Merge pull request #7 from minrk/lint

add and run linter config via pre-commit

.github/workflows/run-tests.yml

@@ -2,7 +2,7 @@ name: JupyterHealth SMART on FHIR test suite
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
 
 jobs:
@@ -13,33 +13,31 @@ jobs:
         python-version: [3.12] # extend if needed
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Use Node.js
-      uses: actions/setup-node@v4
-      with:
-        node-version: '18.x'
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: "pip"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e .[testing]
-    - name: Install SMART sandbox
-      run: | 
-        git clone https://github.com/smart-on-fhir/smart-launcher-v2.git
-        cd smart-launcher-v2
-        git switch -c aa0f3b1 # Fix the version we use for the sandbox
-        npm ci
-        npm run build
-      env: 
-        PORT: 5555
-    - name: Run tests
-      run: |
-        pytest tests/
-      env: 
-        SANDBOX_DIR: ${{ github.workspace }}/smart-launcher-v2
-
-
+      - uses: actions/checkout@v4
+      - name: Use Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "18.x"
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[testing]
+      - name: Install SMART sandbox
+        run: |
+          git clone https://github.com/smart-on-fhir/smart-launcher-v2.git
+          cd smart-launcher-v2
+          git switch -c aa0f3b1 # Fix the version we use for the sandbox
+          npm ci
+          npm run build
+        env:
+          PORT: 5555
+      - name: Run tests
+        run: |
+          pytest tests/
+        env:
+          SANDBOX_DIR: ${{ github.workspace }}/smart-launcher-v2

.gitignore

@@ -1,5 +1,35 @@
-jupyterhub-proxy.pid
-jupyterhub_cookie_secret
 *.key
 *.key.pub
 *.egg-info
+
+node_modules
+*.py[co]
+*~
+.cache
+.DS_Store
+/build
+dist
+docs/_build
+docs/build
+
+.ipynb_checkpoints
+.virtual_documents
+
+
+jupyterhub_cookie_secret
+jupyterhub.sqlite
+jupyterhub.sqlite*
+
+*.egg-info
+MANIFEST
+.coverage
+.coverage.*
+htmlcov
+.idea/
+.vscode/
+.pytest_cache
+pip-wheel-metadata
+oldest-requirements.txt
+jupyterhub-proxy.pid
+
+*.hot-update*

.pre-commit-config.yaml

@@ -0,0 +1,49 @@
+# pre-commit is a tool to perform a predefined set of tasks manually and/or
+# automatically before git commits are made.
+#
+# Config reference: https://pre-commit.com/#pre-commit-configyaml---top-level
+#
+# Common tasks
+#
+# - Run on all files:   pre-commit run --all-files
+# - Register git hooks: pre-commit install --install-hooks
+#
+
+ci:
+  # pre-commit.ci will open PRs updating our hooks once a month
+  autoupdate_schedule: monthly
+
+repos:
+  # autoformat and lint Python code
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.3
+    hooks:
+      - id: ruff
+        types_or:
+          - python
+          - jupyter
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+        types_or:
+          - python
+          - jupyter
+
+  # Autoformat: markdown, yaml, javascript (see the file .prettierignore)
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+
+  # Format toml
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+      - id: taplo-format
+      - id: taplo-lint
+
+  # Autoformat and linting, misc. details
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer

README.md

@@ -1,6 +1,8 @@
 # SMART on FHIR flow in Jupyter
+
 This repo contains two demos:
- - `server_extension`: a Jupyter server extension that acts as public client for a SMART server.
- - `hub_service`: a JupyterHub service that acts as confidential client for a SMART server and performs asymmetric authentication.
+
+- `server_extension`: a Jupyter server extension that acts as public client for a SMART server.
+- `hub_service`: a JupyterHub service that acts as confidential client for a SMART server and performs asymmetric authentication.
 
 Check the READMEs in the respective folders for more information. Work in progress.

examples/hub_service/README.md

@@ -5,18 +5,21 @@ This project contains a demo of a JupyterHub service that acts as a confidential
 ## Installation
 
 1. Clone this repository:
+
    ```
    git clone https://github.com/jupyterhealth/smart-fhir-jupyter-demo.git
    cd smart-fhir-jupyter-demo/hub_service
    ```
 
 2. Create and activate a virtual environment:
+
    ```
    python -m venv .venv
-   source .venv/bin/activate 
+   source .venv/bin/activate
    ```
 
