Non-reliance on ~/git

[rgerkin]

The shell scripts rely on things being checked out to ~/git (which, to be fair, is what the README directs) but for those of us that like to put files where we want, can we instead use something like an OPENWORM_HOME shell variable? I'm thinking something like this:

So instead of:

python ~/git/BlueBrainProjectShowcase/Channelpedia/NML2ChannelAnalyse.py...

each script would have something like:

OPENWORM_HOME=${OPENWORM_HOME:-~/git/}
python $OPENWORM_HOME/BlueBrainProjectShowcase/Channelpedia/NML2ChannelAnalyse.py...

The VAR=${VAR:-DEFAULT} syntax lets you use the environment variable or a default if doesn't exist. It works in most shells. This way no one has to set the OPENWORM_HOME variable, but if they want then they can and then put muscle_model in the corresponding location. In general, having an OPENWORM_HOME that refers to the top-level directory for all repos (for those of us interested in more than one repo) could be useful.

If anyone likes this I can patch all the scripts.

[rayner]

I'm entirely in favour of this. The README only directs people to put things in ~/git because that's what the shell scripts rely on... :-)

[pgleeson]

I plan to move these analysis scripts out of BlueBrainProjectShowcase next week. It's the wrong place for them. Hoping to make a single NML2 python utilities/bells & whistles package here and will hopefully solve a number of these installation issues.

[rayner]

@pgleeson Ah, okay, thanks. I don't think there's anything else with hard-coded paths, is there?

[pgleeson]

There shouldn't be. Those hard coded paths were just there for testing and not really intended as a recommended installation requirement.

[slarson]

Think this is closed now with #27