forked from enviPath/enviPy
[Feature] Documentation for development setup
## Summary This PR improves the local development setup experience by adding Docker Compose and Makefile for streamlined setup. ## Changes - **Added `docker-compose.yml`**: for one-command PostgreSQL database setup - **Added `Makefile`**: Convenient shortcuts for common dev tasks (\`make setup\`, \`make dev\`, etc.) - **Updated `README.md`**: Quick development setup instructions using Make - - **Added**: RDkit installation pain point documentation - **Fixed**: Made Java feature properly dependent ## Why these changes? The application uses PostgreSQL-specific features (\`ArrayField\`) and requires an anonymous user created by the bootstrap command. This PR makes the setup process trivial for new developers: ```bash cp .env.local.example .env make setup # Starts DB, runs migrations, bootstraps data make dev # Starts development server ``` Java fix: Moved global Java import to inline to avoid everyone having to configure the Java path. Numerous changes to view and settings. - Applied ruff-formatting ## Testing Verified complete setup from scratch works with: - PostgreSQL running in Docker - All migrations applied - Bootstrap data loaded successfully - Anonymous user created - The development server starts correctly. Co-authored-by: Tobias O <tobias.olenyi@tum.de> Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-authored-by: Liam <62733830+limmooo@users.noreply.github.com> Reviewed-on: enviPath/enviPy#143 Reviewed-by: jebus <lorsbach@envipath.com> Reviewed-by: liambrydon <lbry121@aucklanduni.ac.nz> Co-authored-by: t03i <mail+envipath@t03i.net> Co-committed-by: t03i <mail+envipath@t03i.net>
This commit is contained in:
22
.env.local.example
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22
.env.local.example
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@ -0,0 +1,22 @@
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# Django settings
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SECRET_KEY='a-secure-secret-key-for-development'
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DEBUG=True
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ALLOWED_HOSTS=*
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# Database settings (using PostgreSQL for local development)
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POSTGRES_USER=postgres
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POSTGRES_PASSWORD=postgres
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POSTGRES_DB=envipath
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POSTGRES_SERVICE_NAME=localhost
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POSTGRES_PORT=5432
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# Celery settings
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CELERY_BROKER_URL='redis://localhost:6379/0'
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CELERY_RESULT_BACKEND='redis://localhost:6379/0'
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FLAG_CELERY_PRESENT=False
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# Other settings
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LOG_LEVEL='INFO'
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SERVER_URL='http://localhost:8000'
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PLUGINS_ENABLED=True
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EP_DATA_DIR='data'
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@ -16,4 +16,3 @@ POSTGRES_PORT=
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# MAIL
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EMAIL_HOST_USER=
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EMAIL_HOST_PASSWORD=
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6
.gitignore
vendored
6
.gitignore
vendored
@ -5,4 +5,8 @@ static/admin/
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static/django_extensions/
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.env
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debug.log
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scratches/
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scratches/
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data/
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.DS_Store
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30
.pre-commit-config.yaml
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30
.pre-commit-config.yaml
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@ -0,0 +1,30 @@
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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.2.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.13.3
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hooks:
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# Run the linter.
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- id: ruff-check
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types_or: [python, pyi]
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args: [--fix]
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# Run the formatter.
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- id: ruff-format
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types_or: [python, pyi]
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# - repo: local
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# hooks:
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# - id: django-check
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# name: Run Django Check
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# entry: uv run python manage.py check
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# language: system
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# pass_filenames: false
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# types: [python]
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89
README.md
89
README.md
@ -1,2 +1,91 @@
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# enviPy
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## Local Development Setup
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These instructions will guide you through setting up the project for local development.
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### Prerequisites
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- Python 3.11 or later
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- [uv](https://github.com/astral-sh/uv) - A fast Python package installer and resolver.
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- **Docker and Docker Compose** - Required for running the PostgreSQL database.
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- Git
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> **Note:** This application requires PostgreSQL, which uses `ArrayField`. Docker is the recommended way to run PostgreSQL locally.
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### 1. Install Dependencies
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This project uses `uv` to manage dependencies and `poe-the-poet` for task running. First, [install `uv` if you don't have it yet](https://docs.astral.sh/uv/guides/install-python/).
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Then, sync the project dependencies. This will create a virtual environment in `.venv` and install all necessary packages, including `poe-the-poet`.
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```bash
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uv sync --dev
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```
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> **Note on RDkit:** If you have a different version of rdkit installed globally, the dependency installation may fail. If this happens, please uninstall the global version and run `uv sync` again.
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### 2. Set Up Environment File
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Copy the example environment file for local setup:
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```bash
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cp .env.local.example .env
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```
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This file contains the necessary environment variables for local development.
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### 3. Quick Setup with Poe
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The easiest way to set up the development environment is by using the `poe` task runner, which is executed via `uv run`.
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```bash
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uv run poe setup
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```
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This single command will:
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1. Start the PostgreSQL database using Docker Compose.
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2. Run database migrations.
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3. Bootstrap initial data (anonymous user, default packages, models).
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After setup, start the development server:
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```bash
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uv run poe dev
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```
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The application will be available at `http://localhost:8000`.
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#### Other useful Poe commands:
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You can list all available commands by running `uv run poe --help`.
