GENESIS: Documentation

Related Documentation:
Backup Repository

The GENESIS Repositories

For the federated development of the software components of GENESIS, a software buildbot machine houses a monotone server that is connectible over the internet. Source code changes can be properly merged using the functions available on monotone, regardless of the location where the changes have been made (at home, in your office, on the airplane). The build mechanism will always build the most up to date version of the code.

Convenient Access to the Source Code

The easiest way to get the latest version of the source code is via the DeveloperPackage.

It is also possible to manually perform operations that are automated by the DeveloperPackage.

Serving your source code

If you want someone else to sync their code with what you have on your laptop, you can conveniently convert your laptop to a source code server using the command neurospaces_serve (see the DeveloperPackage). Other people can now connect to your laptop using, for example

   neurospaces_sync --repo-sync <ip-address-of-your-laptop>


   neurospaces_pull --repo-pull <ip-address-of-your-laptop>

All these commands accept a “--regex <package-regex>” option to select packages to serve, sync and pull respectively. To interrupt the server and kill all the server processes, use “neurospaces_kill_servers”.

Checking out Code Manually

To check out the latest version of the GENESIS code you must first initialize a local monotone repository via this command:

   mtn db init

There are monotone instances running for different parts of GENESIS on different ports. To target the correct component of our GENESIS system you need to use the following arguments for the remote server. The server address and port number are accessed by, for example, for the backward compatibility layer

Description Package namePort #Repository Name

GENESIS backward compatability layerns-sli 4692

Internal Storage for Models model-container 4693

Single neuron solver heccer 4694

Scheduler ssp 4695

Development Package developer 4696

Project Browser project-browser 4697

Incomplete GUI studio 4698

GShell gshell 4699

User documentation userdocs 4700

Exchange exchange 4701

Publications publications 4702

Experimental Protocols and I/O experiment 4703

RTXI protocol software package rtxi 4704

Python Scheduler sspy 4705

Chemesis-3 chemesis3 4706

Code can be pulled from the monotone server into your local working repository with the command

   mtn pull<port#> ‘‘*’’

The “*” argument pulls all branches from the server into your local repository. To pull a specific branch see the following section. It’s important that each server be synchronized with it’s own local repository. Once the code has been pulled you can checkout one of the branches into your working directory with the command

   mtn --branch=<Branch ID> co source_directory

Synchronizing Databases

To synchronize your monotone repository to the remote server you’ll need to use the sync command with the proper address of the server (as listed in the above table).

   mtn sync<port#> "*"

Now all changes, including logs will be on both the client and server repositories. Note in order to perform this operation you need to be given write access to the repositories on the GENESIS server repository repo-genesis3.


You must know the desired branch when pulling a repository. All branches can be downloaded simultaneously via the “*” argument. We currently use numeric branches that start at zero (0). After pulling a repository you can generate a list of branches available for check out from your local repository via the command

   mtn list branches

Committing Changes

A monotone repository is an annotated database and every change that is made is signed with keys. To be able to commit changes to your local monotone repository you need to generate a key pair. To do this execute the command

   mtn genkey

This stores a your private key in ~/.monotone. To enable this, you will be asked to enter a password which is used to verify your identity when you check in changes. To see all the keys monotone has stored you can do a

   mtn list keys

and also an

   mtn list keys

To commit the changes you have made to your own database repository, cd to the appropriate source directory and execute either

   mtn ci


   mtn commit

Repository Access

To get write access to a repository which you did not initiate, it must be signed with your public key. To export your public key perform the following command

   mtn pubkey > me.pubkey

Send the repository owner your public key for write access. To perform this you must have monotone read in the key from stdin with the read command

   cat me.pubkey | mtn read

If this is successful it will indicate that a packet has been read. You can store several keys in a file this way with the number of successful packets read in being given.