorn", "app:app", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["poetry", "run", "uvicorn", "app:app", "--host", "0.0.0.0", "--port", "8000"]

README.md

@@ -1,2 +1,3 @@
 # spectacles
-API for a clearer look at clarity
+
+API for a clearer look at clarity using FastAPI.

app/config.py

@@ -0,0 +1,29 @@
+import os
+
+import dotenv
+
+dotenv.load_dotenv()
+
+
+class Config:
+    __instance = None
+
+    # Ensure only one instance of Config is created
+    def __new__(cls, *args, **kwargs):
+        if not cls.__instance:
+            cls.__instance = super().__new__(cls, *args, **kwargs)
+        return cls.__instance
+
+    def __init__(self):
+        # Load or set your configuration data here
+        self.SECRET_KEY = os.getenv("SPECTACLES_SECRET_KEY")
+        self.ALGORITHM = os.getenv("SPECTACLES_ALGORITHM")
+        self.ACCESS_TOKEN_EXPIRE_MINUTES = 90
+
+
+config_values = Config()
+
+if not config_values.SECRET_KEY or not config_values.ALGORITHM:
+    raise ValueError(
+        "SPECTACLES_SECRET_KEY and SPECTACLES_ALGORITHM must be set as environmental variables"
+    )

app/main.py

@@ -1,8 +1,6 @@
-import dotenv
 from fastapi import FastAPI
 
-dotenv.load_dotenv()
-
+# from config import config_values
 from .routers import auth
 
 

app/routers/auth.py

@@ -1,5 +1,4 @@
 from datetime import datetime, timedelta, timezone
-import os
 from typing import Annotated
 
 
@@ -9,23 +8,18 @@
 from passlib.context import CryptContext
 from pydantic import BaseModel
 
-# to get a string like this run:
-# openssl rand -hex 32
-
-# Fetch environmental variables
-SECRET_KEY = os.getenv("SPECTACLES_SECRET_KEY")
-ALGORITHM = os.getenv("SPECTACLES_ALGORITHM")
-
-if not SECRET_KEY or not ALGORITHM:
-    raise ValueError("SPECTACLES_SECRET_KEY and SPECTACLES_ALGORITHM must be set as environmental variables")
-
-ACCESS_TOKEN_EXPIRE_MINUTES = 90
-
+from ..config import config_values
 
+# TODO, this is not a database
 clients_db = {
-    "first_client": {"disabled": False, "client_id": "first_client", "client_secret_hashed": "$2b$12$Yqwzj50q0.5brgJAYwOIEO1l10tdgStMZEB41HwRMFzU/h5wuDsh."}
+    "first_client": {
+        "disabled": False,
+        "client_id": "first_client",
+        "client_secret_hashed": "$2b$12$Yqwzj50q0.5brgJAYwOIEO1l10tdgStMZEB41HwRMFzU/h5wuDsh.",
+    }
 }
 
+
 class Token(BaseModel):
     access_token: str
     token_type: str
@@ -34,14 +28,17 @@ class Token(BaseModel):
 class TokenData(BaseModel):
     client_id: str | None = None
 
+
 class Client(BaseModel):
     """Client without the hashed secret, more suitable to view"""
+
     client_id: str
     disabled: bool | None = None
 
 
 class ClientInDB(Client):
     """Client with hashed secret"""
+
     client_secret_hashed: str
 
 
@@ -59,11 +56,13 @@ def verify_client_secret(plain_secret, hashed_secret):
 def get_secret_hash(secret):
     return secret_context.hash(secret)
 
+
 def get_client(db, client_id: str):
     if client_id in db:
         client_dict = db[client_id]
         return ClientInDB(**client_dict)
 
+
 def authenticate_client(clients_db, client_id: str, client_secret: str):
     client: ClientInDB = get_client(clients_db, client_id)
     if not client:
@@ -80,7 +79,9 @@ def create_access_token(data: dict, expires_delta: timedelta | None = None):
     else:
         expire = datetime.now(timezone.utc) + timedelta(minutes=15)
     to_encode.update({"exp": expire})
-    encoded_jwt = jwt.encode(to_encode, SECRET_KEY, algorithm=ALGORITHM)
+    encoded_jwt = jwt.encode(
+        to_encode, config_values.SECRET_KEY, algorithm=config_values.ALGORITHM
+    )
     return encoded_jwt
 
 
@@ -91,23 +92,28 @@ async def get_current_client(token: Annotated[str, Depends(oauth2_scheme)]):
         headers={"WWW-Authenticate": "Bearer"},
     )
     try:
-        payload = jwt.decode(token, SECRET_KEY, algorithms=[ALGORITHM])
-        client_id: str = payload.get("sub")
-        if client_id is None:
+        payload = jwt.decode(
+            token, config_values.SECRET_KEY, algorithms=[config_values.ALGORITHM]
+        )
+        client_id = payload.get("sub")
+        if client_id is None or not isinstance(client_id, str):
             raise credentials_exception
+
         token_data = TokenData(client_id=client_id)
     except JWTError:
         raise credentials_exception
 
     # If we get this far, the token is valid
+    if token_data.client_id is None:
+        raise credentials_exception
     client = get_client(clients_db, client_id=token_data.client_id)
     if client is None:
         raise credentials_exception
     return client
 
 
 async def get_current_active_client(
-    current_client: Annotated[Client, Depends(get_current_client)]
+    current_client: Annotated[Client, Depends(get_current_client)],
 ):
     if current_client.disabled:
         raise HTTPException(status_code=400, detail="Inactive user")
@@ -116,7 +122,7 @@ async def get_current_active_client(
 
 @router.post("/token")
 async def login_for_access_token(
-    form_data: Annotated[OAuth2PasswordRequestForm, Depends()]
+    form_data: Annotated[OAuth2PasswordRequestForm, Depends()],
 ) -> Token:
     client = authenticate_client(clients_db, form_data.username, form_data.password)
     if not client:
@@ -125,7 +131,7 @@ async def login_for_access_token(
             detail="Incorrect username or password",
             headers={"WWW-Authenticate": "Bearer"},
         )
-    access_token_expires = timedelta(minutes=ACCESS_TOKEN_EXPIRE_MINUTES)
+    access_token_expires = timedelta(minutes=config_values.ACCESS_TOKEN_EXPIRE_MINUTES)
     access_token = create_access_token(
         data={"sub": client.client_id}, expires_delta=access_token_expires
     )
@@ -134,13 +140,13 @@ async def login_for_access_token(
 
 @router.get("/users/me/", response_model=Client)
 async def read_users_me(
-    current_client: Annotated[Client, Depends(get_current_active_client)]
+    current_client: Annotated[Client, Depends(get_current_active_client)],
 ):
     return current_client
 
 
 @router.get("/users/me/items/")
 async def read_own_items(
-    current_client: Annotated[Client, Depends(get_current_active_client)]
+    current_client: Annotated[Client, Depends(get_current_active_client)],
 ):
-    return [{"item_id": "Foo", "owner": current_client.client_id}]
+    return [{"item_id": "Foo", "owner": current_client.client_id}]