[WIP] Docker build

[TomekFraczek]

Optional pull request/up for discussion

To simplify the build process and make the application more operating system agnostic, I've wrapped the install in a docker container, built out of a series of dockerfiles.

Primarily, this allows the code to work in the exact same way on every machine, and to be isolated in it's own, safe environment. Additionally, the build/install process on new machines will be reduced to a one-liner (not counting network configurations), and can be easily extended to include a stable production version (related to https://github.com/carmenalab/brain-python-interface/issues/26).

For development purposes, the build process was split into several stages: base, python and code.

• base: build the os-level dependencies and directory strcture
• python: build the python dependencies, set up python variables
• code: build source-code based dependencies, run configuration and database setup

This allows the docker image to be rebuilt at any of the three levels, so as few as possible of the installs are repeated. Together with dockerfile caching, this allows for very quick build times.

Other related upgrades:

• Optimize ubuntu packages, remove redundacies
• Updated rabbit-mq install process (repository moved, settings updated)
• Use requirements.txt file in install proceess
• Move more packages to pip install (i.e. scipy, numpy)
• Update of django database setup (as per https://github.com/carmenalab/brain-python-interface/issues/21) Now uses makemigrations and migrate instead of syncdb
• Automatically fix bash scripts broken by editing in windows (remove /r line endings)
• Fully automatic install process with (settable) default values, config available at any later time. On Linux, use : ./config.sh <image_name>. On windows use: config.bat <image_name>

TODO

As of right now, the install is incomplete, as it is still missing some packages. Packages to still be added:

• [ ] OpenGL-accelerate
• [ ] plexon
• [ ] Phigets

Testing and Setup

• [x] Clean up imports
• [ ] Verify and auto-setup connectivity

What do you think? Is this a valuable way to go?

[sgowda]

This is cool, thanks for taking a stab at it! Docker install would be helpful and low risk since if you wanted you can always install it the hard way. I think it would be good to check (sometime closer to merge) that the config allows access to files outside of the container, like data files -- I have had some issues with that previously with Docker.

[TomekFraczek]

Thanks! I'll keep an eye out for that issue.

Just to clarify though, do you mean to make sure that the docker image can write data files outside of the image?

[sgowda]

the docker image should be able to both read and write files outside of the container. writing is needed for saving behavioral data generated during the experiment, reading is needed for analyses which need to open data files and reference task source code.