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```bash
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uv run poe db-up # Start PostgreSQL only
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uv run poe db-down # Stop PostgreSQL
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uv run poe migrate # Run migrations only
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uv run poe bootstrap # Bootstrap data only
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uv run poe shell # Open the Django shell
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uv run poe clean # Remove database volumes (WARNING: destroys all data)
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```
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### Troubleshooting
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* **Docker Connection Error:** If you see an error like `open //./pipe/dockerDesktopLinuxEngine: The system cannot find the file specified` (on Windows), it likely means your Docker Desktop application is not running. Please start Docker Desktop and try the command again.
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* **SSH Keys for Git Dependencies:** Some dependencies are installed from private git repositories and require SSH authentication. Ensure your SSH keys are configured correctly for Git.
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* For a general guide, see [GitHub's official documentation](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent).
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* **Windows Users:** If `uv sync` hangs while fetching git dependencies, you may need to explicitly configure Git to use the Windows OpenSSH client and use the `ssh-agent` to manage your key's passphrase.
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1. **Point Git to the correct SSH executable:**
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```powershell
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git config --global core.sshCommand "C:/Windows/System32/OpenSSH/ssh.exe"
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```
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2. **Enable and use the SSH agent:**
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```powershell
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# Run these commands in an administrator PowerShell
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Get-Service ssh-agent | Set-Service -StartupType Automatic -PassThru | Start-Service
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# Add your key to the agent. It will prompt for the passphrase once.
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ssh-add
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```
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20
docker-compose.dev.yml
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20
docker-compose.dev.yml
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@ -0,0 +1,20 @@
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services:
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db:
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image: postgres:15
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container_name: envipath-postgres
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environment:
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POSTGRES_USER: postgres
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POSTGRES_PASSWORD: postgres
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POSTGRES_DB: envipath
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ports:
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- "5432:5432"
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volumes:
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- postgres_data:/var/lib/postgresql/data
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U postgres"]
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interval: 5s
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timeout: 5s
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retries: 5
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volumes:
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postgres_data:
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@ -9,6 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
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For the full list of settings and their values, see
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https://docs.djangoproject.com/en/4.2/ref/settings/
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"""
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import os
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from pathlib import Path
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@ -20,33 +21,35 @@ from sklearn.tree import DecisionTreeClassifier
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# Build paths inside the project like this: BASE_DIR / 'subdir'.
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BASE_DIR = Path(__file__).resolve().parent.parent
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load_dotenv(BASE_DIR / '.env', override=False)
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load_dotenv(BASE_DIR / ".env", override=False)
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# Quick-start development settings - unsuitable for production
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# See https://docs.djangoproject.com/en/4.2/howto/deployment/checklist/
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# SECURITY WARNING: keep the secret key used in production secret!
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SECRET_KEY = '7!VTW`aZqg/UBLsM.P=m)2]lWqg>{+:xUgG1"WO@bCyaHR2Up8XW&g<*3.F4l2gi9c.E3}dHyA0D`&z?u#U%^7HYbj],eP"g_MS|3BNMD[mI>s#<i/%2ngZ~Oy+/w&@]'
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SECRET_KEY = os.environ.get("SECRET_KEY", "secret-key")
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# SECURITY WARNING: don't run with debug turned on in production!
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DEBUG = os.environ.get('DEBUG', 'False') == 'True'
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ALLOWED_HOSTS = os.environ['ALLOWED_HOSTS'].split(',')
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DEBUG = os.environ.get("DEBUG", "False") == "True"
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ALLOWED_HOSTS = os.environ["ALLOWED_HOSTS"].split(",")
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# Application definition
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INSTALLED_APPS = [
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'django.contrib.admin',
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'django.contrib.auth',
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'django.contrib.contenttypes',
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'django.contrib.sessions',
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'django.contrib.messages',
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'django.contrib.staticfiles',
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"django.contrib.admin",
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"django.contrib.auth",
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"django.contrib.contenttypes",
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"django.contrib.sessions",
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"django.contrib.messages",
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"django.contrib.staticfiles",
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# 3rd party
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'django_extensions',
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'oauth2_provider',
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"django_extensions",
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"oauth2_provider",
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# Custom
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'epdb',
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'migration',
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"epdb",
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"migration",
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]
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AUTHENTICATION_BACKENDS = [
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@ -54,42 +57,42 @@ AUTHENTICATION_BACKENDS = [
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]
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MIDDLEWARE = [
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'django.middleware.security.SecurityMiddleware',
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'django.contrib.sessions.middleware.SessionMiddleware',
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'django.middleware.common.CommonMiddleware',
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'django.middleware.csrf.CsrfViewMiddleware',
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'django.contrib.auth.middleware.AuthenticationMiddleware',
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'django.contrib.messages.middleware.MessageMiddleware',
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'django.middleware.clickjacking.XFrameOptionsMiddleware',
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'oauth2_provider.middleware.OAuth2TokenMiddleware',
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"django.middleware.security.SecurityMiddleware",
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"django.contrib.sessions.middleware.SessionMiddleware",
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"django.middleware.common.CommonMiddleware",
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"django.middleware.csrf.CsrfViewMiddleware",
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"django.contrib.auth.middleware.AuthenticationMiddleware",
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"django.contrib.messages.middleware.MessageMiddleware",
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"django.middleware.clickjacking.XFrameOptionsMiddleware",
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"oauth2_provider.middleware.OAuth2TokenMiddleware",
