Moving condition to the environment directory

[eagmon]

We currently keep data on environments in reconstruction/ecoli/flat/condition/. This includes media/ -- lists of molecular concentrations for each media environment; timeseries/ -- timelines of times and media conditions to support environmental shifts; and environment_molecules.tsv -- a list of all molecules that could be present in the environment. These molecules are all currently labeled with [p] or [c] to support interaction with FBA, which had these as the external exchange molecules. /condition/ also includes condition_defs.tsv which provides a look up table for doubling time, and tf_condition.tsv.

I would like to move towards better handling of the environment, which will include moving reconstruction/ecoli/flat/condition/ to environment/condition/, under the environment base directory. This new directory should probably not include condition_defs.tsv and tf_condition.tsv, which deal with internal wcEcoli parameters.

For media, the location labels will all be dropped. When the environmental molecules are passed to wcEcoli, the appropriate label will need to be re-added to represent transport across the outer membrane.

There might be some complications in moving the condition directory into the environment directory, but it will be worth it for the sake of conceptual and technical simplicity. I still want wcEcoli to support simulations without the agent framework, so the parca will need to see the available media and timeline in order to build up sim_data.

I'm still thinking through the details of how to do this, so any thoughts are welcome!

[ghost]

slightly off-topic, but are we going to be moving our environment timelines for the surrogate models to environment/condition/?

[eagmon]

@lt5bf -- yes, I think we should have a new environment/condition/ that contains timelines and media. I will need to do some work to migrate reconstruction/ecoli/flat/condition/ into that directory.