Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Feb 10 16:55
    wasade commented #855
  • Feb 10 16:31
    guillaume-gricourt commented #855
  • Feb 10 16:19
    wasade commented #855
  • Feb 10 12:07
    guillaume-gricourt edited #855
  • Feb 10 12:04
    guillaume-gricourt opened #855
  • Jan 26 20:25
    MaryoHg commented #852
  • Jan 11 19:18
    wasade commented #854
  • Jan 11 14:59
    antgonza opened #854
  • Dec 02 2020 21:24

    wasade on master

    Maybe the builds work now? (compare)

  • Dec 02 2020 21:18

    wasade on master

    activate for running too (compare)

  • Dec 02 2020 21:14

    wasade on master

    docs to 3.7 (compare)

  • Dec 02 2020 21:11

    wasade on master

    bash (compare)

  • Dec 02 2020 21:06

    wasade on master

    kick (compare)

  • Dec 02 2020 21:02

    wasade on master

    try incubator (compare)

  • Dec 02 2020 20:48

    wasade on master

    using a different python (compare)

  • Dec 02 2020 20:22

    wasade on master

    asd (compare)

  • Dec 02 2020 20:20

    wasade on master

    not sure whats going on (compare)

  • Dec 02 2020 20:05

    wasade on master

    conda activate? (compare)

  • Dec 02 2020 19:52

    wasade on master

    env update to install (compare)

  • Dec 02 2020 19:47

    wasade on master

    Update not upgrade (compare)

Yoshiki Vázquez Baeza
@ElDeveloper
bash autocomplete is plain magic
Jai Ram Rideout
@jairideout
:sparkles:
Greg Caporaso
@gregcaporaso
k, website is updated. can someone review/merge #678 to bump the version?
Daniel McDonald
@wasade
reviewing/merging
@jairideout, is there a good way to associate that with a specific env? not seeing anyway to have env vars specific to environments without manually modifying activate
merged
Jai Ram Rideout
@jairideout
not sure, it'd be cool if conda had a postactivate hook for stuff like this
Greg Caporaso
@gregcaporaso
i’m gonna send a note to the dev lists in a minute with tweetable link and some notes
Jai Ram Rideout
@jairideout
biom is using click's bash autocomplete support, see here for more details: http://click.pocoo.org/5/bashcomplete/
Jai Ram Rideout
@jairideout
@gregcaporaso here's the link to Jenkins' progress: http://ci.qiime.org/job/QIIME/979/console
Daniel McDonald
@wasade
@jairideout, ya, just wish there were easy hooks in conda as dropping something into ~/.bash_profile won’t work
…well, you could hack it i suppose. bash doesn’t actually care if the executable is present, would just need to precompute the completion scripts
Yoshiki Vázquez Baeza
@ElDeveloper
Greg Caporaso
@gregcaporaso
wow. those are going to change the world. i do have to ask: why was that hard?
all went well with the jenkins test against the 2.1.5 release, so i think we can check this one off. thanks again for all of the work on this @jairideout, @ebolyen and @wasade! :beers:
Greg Caporaso
@gregcaporaso
i did this to get my auto complete to work in my conda env
seems to be working
Evan Bolyen
@ebolyen
:beers:
Daniel McDonald
@wasade
@gregcaporaso, the issue with the activation script is that you can’t just put it into ~/.bash_profile or ~/.bashrc unless it falls after source activate <your_env_that_contains_biom>
Greg Caporaso
@gregcaporaso
it seemed to work for me - i was surprised. maybe i did something wrong and it’s actually not working
Daniel McDonald
@wasade
did you do it prior to an activate?
or following?
Greg Caporaso
@gregcaporaso
no, it’s working, but i don’t understand how
Daniel McDonald
@wasade
i mean in your ~/.bash_profile or something
Greg Caporaso
@gregcaporaso
i put the line in bashrc, log out, log back in, activate my env, and tab completion works
Daniel McDonald
@wasade
very odd
Greg Caporaso
@gregcaporaso
and biom is not available outside of my env
i guess click is just magic?
Daniel McDonald
@wasade
I get: "-bash: biom: command not found"
if i do it outside of an env
can you open a new terminal, not activate an environment, and send the output from which biom?
Greg Caporaso
@gregcaporaso
no output
Daniel McDonald
@wasade
that’s total voodoo unless it caches somewhere, but that doesn’t appear to be the case from testing
weird
thanks
Greg Caporaso
@gregcaporaso
sounds like that’s what it’s doing, from the description at the link i sent
Daniel McDonald
@wasade
the command source foo calls foo as though it were a program
click intercepts the call with a hook
then generates the necessary COMP_WORDS blah blah
it cannot work if foo is not in the path
but if its working for you, then awesome :)
Greg Caporaso
@gregcaporaso
source biom is used to create the shell script in the env
Daniel McDonald
@wasade
the click codebase is elegant btw… it’s worth a traversal if you haven’t had a chance to read through any of it
Greg Caporaso
@gregcaporaso
you then run the shell script from outside the env
i have looked through parts, it’s really nice
Daniel McDonald
@wasade
ohhh, i see now
heh
bam, okay, got it working
had my blinders on and only saw the “Activation” section, not the “Activation script"