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]
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OAUTH2_PROVIDER = {
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"PKCE_REQUIRED": False, # Accept PKCE requests but dont require them
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}
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if os.environ.get('REGISTRATION_MANDATORY', False) == 'True':
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MIDDLEWARE.append('epdb.middleware.login_required_middleware.LoginRequiredMiddleware')
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if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
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MIDDLEWARE.append("epdb.middleware.login_required_middleware.LoginRequiredMiddleware")
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ROOT_URLCONF = 'envipath.urls'
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ROOT_URLCONF = "envipath.urls"
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TEMPLATES = [
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{
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'BACKEND': 'django.template.backends.django.DjangoTemplates',
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'DIRS': (os.path.join(BASE_DIR, 'templates'),),
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'APP_DIRS': True,
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'OPTIONS': {
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'context_processors': [
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'django.template.context_processors.debug',
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'django.template.context_processors.request',
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'django.contrib.auth.context_processors.auth',
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'django.contrib.messages.context_processors.messages',
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"BACKEND": "django.template.backends.django.DjangoTemplates",
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"DIRS": (os.path.join(BASE_DIR, "templates"),),
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"APP_DIRS": True,
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"OPTIONS": {
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"context_processors": [
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"django.template.context_processors.debug",
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"django.template.context_processors.request",
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"django.contrib.auth.context_processors.auth",
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"django.contrib.messages.context_processors.messages",
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],
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},
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},
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]
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WSGI_APPLICATION = 'envipath.wsgi.application'
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WSGI_APPLICATION = "envipath.wsgi.application"
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# Database
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# https://docs.djangoproject.com/en/4.2/ref/settings/#databases
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@ -97,11 +100,11 @@ WSGI_APPLICATION = 'envipath.wsgi.application'
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DATABASES = {
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"default": {
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"ENGINE": "django.db.backends.postgresql",
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"USER": os.environ['POSTGRES_USER'],
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"NAME": os.environ['POSTGRES_DB'],
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"PASSWORD": os.environ['POSTGRES_PASSWORD'],
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"HOST": os.environ['POSTGRES_SERVICE_NAME'],
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"PORT": os.environ['POSTGRES_PORT']
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"USER": os.environ["POSTGRES_USER"],
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"NAME": os.environ["POSTGRES_DB"],
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"PASSWORD": os.environ["POSTGRES_PASSWORD"],
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"HOST": os.environ["POSTGRES_SERVICE_NAME"],
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"PORT": os.environ["POSTGRES_PORT"],
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}
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}
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@ -109,96 +112,84 @@ DATABASES = {
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# https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
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AUTH_PASSWORD_VALIDATORS = [
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{
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'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator',
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},
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{
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'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',
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},
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{
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'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
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},
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{
|
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'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
|
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},
|
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{"NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"},
|
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{"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
|
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{"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
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{"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
|
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]
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# Internationalization
|
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# https://docs.djangoproject.com/en/4.2/topics/i18n/
|
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LANGUAGE_CODE = 'en-us'
|
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LANGUAGE_CODE = "en-us"
|
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|
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TIME_ZONE = 'UTC'
|
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TIME_ZONE = "UTC"
|
||||
|
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USE_I18N = True
|
||||
|
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USE_TZ = True
|
||||
|
||||
|
||||
|
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# Default primary key field type
|
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# https://docs.djangoproject.com/en/4.2/ref/settings/#default-auto-field
|
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|
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DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
|
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DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
|
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|
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if DEBUG:
|
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EMAIL_BACKEND = 'django.core.mail.backends.console.EmailBackend'
|
||||
EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
|
||||
else:
|
||||
EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
|
||||
EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
|
||||
EMAIL_USE_TLS = True
|
||||
EMAIL_HOST = 'mail.gandi.net'
|
||||
EMAIL_HOST_USER = os.environ['EMAIL_HOST_USER']
|
||||
EMAIL_HOST_PASSWORD = os.environ['EMAIL_HOST_PASSWORD']
|
||||
EMAIL_HOST = "mail.gandi.net"
|
||||
EMAIL_HOST_USER = os.environ["EMAIL_HOST_USER"]
|
||||
EMAIL_HOST_PASSWORD = os.environ["EMAIL_HOST_PASSWORD"]
|
||||
EMAIL_PORT = 587
|
||||
|
||||
AUTH_USER_MODEL = "epdb.User"
|
||||
ADMIN_APPROVAL_REQUIRED = os.environ.get('ADMIN_APPROVAL_REQUIRED', 'False') == 'True'
|
||||
ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") == "True"
|
||||
|
||||
# # SESAME
|
||||
# SESAME_MAX_AGE = 300
|
||||
# # TODO set to "home"
|
||||
# LOGIN_REDIRECT_URL = "/"
|
||||
LOGIN_URL = '/login/'
|
||||
LOGIN_URL = "/login/"
|
||||
|
||||
SERVER_URL = os.environ.get('SERVER_URL', 'http://localhost:8000')
|
||||
SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
|
||||
|
||||
CSRF_TRUSTED_ORIGINS = [SERVER_URL]
|
||||
|
||||
AMBIT_URL = 'http://localhost:9001'
|
||||
DEFAULT_VALUES = {
|
||||
'description': 'no description'
|
||||
}
|
||||
AMBIT_URL = "http://localhost:9001"
|
||||
DEFAULT_VALUES = {"description": "no description"}
|
||||
|
||||
EP_DATA_DIR = os.environ['EP_DATA_DIR']
|
||||
MODEL_DIR = os.path.join(EP_DATA_DIR, 'models')
|
||||
EP_DATA_DIR = os.environ["EP_DATA_DIR"]
|
||||
if not os.path.exists(EP_DATA_DIR):
|
||||
os.mkdir(EP_DATA_DIR)
|
||||
|
||||
MODEL_DIR = os.path.join(EP_DATA_DIR, "models")
|
||||
if not os.path.exists(MODEL_DIR):
|
||||
os.mkdir(MODEL_DIR)
|
||||
|
||||
STATIC_DIR = os.path.join(EP_DATA_DIR, 'static')
|
||||
STATIC_DIR = os.path.join(EP_DATA_DIR, "static")
|
||||
if not os.path.exists(STATIC_DIR):
|
||||
os.mkdir(STATIC_DIR)
|
||||
|
||||
LOG_DIR = os.path.join(EP_DATA_DIR, 'log')
|
||||
LOG_DIR = os.path.join(EP_DATA_DIR, "log")
|
||||
if not os.path.exists(LOG_DIR):
|
||||
os.mkdir(LOG_DIR)
|
||||
|
||||
PLUGIN_DIR = os.path.join(EP_DATA_DIR, 'plugins')
|
||||
PLUGIN_DIR = os.path.join(EP_DATA_DIR, "plugins")
|
||||
if not os.path.exists(PLUGIN_DIR):
|
||||
os.mkdir(PLUGIN_DIR)
|
||||
|
||||
# Set this as our static root dir
|
||||
STATIC_ROOT = STATIC_DIR
|
||||
|
||||
STATIC_URL = '/static/'
|
||||
STATIC_URL = "/static/"
