Add script for setting up an AMI

[aboucaud]

This PR adds both a bash script and a conda environment file to store the generic RAMP dependencies.

The idea is to add to every kit a file named ami_environment.yml containing the conda dependencies (channels, dependencies & pip-only requirements) so an AMI can easily be setup for this particular kit with three simple shell commands

git clone https://github.com/paris-saclay-cds/ramp-backend.git
cd ramp-backend
./scripts/ami_setup.sh <kit_name> scripts/ramp_environment.yml

[kegl]

Great, just let's not call it "ami", it should be generic setup for any (ubuntu) backend.

[aboucaud]

Name changed to ubuntu_setup.sh..

[jorisvandenbossche]

let's not call it "ami",

It's maybe more a comment for the autism repo, but shouldn't we then call it there differently as well? (eg ramp_environment.yml as the file here)

[jorisvandenbossche]

conda update pip ?

[aboucaud]

Last time I tried, the conda version of pip was an old one, and pip was complaining there was a newer version to be install with this command.

I guess that was a lazy choice to avoid a warning.

[jorisvandenbossche]

Should check, but I think you could even leave out the --name base

[aboucaud]

True only if the environment file does not have a different name specified.
This is for corner cases.

[jorisvandenbossche]

the file is called .py, but should this be .sh or something similar ?

[aboucaud]

oups.. 😄

[jorisvandenbossche]

What is this file used for?

[aboucaud]

I still had in mind we should separate the "backend" requirements for the moment.

Since we install ramp-backend and ramp-workflow via pip, all of their dependencies are also installed via pip by default. If we specify their dependencies in this file, we then can use conda for most of these dependencies.

[jorisvandenbossche]

Ah, missed it in the script that you do the conda env update twice, with this one and the one of the kit

[jorisvandenbossche]

I think ramp-workflow is not a dependency of ramp-backend? So maybe leave it here to only ramp-backend, so we have less duplication between this env file and the one in the starting kit?

[aboucaud]

is it not better the other way around ?
keep ramp-workflow here and remove it from the ami_env.yml

[jorisvandenbossche]

Hmm, not sure. Keeping it in the starting kit makes that more complete for people who want to check or replicate the same environment for the challenge.

[aboucaud]

ok then

[jorisvandenbossche]

this will not really work as desired I think since you defined psycopg2-binary as the dependency in setup.py (of ramp-backend). But I think it is actually better to change setup.py to use just psycopg2

[aboucaud]

Thanks for catching the mismatch.

I switched from psycopg2 to psycopg2-binary because it was advised in a Warning message. I have to check if both exist within conda though.

[jorisvandenbossche]

conda already provides binary packages, so there should not exist such a thing (It's rather strange practice of the psycopg2 devs to do this I think)