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# Tilo
A visual explorer for the biological Tree of Life.
[Available online](https://terryt.dev/tilo/).
## Project Overview
The UI is largely coded in Typescript, using the [Vue](https://vuejs.org)
framework, with [Vite](https://vitejs.dev) as the build tool. Much of
the styling is done using [Tailwind](https://tailwindcss.com). Packages
are managed using [npm](https://www.npmjs.com) and [Node.js](https://nodejs.org).
On the server side, tree data is served and generated using Python, with
packages managed using [Pip](https://pypi.org/project/pip). Tree data is
stored using [Sqlite](https://www.sqlite.org).
## Files
### Project Level
- **package.json**: Contains npm project information, such as package dependencies.
- **package-lock.json**: Auto-generated by npm. Used for replicable installations.
- **LICENCE.txt**: This project's license (MIT).
### Client & Server
- **src**: Contains most of the client-side code.
- **index.html**: Holds code for the main page, into which code from 'src' will be included.
- **public**: Contains files to be copied unchanged in the production-build of the UI.
- **backend**: Contains code for the server, and for generating tree-of-life data.
### Configuration
- **vite.config.js**: For configuring Vite.
- **tailwind.config.js**: For configuring Tailwind.
- **postcss.config.js**: For configuring Tailwind.
- **tsconfig.json**: For configuring Typescript.
### Other
- **.gitignore**: Lists files to be ignored if using [Git](https://git-scm.com/downloads).
- **DEPLOY.md**: Instructions for deployment on an Apache server on Ubuntu.
- **prebuild.sh**: Bash script for automating some steps of deployment.
## Setup Instructions
Note: Running your own version of the client and server should be straightforward,
but generating the database that they use takes a long time. More details are
in `backend/tolData/README.md`.
### Client Side
1. If you don't have npm or Node.js installed, you can download a Node installer from
<https://nodejs.org/en/download>, which includes npm. This project was coded using version 16.
1. In this directory, run the command `npm install`, which install packages listed in
package.json, creating a `node_modules` directory to hold them.
1. Running `npm run dev` starts the dev server.
### Server Side
1. If you don't have Python 3 installed, see <https://www.python.org/downloads>.
The package manager Pip is included.
1. The database used by the server is generated using scripts in `backend/tol_data/`.
See it's README for instructions. You'll likely need to install a few
packages using Pip.
1. The dev server is started by running `./server.py` in the `backend/` directory.
To run it, you'll need to install jsonpickle. This can be done using
`python -m pip install jsonpickle`.
If you want to keep the installed package separate from your system's packages,
it's common practice to use [venv](https://docs.python.org/3/tutorial/venv.html).
### Running Tilo
1. In `backend/`, run `./server.py`, which starts a basic HTTP server that provides
tree-of-life data on port 8000.
1. In this directory, or somewhere in `src/`, run `npm run dev`. This starts a dev server that
provides Tilo's user interface on port 3000.
1. Open a web browser, and navigate to <http://localhost:3000>.
## Deploying the Website
This is significantly dependent on the server platform. `DEPLOY.md` contains
instructions for deployment on an Apache server on an Ubuntu system.
## Licence
Tilo is licensed under the [MIT Licence](https://github.com/terry06890/tilo/blob/main/LICENCE.txt).
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