|
||||
|
||||
# Where the sources are stored...
|
||||
STATICFILES_DIRS = (
|
||||
BASE_DIR / 'static',
|
||||
)
|
||||
STATICFILES_DIRS = (BASE_DIR / "static",)
|
||||
|
||||
FIXTURE_DIRS = (
|
||||
BASE_DIR / 'fixtures',
|
||||
)
|
||||
FIXTURE_DIRS = (BASE_DIR / "fixtures",)
|
||||
|
||||
# Logging
|
||||
LOGGING = {
|
||||
@ -206,8 +197,8 @@ LOGGING = {
|
||||
"disable_existing_loggers": True,
|
||||
"formatters": {
|
||||
"simple": {
|
||||
'format': '[%(asctime)s] %(levelname)s %(module)s - %(message)s',
|
||||
'datefmt': '%Y-%m-%d %H:%M:%S',
|
||||
"format": "[%(asctime)s] %(levelname)s %(module)s - %(message)s",
|
||||
"datefmt": "%Y-%m-%d %H:%M:%S",
|
||||
},
|
||||
},
|
||||
"handlers": {
|
||||
@ -220,7 +211,7 @@ LOGGING = {
|
||||
"level": "DEBUG", # Or higher
|
||||
"class": "logging.FileHandler",
|
||||
"filename": os.path.join(LOG_DIR, "debug.log"),
|
||||
"formatter": "simple"
|
||||
"formatter": "simple",
|
||||
},
|
||||
},
|
||||
"loggers": {
|
||||
@ -228,66 +219,66 @@ LOGGING = {
|
||||
"epdb": {
|
||||
"handlers": ["file"], # "console",
|
||||
"propagate": True,
|
||||
"level": os.environ.get('LOG_LEVEL', 'INFO')
|
||||
"level": os.environ.get("LOG_LEVEL", "INFO"),
|
||||
},
|
||||
# For everything under envipath/ loaded via getlogger(__name__)
|
||||
'envipath': {
|
||||
'handlers': ['file', 'console'],
|
||||
'propagate': True,
|
||||
'level': os.environ.get('LOG_LEVEL', 'INFO')
|
||||
"envipath": {
|
||||
"handlers": ["file", "console"],
|
||||
"propagate": True,
|
||||
"level": os.environ.get("LOG_LEVEL", "INFO"),
|
||||
},
|
||||
# For everything under utilities/ loaded via getlogger(__name__)
|
||||
'utilities': {
|
||||
'handlers': ['file', 'console'],
|
||||
'propagate': True,
|
||||
'level': os.environ.get('LOG_LEVEL', 'INFO')
|
||||
"utilities": {
|
||||
"handlers": ["file", "console"],
|
||||
"propagate": True,
|
||||
"level": os.environ.get("LOG_LEVEL", "INFO"),
|
||||
},
|
||||
},
|
||||
}
|
||||
|
||||
# Flags
|
||||
ENVIFORMER_PRESENT = os.environ.get('ENVIFORMER_PRESENT', 'False') == 'True'
|
||||
ENVIFORMER_DEVICE = os.environ.get('ENVIFORMER_DEVICE', 'cpu')
|
||||
ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
|
||||
ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
|
||||
|
||||
# If celery is not present set always eager to true which will cause delayed tasks to block until finished
|
||||
FLAG_CELERY_PRESENT = os.environ.get('FLAG_CELERY_PRESENT', 'False') == 'True'
|
||||
FLAG_CELERY_PRESENT = os.environ.get("FLAG_CELERY_PRESENT", "False") == "True"
|
||||
if not FLAG_CELERY_PRESENT:
|
||||
CELERY_TASK_ALWAYS_EAGER = True
|
||||
|
||||
# Celery Configuration Options
|
||||
CELERY_TIMEZONE = "Europe/Berlin"
|
||||
# Celery Configuration
|
||||
CELERY_BROKER_URL = 'redis://localhost:6379/0' # Use Redis as message broker
|
||||
CELERY_RESULT_BACKEND = 'redis://localhost:6379/1'
|
||||
CELERY_ACCEPT_CONTENT = ['json']
|
||||
CELERY_TASK_SERIALIZER = 'json'
|
||||
CELERY_BROKER_URL = "redis://localhost:6379/0" # Use Redis as message broker
|
||||
CELERY_RESULT_BACKEND = "redis://localhost:6379/1"
|
||||
CELERY_ACCEPT_CONTENT = ["json"]
|
||||
CELERY_TASK_SERIALIZER = "json"
|
||||
|
||||
MODEL_BUILDING_ENABLED = os.environ.get('MODEL_BUILDING_ENABLED', 'False') == 'True'
|
||||
APPLICABILITY_DOMAIN_ENABLED = os.environ.get('APPLICABILITY_DOMAIN_ENABLED', 'False') == 'True'
|
||||
MODEL_BUILDING_ENABLED = os.environ.get("MODEL_BUILDING_ENABLED", "False") == "True"
|
||||
APPLICABILITY_DOMAIN_ENABLED = os.environ.get("APPLICABILITY_DOMAIN_ENABLED", "False") == "True"
|
||||
DEFAULT_RF_MODEL_PARAMS = {
|
||||
'base_clf': RandomForestClassifier(
|
||||
"base_clf": RandomForestClassifier(
|
||||
n_estimators=100,
|
||||
max_features='log2',
|
||||
max_features="log2",
|
||||
random_state=42,
|
||||
criterion='entropy',
|
||||
criterion="entropy",
|
||||
ccp_alpha=0.0,
|
||||
max_depth=3,
|
||||
min_samples_leaf=1
|
||||
min_samples_leaf=1,
|
||||
),
|
||||
'num_chains': 10,
|
||||
"num_chains": 10,
|
||||
}
|
||||
|
||||
DEFAULT_MODEL_PARAMS = {
|
||||
