Leiden Ice Database

A Python Flask project that uses NumPy and D3.js to show IR spectra of ice.

Setting up a development environment can be a time-consuming process, so this project includes a fully configured Vagrant set-up (read Development Environment Set-up below). It's highly recommended that you use this.

Development Environment Set-up

Prerequisites

This project includes a Vagrant configuration file that allows you to easily set up a development environment. Vagrant uses VirtualBox by default, so also make sure you have that installed.

Are you using a Leiden Observatory computer? Make sure you set VirtualBox to store its VMs outside your home (~/) directory, because the home folder is limited to 2GB. Open VirtualBox and click File->Preferences, then under the General tab pick a different Default Machine Folder. For example, use /data1/icemachine instead.

Also verify you have a Terminal and git installed.

Install machine

Open a terminal and run the following commands and keep on reading.

git clone https://github.com/bartolsthoorn/ice-database
cd ice-database
vagrant up

Vagrant will now install a new Debian machine, including all the requirements for this project (this might take ~15 min). This is called provisioning. Once this is done, connect to the newly made machine with the command below.

Seeing warnings? The vagrant up might show warnings like default: dpkg-preconfigure: unable to re-open stdin: No such file or directory and default: stdin: is not a tty, and perhaps other warnings. This is usually nothing to worry about and we'll test the set-up later.

If for any reason the provisioning process fails, it's always possible to run vagrant provision again. The provisioning scripts are idempotent, which means that you can run them again without getting into trouble (it checks what's already installed).

vagrant ssh

You should now be connected to the fully configured machine. To make sure everything is installed, run the following commands.

pyenv versions
cd /vagrant && python --version
python app.py

The /vagrant folder is a shared folder between the virtual machine and your developer machine.

Developing

This set-up features a ViM configuration, so you could use this as your editor. This is not at all required though, it's handy to know that the /vagrant folder on the virtual machine is actually the same folder as this repository. So you can freely edit the files on your host machine with your favourite editor and just run python / server using the virtual machine.

Delete machine

To delete a vagrant machine use vagrant destroy (this will delete all its data as well). To rebuild use vagrant up again.

Starting the production server

ssh icedb.strw.leidenuniv.nl
cd /data/icedb/ice-database
gunicorn application:app -b 0.0.0.0:5000 --pid ../gunicorn -D