Add docker

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+	"recommendations": [
+		"svelte.svelte-vscode",
+		"ms-python.vscode-pylance",
+		"ms-python.python",
+		"charliermarsh.ruff"
+	]
+}

.vscode/settings.json

@@ -1,6 +1,16 @@
 {
+	"python.defaultInterpreterPath": "backend/.venv/bin/python",
+	"autoDocstring.docstringFormat": "google",
+	"editor.wordWrapColumn": 100,
+	"eslint.validate": ["javascript", "javascriptreact", "svelte"],
+	"python.testing.pytestEnabled": true,
+	"editor.defaultFormatter": "esbenp.prettier-vscode",
+	"python.analysis.typeCheckingMode": "basic",
+	"editor.formatOnSave": true,
 	"[python]": {
-		"editor.defaultFormatter": "ms-python.black-formatter"
+		"editor.defaultFormatter": "charliermarsh.ruff"
 	},
-	"python.formatting.provider": "none"
+	"[json]": {
+		"editor.defaultFormatter": "esbenp.prettier-vscode"
+	}
 }

DEVELOPMENT.md

@@ -2,34 +2,55 @@
 
 By the time you finish this guide, you will be able to run the JS frontend [Svelte](https://kit.svelte.dev/) and the Python backend [FastAPI](https://fastapi.tiangolo.com/).
 
-> **Note**
-> We use bash for everything and **NOT** Powershell
+Note that we use `docker-compose` as defined in the `docker-compose.yml`.
 
 ## Installation
 
-### Backend
+> **Important**
+> You must have [Docker Desktop](https://www.docker.com/products/docker-desktop/) GUI installed and the `docker-compose` bash command.
 
-> **Warning**
+You can run everything by doing
+
+```bash
+make
+```
+
+and navigate to [http://0.0.0.0:5173](http://0.0.0.0:5173) webserver.
+
+That's it. This will spin up a docker container with the backend, database, and frontend servers running.
+
+To turn it off do
+
+```bash
+make down
+```
+Check out the [`Makefile`](./Makefile) for more shortcuts like this.
+
+If you want intellisense/autocomplete in VSCode, continue to the rest of the installation. Otherwise you are done. Totally optional, but I'd do it for autocomplete.
+
+### Backend 
+
+> **Important**
 > Before you do anything, make sure you have [Python](https://www.python.org/downloads/) installed.
 
 Then install the [Poetry Python Package Manager](https://python-poetry.org/) by doing 
 
 ```bash
-cd backend
 pip3 install poetry
 ```
 
 Then install the packages listed under [`pyproject.toml`](./backend/pyproject.toml) by doing 
 
 ```bash
+poetry config virtualenvs.in-project true # required for the .venv to get created
 poetry install
 ```
 
 **🥳 You're done with the backend installation!**
 
 ### Frontend
 
-> **Warning**
+> **Important**
 > Before you do anything, make sure you first have [Node](https://nodejs.org/en/download) installed.
 
 If you haven't already, also install [Yarn](https://classic.yarnpkg.com/lang/en/docs/install/#mac-stable) globally as the package manager for node by doing 
@@ -47,36 +68,14 @@ yarn install
 
 **🥳 You're done with the frontend installation!**
 
-## Running the Development Servers 
-
-It's very simple! You need two terminals open:
-
-On the first terminal, run the backend
-
-```bash
-cd backend
-poetry run dev
-```
-
-which will run the [ `server.py` ](./backend/src/server.py) HTTP server on localhost port 8000.
-
-Then, in the other terminal, run the frontend development server
-
-```bash
-cd frontend
-yarn dev --open
-```
-
-which should open up your browser to the user interface at [http://localhost:5173/](http://localhost:5173/).
-
-**🥳 You now should be up an running!**
-
-In the future, from the root directory you can use make commands to quickly run things instead of having to `cd` to different places and run different commands. Check out [`Makefile`](./Makefile). 
-
-But don't use it unless you understand what it's running.
 
 ## Navigating the codebase
 
+> **Warning**
+> Ignore the build script in the video, they are outdated
+> We use docker now through `make`
+> Additionally the host has changed from `localhost` to `0.0.0.0`
+
 I'll explain top-down how to understand the structure of this repository. First of all, you want to mainly pay attention to the [`frontend`](./frontend/) then the [`backend`](./backend/) code. I'll explain:
 
 ### Frontend
@@ -114,38 +113,13 @@ Check out the FastAPI docs for more info.
 
 Once we created the HTTP endpoints in the backend, we can call 
 ```bash
-cd frontend
-yarn openapi
+make api
 ```
 
 which generates frontend bindings/functions we can use in the frontend. See the [`+page.svelte`](./frontend/src/routes/page.svelte) for an example usage with the `Backend` object (generated from the command above). You'll see in the network tab that it just makes a `fetch` call to the backend.
 