'base_clf': DecisionTreeClassifier(
|
||||
criterion='entropy',
|
||||
"base_clf": DecisionTreeClassifier(
|
||||
criterion="entropy",
|
||||
max_depth=3,
|
||||
min_samples_split=5,
|
||||
# min_samples_leaf=5,
|
||||
max_features='sqrt',
|
||||
max_features="sqrt",
|
||||
# class_weight='balanced',
|
||||
random_state=42
|
||||
random_state=42,
|
||||
),
|
||||
'num_chains': 10,
|
||||
"num_chains": 10,
|
||||
}
|
||||
|
||||
DEFAULT_MAX_NUMBER_OF_NODES = 30
|
||||
@ -295,9 +286,10 @@ DEFAULT_MAX_DEPTH = 5
|
||||
DEFAULT_MODEL_THRESHOLD = 0.25
|
||||
|
||||
# Loading Plugins
|
||||
PLUGINS_ENABLED = os.environ.get('PLUGINS_ENABLED', 'False') == 'True'
|
||||
PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
|
||||
if PLUGINS_ENABLED:
|
||||
from utilities.plugin import discover_plugins
|
||||
|
||||
CLASSIFIER_PLUGINS = discover_plugins(_cls=Classifier)
|
||||
PROPERTY_PLUGINS = discover_plugins(_cls=Property)
|
||||
DESCRIPTOR_PLUGINS = discover_plugins(_cls=Descriptor)
|
||||
@ -306,59 +298,59 @@ else:
|
||||
PROPERTY_PLUGINS = {}
|
||||
DESCRIPTOR_PLUGINS = {}
|
||||
|
||||
SENTRY_ENABLED = os.environ.get('SENTRY_ENABLED', 'False') == 'True'
|
||||
SENTRY_ENABLED = os.environ.get("SENTRY_ENABLED", "False") == "True"
|
||||
if SENTRY_ENABLED:
|
||||
import sentry_sdk
|
||||
|
||||
def before_send(event, hint):
|
||||
# Check if was a handled exception by one of our loggers
|
||||
if event.get('logger'):
|
||||
for log_path in LOGGING.get('loggers').keys():
|
||||
if event['logger'].startswith(log_path):
|
||||
if event.get("logger"):
|
||||
for log_path in LOGGING.get("loggers").keys():
|
||||
if event["logger"].startswith(log_path):
|
||||
return None
|
||||
|
||||
return event
|
||||
|
||||
sentry_sdk.init(
|
||||
dsn=os.environ.get('SENTRY_DSN'),
|
||||
dsn=os.environ.get("SENTRY_DSN"),
|
||||
# Add data like request headers and IP for users,
|
||||
# see https://docs.sentry.io/platforms/python/data-management/data-collected/ for more info
|
||||
send_default_pii=True,
|
||||
environment=os.environ.get('SENTRY_ENVIRONMENT', 'development'),
|
||||
environment=os.environ.get("SENTRY_ENVIRONMENT", "development"),
|
||||
before_send=before_send,
|
||||
)
|
||||
|
||||
# compile into digestible flags
|
||||
FLAGS = {
|
||||
'MODEL_BUILDING': MODEL_BUILDING_ENABLED,
|
||||
'CELERY': FLAG_CELERY_PRESENT,
|
||||
'PLUGINS': PLUGINS_ENABLED,
|
||||
'SENTRY': SENTRY_ENABLED,
|
||||
'ENVIFORMER': ENVIFORMER_PRESENT,
|
||||
'APPLICABILITY_DOMAIN': APPLICABILITY_DOMAIN_ENABLED,
|
||||
"MODEL_BUILDING": MODEL_BUILDING_ENABLED,
|
||||
"CELERY": FLAG_CELERY_PRESENT,
|
||||
"PLUGINS": PLUGINS_ENABLED,
|
||||
"SENTRY": SENTRY_ENABLED,
|
||||
"ENVIFORMER": ENVIFORMER_PRESENT,
|
||||
"APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED,
|
||||
}
|
||||
|
||||
# path of the URL are checked via "startswith"
|
||||
# -> /password_reset/done is covered as well
|
||||
LOGIN_EXEMPT_URLS = [
|
||||
'/register',
|
||||
'/api/legacy/',
|
||||
'/o/token/',
|
||||
'/o/userinfo/',
|
||||
'/password_reset/',
|
||||
'/reset/',
|
||||
'/microsoft/',
|
||||
"/register",
|
||||
"/api/legacy/",
|
||||
"/o/token/",
|
||||
"/o/userinfo/",
|
||||
"/password_reset/",
|
||||
"/reset/",
|
||||
"/microsoft/",
|
||||
]
|
||||
|
||||
# MS AD/Entra
|
||||
MS_ENTRA_ENABLED = os.environ.get('MS_ENTRA_ENABLED', 'False') == 'True'
|
||||
MS_ENTRA_ENABLED = os.environ.get("MS_ENTRA_ENABLED", "False") == "True"
|
||||
if MS_ENTRA_ENABLED:
|
||||
# Add app to installed apps
|
||||
INSTALLED_APPS.append('epauth')
|
||||
INSTALLED_APPS.append("epauth")
|
||||
# Set vars required by app
|
||||
MS_ENTRA_CLIENT_ID = os.environ['MS_CLIENT_ID']
|
||||
MS_ENTRA_CLIENT_SECRET = os.environ['MS_CLIENT_SECRET']
|
||||
MS_ENTRA_TENANT_ID = os.environ['MS_TENANT_ID']
|
||||
MS_ENTRA_CLIENT_ID = os.environ["MS_CLIENT_ID"]
|
||||
MS_ENTRA_CLIENT_SECRET = os.environ["MS_CLIENT_SECRET"]
|
||||
MS_ENTRA_TENANT_ID = os.environ["MS_TENANT_ID"]
|
||||
MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
|
||||
MS_ENTRA_REDIRECT_URI = os.environ['MS_REDIRECT_URI']
