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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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Bioconda Contribution Fest: 2-3 November #2277

Closed bgruening closed 7 years ago

bgruening commented 8 years ago

With all the changes that will come in the next weeks and a few open issues concerning the overall quality of our packages I thought about organizing an online contribution fest. Maybe over one or two days, where we all gather together (online) and work on some specific tasks.

Our first Contribution Fest will be on the 2-3 November! We will have an IRC channel (maybe gitter?) and a google hangout in place.

We will start with a short presentation of all ideas and try to create small groups to tackle problems small groups. I guess it's a good idea if you fork bioconda-recipes and get your own travis setup up and running so we avoid the travis bottleneck.

Some ideas on what we can work on:

Moreover, we have some issue that could be worked on: https://github.com/bioconda/bioconda-recipes/labels/hackathon

PreHack preparation:

tomkinsc commented 8 years ago

This is a great idea; I will happily participate to the extent I have time available.

jmchilton commented 8 years ago

I'd participate in some capacity.

daler commented 8 years ago

Good idea. I may not be able to do things synchronously due to time constraints, but would be happy to participate otherwise.

bgruening commented 8 years ago

@daler this could be a chance to see PR all 24h :)

brwnj commented 8 years ago

What are your specific task ideas so far? In any case, I'd participate.

On Sun, Sep 4, 2016, 7:16 AM Björn Grüning notifications@github.com wrote:

@daler https://github.com/daler this could be a chance to see PR all 24h :)

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bgruening commented 8 years ago

@brwnj I have added a few ideas to the top post.

eggzilla commented 8 years ago

Hey, I will also contribute. Especially #1860 sounds interesting for me :-)

dkoppstein commented 8 years ago

Would be happy to contribute! I think weekends might be easier for me, but perhaps we should find a consensus time.

On Sun, Sep 4, 2016, 8:09 AM Florian Eggenhofer notifications@github.com wrote:

Hey, I will also contribute. Especially #1860 https://github.com/bioconda/bioconda-recipes/issues/1860 sounds interesting for me :-)

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leobiscassi commented 8 years ago

Hi all, I'm in! :smiley:

nturaga commented 8 years ago

I will try participate too.

tiagoantao commented 8 years ago

I am very pressed for time, but I will try to participate

tiagoantao commented 8 years ago

Idea:

2282 (age of packages)

jerowe commented 8 years ago

I would be very interested, but it depends on when.

On Sep 5, 2016 4:08 AM, "Tiago Antao" notifications@github.com wrote:

Idea:

2282 https://github.com/bioconda/bioconda-recipes/issues/2282 (age of

packages)

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cbrueffer commented 8 years ago

Same here; interested but depends on date/time.

johanneskoester commented 8 years ago

I'm in of course. My time is very limited at the moment, but I'll try to join!!

mdehollander commented 8 years ago

I am also interested. My contribution depends as well on the time i have available and my knowledge of the bioconda system

jrderuiter commented 8 years ago

I am also interested, time and familiarity with the bioconda system permitting! On Mon, 5 Sep 2016 at 11:46, Mattias de Hollander notifications@github.com wrote:

I am also interested. My contribution depends as well on the time i have available and my knowledge of the bioconda system

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zachcp commented 8 years ago

bioconda has been a great resource to me. I'd be interested in helping.

Another potential issue to flag, related to #1860 is what to do with packages that were added to bioconda early on but are now upstream. (r-ggplot2, click, others? probably many now). maybe these should be pruned?

endrebak commented 8 years ago

Is someone working on upgrading R and Rpy? If so I'll join you. We should make our own TODO-thread for this. I cannot do it alone: someone with a more complete understanding of R, Rpy2, anaconda and its quirks is needed.

abretaud commented 8 years ago

I'll try to join if I have time!

lucapinello commented 8 years ago

This is a great idea!

olgabot commented 8 years ago

This is great! I've been wanting to contribute more to bioconda so a sprint like this would be great!

On Wed, Sep 7, 2016, 10:32 Luca Pinello notifications@github.com wrote:

This is a great idea!

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tseemann commented 8 years ago

I'd like to - might be able to join depending on timing.