-## FAQ
-
-### How to add JavaScript packages to the frontend?
-
-```bash
-cd frontend
-yarn add npm_package_name
-```
-
-for example if I wanted to install [D3](https://www.npmjs.com/package/d3):
-
-```bash
-cd frontend
-yarn add d3
-```
+### Database
 
-### How to add Python packages to the backend?
+We use a PostgreSQL database, but this can be swapped out later by changing the [`db.py`](./backend/src/db.py).
 
-```bash
-cd backend
-poetry add pypi_package_name
-```
-
-for example if I wanted to install [PyTorch](https://pypi.org/project/torch/):
-
-```bash
-cd backend
-poetry add torch
-```
+The starting scheme is here in [`init.sql`](./backend/init.sql) for the initial tables to be created.

Makefile

@@ -1,14 +1,29 @@
-install-front:
-	cd frontend; yarn install
+all: up
 
-install-back:
-	cd backend; poetry install
+up:
+	docker-compose up -d
 
-front:
-	cd frontend; yarn dev --open
+down:
+	docker-compose down
 
-back:
-	cd backend; poetry run dev
+restart:
+	make down
+	make up
 
-api: # the backend server needs to be running too
+hard-restart:
+	make down
+	docker-compose up --build -d	
+
+api: # generates the api for the frontend to call the backend 
 	cd frontend; yarn openapi
+
+install:
+	pip3 intall poetry
+	poetry config virtualenvs.in-project true
+	@echo "Install Docker Desktop https://www.docker.com/products/docker-desktop/"
+	@echo "and make sure `docker-compose` is available as a bash command"
+
+restart-venv:
+	cd backend; poetry config virtualenvs.in-project true;
+	cd backend; poetry env list; poetry env remove --all; 
+	cd backend; poetry install

README.md

@@ -2,38 +2,16 @@
 
 **A user friendly system to discover insights into venom protein data.**
 
-<!-- ## Live Deployments
-- [Venome Docs](https://venome.vercel.app) contains the live deployment of [`docs`](./docs/README.md) -->
-
 ## Structure
 
+-   [`docker-compose.yml`](./docker-compose.yml) contains the Docker container build
 -   [`frontend`](./frontend/README.md) contains the user interface in Svelte/JS
 -   [`backend`](./backend/README.md) contains the HTTP server and Database
-<!-- -   [`docs`](./docs/README.md) contains the documentation website generator (starlight/astro)
--   [`wip`](/wip/README.md) contains 🚧work-in-progress🚧 documents -->
 
 
 ## Quick start
 
-For an in depth guide of the installation and running, go to [`DEVELOPMENT.md`](./DEVELOPMENT.md).
-
-If you have everything nicely installed, then you can quickly do:
-
-### Frontend
-
-```bash
-cd frontend
-yarn install
-yarn dev 
-```
-
-### Backend
-
-```bash
-cd backend
-poetry install
-poetry run dev
-```
+Go to [`DEVELOPMENT.md`](./DEVELOPMENT.md) to get up and running.
 
 ## Resources
 

backend/.dockerignore

@@ -0,0 +1 @@
+.venv

backend/.gitignore

@@ -1 +1,2 @@
-__pycache__/
+__pycache__/
+.venv

backend/Dockerfile

@@ -0,0 +1,13 @@
+FROM python:3.11
+
+WORKDIR /app
+
+COPY . /app/
+
+RUN pip install poetry
+
+RUN poetry config virtualenvs.in-project true
+
+RUN poetry install
+
+EXPOSE 8000

backend/README.md

@@ -1,16 +1,13 @@
 # Backend
 
-## Development
-
-First install the python libraries
+## Add packages
 
 ```bash
-cd backend
-pip3 install -r requirements.txt
+poetry add py_package_name
 ```
 
-Then, run the HTTP server by
+Note you'll need to rebuild the docker container after adding a new package
 
 ```bash
-python3 server.py
-```
+make hard-restart
+```

backend/init.sql

@@ -0,0 +1,7 @@
+-- protein entries (basic) has name and id for a start
+--      TODO: add more info for the protein entries (like PDB, other protein info, markdown text)
+--      NOTE: text is like varchar but without a length limit
+CREATE TABLE protein_entries (
+    id integer GENERATED ALWAYS AS IDENTITY PRIMARY KEY,
+    name text NOT NULL UNIQUE
+);

backend/pyproject.toml

@@ -11,6 +11,8 @@ python = ">=3.9,<3.13"
 numpy = "^1.26.1"
 uvicorn = "^0.23.2"
 fastapi = "^0.104.0"
+psycopg = "^3.1.12"
+psycopg-pool = "^3.1.8"
 
 
 [build-system]
@@ -19,4 +21,4 @@ build-backend = "poetry.core.masonry.api"
 
 
 [tool.poetry.scripts]
-dev = "src.server:main" # run src/server.py at main()
+dev = "src.server:poetry_run_dev"