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biocore/biom-format

The Biological Observation Matrix (BIOM) Format Project

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Repo info

Activity

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)
Dec 02 2020 19:42

wasade on master

Don't lint twice (compare)
Dec 02 2020 19:40

wasade on master

Adjusting testing config (compare)
Dec 02 2020 19:34

wasade on master

Initial GH action build/lint/te… (compare)
Nov 16 2020 20:25

wasade on 2.1.10

(compare)
Nov 16 2020 20:23

wasade on master

Normalize metadata on parse (#8… (compare)
Nov 16 2020 20:23

wasade closed #853

Daniel McDonald

@wasade

@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

http://youtu.be/zcvbHJ1BZ9s

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 :)

https://github.com/mitsuhiko/click/blob/master/click/core.py#L694

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"

Daniel McDonald

@wasade

btw

we can make in rain rainbows

http://click.pocoo.org/5/utils/#ansi-colors

Jai Ram Rideout

@jairideout

interesting, thanks @gregcaporaso for finding that alternative way to generate the autocomplete script! and very cool re: ansi colors :)