 3. Install the required dependencies:
+
    ```
    pip install -e .
    ```
@@ -30,6 +33,7 @@ This project contains a demo of a JupyterHub service that acts as a confidential
 ## Configuration
 
 1. Update the `jupyterhub_config.py` file with your SMART on FHIR server details:
+
    - Set the `fhir_base_url` to the sandbox server's URL
 
 2. As a confidential client, this needs a public/private key pair. For demo purposes, the script takes care of generating this keypair.
@@ -39,4 +43,5 @@ This project contains a demo of a JupyterHub service that acts as a confidential
 Once authenticated, users can make requests to the FHIR server through the service. The service handles token management and SMART on FHIR authentication flow.
 
 Example:
-- Accessing `http://localhost:8000/hub/fhir` will fetch Condition resources from the FHIR server.
+
+- Accessing `http://localhost:8000/hub/fhir` will fetch Condition resources from the FHIR server.

examples/hub_service/jupyterhub_config.py

@@ -1,5 +1,4 @@
 import requests
-
 from oauthenticator.generic import GenericOAuthenticator
 
 c = get_config()  # noqa

examples/server_extension/README.md

@@ -1,6 +1,6 @@
 # SMART App demo with Jupyter
 
-This is a Jupyter server extension that fetches data from a SMART on FHIR endpoint. 
+This is a Jupyter server extension that fetches data from a SMART on FHIR endpoint.
 
 _work in progress_
 
@@ -9,15 +9,17 @@ _work in progress_
 ## Local Installation with pip
 
 1. Clone the repository:
+
    ```
    git clone https://github.com/jupyterhealth/smart-fhir-jupyter-demo.git
    cd smart-fhir-jupyter-demo/server_extension
    ```
 
 2. Create and activate a virtual environment:
+
    ```
    python -m venv .venv
-   source .venv/bin/activate 
+   source .venv/bin/activate
    ```
 
 3. Install the Jupyter server extension:
@@ -28,6 +30,7 @@ _work in progress_
 ## Installation with Docker
 
 1. Clone the repository:
+
    ```
    git clone https://github.com/jupyterhealth/smart-fhir-jupyter-demo.git
    cd smart-fhir-jupyter-demo/server_extension
@@ -45,20 +48,23 @@ _work in progress_
 1. Ensure you're in the project directory and your virtual environment is activated.
 
 2. Enable the server extension:
+
    ```
    jupyter server extension enable jupyter_smart_on_fhir.server_extension
    ```
 
-2. Start the Jupyter server:
+3. Start the Jupyter server:
+
    ```
    jupyter server
    ```
 
-3. Open a web browser and navigate to `http://localhost:8888` to access the Jupyter interface.
+4. Open a web browser and navigate to `http://localhost:8888` to access the Jupyter interface.
 
 ## Running with Docker
 
 1. Run the Docker container:
+
    ```
    docker run -p 8888:8888 smart-server-extension
    ```
@@ -71,7 +77,3 @@ _work in progress_
    ```
    http://localhost:8888/extension/fhir
    ```
-
-
-
-

jupyter_smart_on_fhir/auth.py

@@ -1,11 +1,12 @@
-from dataclasses import dataclass, asdict
-import requests
-import secrets
-import jwt
 import json
 import os
+import secrets
+from dataclasses import asdict, dataclass
 from pathlib import Path
 
+import jwt
+import requests
+
 
 @dataclass
 class SMARTConfig:
@@ -47,7 +48,7 @@ def generate_state(next_url=None) -> dict:
 def get_jwks_from_key(key_file: Path, key_id: str = "1") -> str:
     """Generate a JWKS from a public key file. Not required for end users, but useful for development"""
     try:
-        with open(key_file + ".pub", "r") as f:
+        with open(key_file + ".pub") as f:
             public_key = f.read()
     except FileNotFoundError as e:
         raise FileNotFoundError(

jupyter_smart_on_fhir/hub_service.py

@@ -4,25 +4,27 @@
 - Asymmetric authentication
 """
 
+import base64
 import os
-import time
 import secrets
+import time
 from functools import wraps
+from urllib.parse import urlencode
+
+import jwt
+import requests
+from cryptography.fernet import Fernet, InvalidToken
 from flask import (
     Flask,
     Response,
+    current_app,
     make_response,
     redirect,
     request,
     session,
-    current_app,
 )
-import requests
-from urllib.parse import urlencode
-import jwt
-import base64
+
 from jupyter_smart_on_fhir.auth import SMARTConfig, generate_state, validate_keys
-from cryptography.fernet import Fernet, InvalidToken
 
 prefix = os.environ.get("JUPYTERHUB_SERVICE_PREFIX", "/")
 

jupyter_smart_on_fhir/server_extension.py

@@ -1,14 +1,16 @@
-from jupyter_server.extension.application import ExtensionApp
-from jupyter_server.base.handlers import JupyterHandler
-import tornado
-import requests
+import base64
+import hashlib
 import secrets
 from urllib.parse import urlencode, urljoin
-import hashlib
-import base64
-from jupyter_smart_on_fhir.auth import SMARTConfig, generate_state
+
+import requests
+import tornado
+from jupyter_server.base.handlers import JupyterHandler
+from jupyter_server.extension.application import ExtensionApp
 from traitlets import List, Unicode
 
+from jupyter_smart_on_fhir.auth import SMARTConfig, generate_state
+
 smart_path = "/smart"
 login_path = "/smart/login"
 callback_path = "/smart/oauth_callback"