|
||||
MS_ENTRA_SCOPES = os.environ.get('MS_SCOPES', '').split(',')
|
||||
MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
|
||||
MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
|
||||
|
||||
@ -151,7 +151,7 @@ class Command(BaseCommand):
|
||||
mapping = {}
|
||||
for p in packages:
|
||||
print(f"Importing {p}...")
|
||||
package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p).read())
|
||||
package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p, encoding='utf-8').read())
|
||||
imported_package = self.import_package(package_data, admin)
|
||||
mapping[p.replace('.json', '')] = imported_package
|
||||
|
||||
|
||||
@ -12,7 +12,8 @@ from epdb.logic import PackageManager
|
||||
from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
|
||||
from epdb.views import get_base_context, _anonymous_or_real
|
||||
from utilities.chem import FormatConverter
|
||||
from envipy_ambit import apply
|
||||
|
||||
|
||||
from rdkit import Chem
|
||||
from rdkit.Chem.MolStandardize import rdMolStandardize
|
||||
|
||||
@ -31,11 +32,19 @@ def normalize_smiles(smiles):
|
||||
|
||||
|
||||
def run_both_engines(SMILES, SMIRKS):
|
||||
from envipy_ambit import apply
|
||||
|
||||
ambit_res = apply(SMIRKS, SMILES)
|
||||
# ambit_res, ambit_errors = FormatConverter.sanitize_smiles([str(s) for s in ambit_res])
|
||||
|
||||
ambit_res = list(set([normalize_smiles(str(x)) for x in
|
||||
FormatConverter.sanitize_smiles([str(s) for s in ambit_res])[0]]))
|
||||
ambit_res = list(
|
||||
set(
|
||||
[
|
||||
normalize_smiles(str(x))
|
||||
for x in FormatConverter.sanitize_smiles([str(s) for s in ambit_res])[0]
|
||||
]
|
||||
)
|
||||
)
|
||||
|
||||
products = FormatConverter.apply(SMILES, SMIRKS)
|
||||
|
||||
@ -46,22 +55,39 @@ def run_both_engines(SMILES, SMIRKS):
|
||||
|
||||
all_rdkit_prods = list(set(all_rdkit_prods))
|
||||
# all_rdkit_res, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
|
||||
all_rdkit_res = list(set([normalize_smiles(str(x)) for x in
|
||||
FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]]))
|
||||
all_rdkit_res = list(
|
||||
set(
|
||||
[
|
||||
normalize_smiles(str(x))
|
||||
for x in FormatConverter.sanitize_smiles(
|
||||
[str(s) for s in all_rdkit_prods]
|
||||
)[0]
|
||||
]
|
||||
)
|
||||
)
|
||||
# return ambit_res, ambit_errors, all_rdkit_res, rdkit_errors
|
||||
return ambit_res, 0, all_rdkit_res, 0
|
||||
|
||||
|
||||
def migration(request):
|
||||
if request.method == 'GET':
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
|
||||
if os.path.exists(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json') and request.GET.get(
|
||||
"force") is None:
|
||||
migration_status = json.load(open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json'))
|
||||
if (
|
||||
os.path.exists(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
|
||||
and request.GET.get("force") is None
|
||||
):
|
||||
migration_status = json.load(
|
||||
open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
|
||||
)
|
||||
else:
|
||||
|
||||
BBD = Package.objects.get(url='http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
|
||||
ALL_SMILES = [cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)]
|
||||
BBD = Package.objects.get(
|
||||
url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
|
||||
)
|
||||
ALL_SMILES = [
|
||||
cs.smiles
|
||||
for cs in CompoundStructure.objects.filter(compound__package=BBD)
|
||||
]
|
||||
RULES = SimpleAmbitRule.objects.filter(package=BBD)
|
||||
|
||||
results = list()
|
||||
@ -71,7 +97,7 @@ def migration(request):
|
||||
total = 0
|
||||
|
||||
for i, r in enumerate(RULES):
|
||||
logger.debug(f'\r{i + 1:03d}/{num_rules}')
|
||||
logger.debug(f"\r{i + 1:03d}/{num_rules}")
|
||||
res = True
|
||||
for smiles in ALL_SMILES:
|
||||
try:
|
||||
@ -81,13 +107,19 @@ def migration(request):
|
||||
except Exception as e:
|
||||
logger.error(e)
|
||||
|
||||
results.append({
|
||||
'name': r.name,
|
||||
'detail_url': s.SERVER_URL + '/migration/' + r.url.replace('https://envipath.org/', '').replace('http://localhost:8000/', ''),
