These are chat archives for dereneaton/ipyrad

28th
Jan 2016
Isaac Overcast
@isaacovercast
Jan 28 2016 01:23 UTC
Isaac Overcast
@isaacovercast
Jan 28 2016 01:56 UTC
You want to change data.dirs.working as well? data.dirs.project?
Deren Eaton
@dereneaton
Jan 28 2016 02:08 UTC
yeah. sounds good.
Isaac Overcast
@isaacovercast
Jan 28 2016 02:37 UTC
heavy load on the system may cause _launch() to take longer than ten seconds. I'm running a big job and saw from a CLI run and was confused, took me a second to figure it out because i ran it again and it worked. Think this is a use case worth covering? Maybe just add some text at the end of the error message about how pegged cpu can cause ipcluster to flip, so just try again?
Isaac Overcast
@isaacovercast
Jan 28 2016 03:38 UTC
Obv after 10 seconds _launch bails and tells you to run ipcluster for API mode, which will confuse CLI users.
Isaac Overcast
@isaacovercast
Jan 28 2016 03:55 UTC
creating the new paramsdict[0] for assembly_name. got any preference for a default?
My default default is 'wat' lol, but that's prob not great :p
Isaac Overcast
@isaacovercast
Jan 28 2016 04:09 UTC
for cli users If assembly_name is unset I'm going to throw an ipyrad error and force them to choose a name. was contemplating setting a default but it's too risky.
Isaac Overcast
@isaacovercast
Jan 28 2016 04:17 UTC
Alternatively we could handle it the same way as project_dir, where it just takes whatever fuckin dir your running from and uses that as the name.
Isaac Overcast
@isaacovercast
Jan 28 2016 05:18 UTC
Huge merge: df4a7cd
df4a7cd..a12105c
ah fuck, you get it... Big merge, changed working_directory to project_dir and added paramsdict[0] = "assembly_name"
Kills all current assemblies. Kills current params.txt, but if you mod it to have a [0] line it works fine. Tested and works good for CLI but haven't tested API much. data.get_params() and data.set_params() probably need a look, but i'm 95% confident they'll work.
Deren Eaton
@dereneaton
Jan 28 2016 16:40 UTC
Cool, Ive been checking it out.
I'm a little confused about how 'assembly_name' is going to work with the CLI and API, there is redundancy with self.name... I won't have time to test around with it for a few days though.
Isaac Overcast
@isaacovercast
Jan 28 2016 16:53 UTC
Yeah, there is redundancy. I don't imagine API users will directly use 'assembly_name' that much.
How's this look, i think it's the best we can do:
conda install --channel ipyrad ipyrad
This works too:
conda install -c ipyrad ipyrad
Deren Eaton
@dereneaton
Jan 28 2016 16:56 UTC
yeah, I dig it
does it work to only parse assembly_name from the params.txt file for setting self.name, but then not adding it to the paramsdict? Seems we don't want it in there if changing it will only mess things up.
Deren Eaton
@dereneaton
Jan 28 2016 17:36 UTC
OK, I spelled out my thoughts more clearly in #96