|
||||
'id': str(r.uuid),
|
||||
'url': r.url,
|
||||
'status': res,
|
||||
})
|
||||
results.append(
|
||||
{
|
||||
"name": r.name,
|
||||
"detail_url": s.SERVER_URL
|
||||
+ "/migration/"
|
||||
+ r.url.replace("https://envipath.org/", "").replace(
|
||||
"http://localhost:8000/", ""
|
||||
),
|
||||
"id": str(r.uuid),
|
||||
"url": r.url,
|
||||
"status": res,
|
||||
}
|
||||
)
|
||||
|
||||
if res:
|
||||
success += 1
|
||||
@ -95,32 +127,37 @@ def migration(request):
|
||||
error += 1
|
||||
|
||||
total += 1
|
||||
results = sorted(results, key=lambda x: (x['status'], x['name']))
|
||||
results = sorted(results, key=lambda x: (x["status"], x["name"]))
|
||||
|
||||
migration_status = {
|
||||
'results': results,
|
||||
'success': success,
|
||||
'error': error,
|
||||
'total': total
|
||||
"results": results,
|
||||
"success": success,
|
||||
"error": error,
|
||||
"total": total,
|
||||
}
|
||||
|
||||
json.dump(migration_status, open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json', 'w'))
|
||||
json.dump(
|
||||
migration_status,
|
||||
open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json", "w"),
|
||||
)
|
||||
|
||||
for r in migration_status['results']:
|
||||
r['detail_url'] = r['detail_url'].replace('http://localhost:8000', s.SERVER_URL)
|
||||
for r in migration_status["results"]:
|
||||
r["detail_url"] = r["detail_url"].replace(
|
||||
"http://localhost:8000", s.SERVER_URL
|
||||
)
|
||||
|
||||
context.update(**migration_status)
|
||||
|
||||
return render(request, 'migration.html', context)
|
||||
return render(request, "migration.html", context)
|
||||
|
||||
|
||||
def migration_detail(request, package_uuid, rule_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
|
||||
if request.method == 'GET':
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
|
||||
BBD = Package.objects.get(name='EAWAG-BBD')
|
||||
BBD = Package.objects.get(name="EAWAG-BBD")
|
||||
STRUCTURES = CompoundStructure.objects.filter(compound__package=BBD)
|
||||
rule = Rule.objects.get(package=BBD, uuid=rule_uuid)
|
||||
|
||||
@ -132,8 +169,9 @@ def migration_detail(request, package_uuid, rule_uuid):
|
||||
|
||||
all_prods = set()
|
||||
for structure in STRUCTURES:
|
||||
|
||||
ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = run_both_engines(structure.smiles, smirks)
|
||||
ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = run_both_engines(
|
||||
structure.smiles, smirks
|
||||
)
|
||||
|
||||
for x in ambit_smiles:
|
||||
all_prods.add(x)
|
||||
@ -152,13 +190,13 @@ def migration_detail(request, package_uuid, rule_uuid):
|
||||
|
||||
if len(ambit_smiles) or len(rdkit_smiles):
|
||||
temp = {
|
||||
'url': structure.url,
|
||||
'id': str(structure.uuid),
|
||||
'name': structure.name,
|
||||
'initial_smiles': structure.smiles,
|
||||
'ambit_smiles': sorted(list(ambit_smiles)),
|
||||
'rdkit_smiles': sorted(list(rdkit_smiles)),
|
||||
'status': set(ambit_smiles) == set(rdkit_smiles),
|
||||
"url": structure.url,
|
||||
"id": str(structure.uuid),
|
||||
"name": structure.name,
|
||||
"initial_smiles": structure.smiles,
|
||||
"ambit_smiles": sorted(list(ambit_smiles)),
|
||||
"rdkit_smiles": sorted(list(rdkit_smiles)),
|
||||
"status": set(ambit_smiles) == set(rdkit_smiles),
|
||||
}
|
||||
detail = f"""
|
||||
BT: {bt_rule_name}
|
||||
@ -177,29 +215,32 @@ def migration_detail(request, package_uuid, rule_uuid):
|
||||
rdkit_errors: {rdkit_errors}
|
||||
"""
|
||||
|
||||
temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
|
||||
temp["detail"] = "\n".join([x.strip() for x in detail.split("\n")])
|
||||
|
||||
results.append(temp)
|
||||
|
||||
res &= partial_res
|
||||
|
||||
results = sorted(results, key=lambda x: x['status'])
|
||||
context['results'] = results
|
||||
context['res'] = res
|
||||
context['bt_rule_name'] = bt_rule_name
|
||||
return render(request, 'migration_detail.html', context)
|
||||
results = sorted(results, key=lambda x: x["status"])
|
||||
context["results"] = results
|
||||
context["res"] = res
|
||||
context["bt_rule_name"] = bt_rule_name
|
||||
return render(request, "migration_detail.html", context)
|
||||
|
||||
|
||||
def compare(request):
|
||||
context = get_base_context(request)
|
||||
|
||||
if request.method == 'GET':
|
||||
context[
|
||||
"smirks"] = "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
|
||||
context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
|
||||
return render(request, 'compare.html', context)
|
||||
if request.method == "GET":
|
||||
context["smirks"] = (
|
||||
"[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
|
||||
)
|
||||
context["smiles"] = (
|
||||
"C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
|
||||
)
|
||||
return render(request, "compare.html", context)
|
||||
|
||||
elif request.method == 'POST':
|
||||
elif request.method == "POST":
|
||||
smiles = request.POST.get("smiles")
|
||||
smirks = request.POST.get("smirks")
|
||||
|
||||
@ -219,9 +260,9 @@ def compare(request):
|
||||
|
||||
rdkit_res, _ = FormatConverter.sanitize_smiles(all_rdkit_prods)
|
||||
context["result"] = True
|
||||
context['ambit_res'] = sorted(set(ambit_res))
|
||||
context['rdkit_res'] = sorted(set(rdkit_res))
|
||||
context['diff'] = sorted(set(ambit_res).difference(set(rdkit_res)))
|
||||
context["ambit_res"] = sorted(set(ambit_res))
|
||||
context["rdkit_res"] = sorted(set(rdkit_res))
|
||||
context["diff"] = sorted(set(ambit_res).difference(set(rdkit_res)))
|
||||
context["smirks"] = smirks
|
||||
context["smiles"] = smiles
|
||||
|
||||
@ -230,7 +271,7 @@ def compare(request):
|
||||
if r.exists():
|
||||
context["rule"] = r.first()
|
||||
|
||||
return render(request, 'compare.html', context)
|
||||
return render(request, "compare.html", context)
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
return HttpResponseNotAllowed(["GET", "POST"])
|
||||
|
||||
@ -38,3 +38,53 @@ envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
|
||||
|
||||
[project.optional-dependencies]
|
||||
ms-login = ["msal>=1.33.0"]
|
||||
dev = [
|
||||
"poethepoet>=0.37.0",
|
||||
"pre-commit>=4.3.0",
|
||||
"ruff>=0.13.3",
|
||||
]
|
||||
|
||||
[tool.ruff]
|
||||
line-length = 100
|
||||
|
||||
[tool.ruff.lint]
|
||||
# Allow fix for all enabled rules (when `--fix`) is provided.
|
||||
fixable = ["ALL"]
|
||||
# Allow unused variables when underscore-prefixed.
|
||||
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
|
||||
|
||||
[tool.ruff.format]
|
||||
docstring-code-format = true
|
||||
|
||||
# 4. Ignore `E402` (import violations) in all `__init__.py` files, and in selected subdirectories.
|
||||
[tool.ruff.lint.per-file-ignores]
|
||||
"__init__.py" = ["E402"]
|
||||
"**/{tests,docs,tools}/*" = ["E402"]
|
||||
|
||||
[tool.poe.tasks]
|
||||
# Main tasks
|
||||
setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
|
||||
dev = { cmd = "python manage.py runserver", help = "Start the development server", deps = ["db-up"] }
|
||||
|
||||
# Database tasks
|
||||
db-up = { cmd = "docker compose -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
|
||||
db-down = { cmd = "docker compose -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
|
||||
|
||||
# Full cleanup tasks
|
||||
clean = { sequence = ["clean-db"], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
|
||||
clean-db = { cmd = "docker compose -f docker-compose.dev.yml down -v", help = "Removes the database container and volume." }
|
||||
|
||||
# Django tasks
|
||||
migrate = { cmd = "python manage.py migrate", help = "Run database migrations" }
|
||||
bootstrap = { shell = """
|
||||
echo "Bootstrapping initial data..."
|
||||
echo "This will take a bit ⏱️. Get yourself some coffee..."
|
||||
python manage.py bootstrap
|
||||
echo "✓ Bootstrap complete"
|
||||
echo ""
|
||||
echo "Default admin credentials:"
|
||||
echo " Username: admin"
|
||||
echo " Email: admin@envipath.com"
|
||||
echo " Password: SuperSafe"
|
||||
""", help = "Bootstrap initial data (anonymous user, packages, models)" }
|
||||
shell = { cmd = "python manage.py shell", help = "Open Django shell" }
|
||||
|
||||
Reference in New Issue
Block a user