I'm a bit behind on Bioconda recent changes however, would need to find out what's been happening.

roryk commented 8 years ago

Down for helping with this!

yesimon commented 8 years ago

I might take some time to look at some OS X issues!

bgruening commented 8 years ago

Wow, what a great response! Thanks so much!!!! What about the 10th and 11th of October - or do we need a doodle?

leobiscassi commented 8 years ago

That's great for me

On Sun, Sep 11, 2016 at 6:53 AM Björn Grüning notifications@github.com wrote:

Wow, what a great response! Thanks so much!!!! What about the 10th and 11th of October - or do we need a doodle?

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Best regards, Léo Biscassi

johanneskoester commented 8 years ago

I'm on vacation from 2 to 15. October. If nothing else works, you can of course still do it without me though.

souravsingh commented 8 years ago

I am really looking forward to this!

bgruening commented 8 years ago

What about the 2-3 November? Is this better?

johanneskoester commented 8 years ago

Works for me!

jerowe commented 8 years ago

Great for me too! I'm excited!

Is there an agenda? Do we all just choose things we want to contribute?

I see that there are ideas listed. I'll quite happily work on moving the perl to a perl- prefix.

dkoppstein commented 8 years ago

We can use the new project board functionality that github recently integrated!

bgruening commented 8 years ago

@bioconda/all let's fix the data for our first online bioconda hackathon: 2-3 November! Looking forward to it!!!!

tseemann commented 8 years ago

Managed to choose the exact dates of our national bioinformatics conference - but that's ok :) http://www.abacbs.org/conference/

bgruening commented 8 years ago

arg, sorry :( Maybe you can organize a break-out session :)

tomkinsc commented 8 years ago

Another idea for the contribution fest would be to start transitioning generic packages (ex. scala) from bioconda to conda-forge, now that we're depending on the latter. It would mean we have fewer to maintain, and would also make generic packages more widely available to others.

bgruening commented 8 years ago

@tomkinsc please add it to the top post.

dkoppstein commented 8 years ago

Any high priority issues that we should add to the backlog for this sprint?

kyleabeauchamp commented 8 years ago

Two more ideas:

  1. Implement security enhancements (e.g. #2327)
  2. Perhaps we should set up a doodle poll for a "kickoff" google hangout of 1 hour, something like the opening session of a conference or a meet-and-greet?
bgruening commented 8 years ago

@kyleabeauchamp added. @dkoppstein I think everyone has a different priority list but we will introduce all our ideas and we are happy for every single contribution ... docu, code, recipes, license cleanups ....

tomkinsc commented 8 years ago

For processes that can be automated, I would advocate adding functions to bioconda-utils so we can easily repeat parts of this effort in the future.

A few potential functions to automate:

For each of these, a package name could be provided, or if omitted all bioconda packages would be used.

bgruening commented 8 years ago

I plan to go over all PR in the next days and label them. For example see this one: https://github.com/bioconda/bioconda-recipes/pull/2562

We need help from someone who owns a Mac and cares about OSX packages. If we can label PR appropriate we can use this hopefully during our hackathon.

gregvonkuster commented 8 years ago

I have a mac and I definitely care about OS X packages - I will participate as much as I can.

bgruening commented 8 years ago

I have collected a few issue and tagged them as hackathon: https://github.com/bioconda/bioconda-recipes/labels/hackathon

Feel free to add more if relevant.

@gregvonkuster thanks!!!

jrderuiter commented 8 years ago

I'm also interested in helping with the OSX packages if I have time! On Sun, 9 Oct 2016 at 14:52, Björn Grüning notifications@github.com wrote:

I have collected a few issue and tagged them as hackathon: https://github.com/bioconda/bioconda-recipes/labels/hackathon

Feel free to add more if relevant.

@gregvonkuster https://github.com/gregvonkuster thanks!!!

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lecorguille commented 8 years ago

I'm in!

vodkatad commented 8 years ago

Will try to join you to get a gist on how to give a hand in the future to this project.

bgruening commented 8 years ago

I updated the description a little bit and I'm starting to get exited only for days left. Please prepare a bioconda-recipes fork that is working with travis to distribute the work load a little bit. Let me know if you have any questions.

claresloggett commented 8 years ago

I might have some blocks of time to contribute but I'm probably in a different timezone to most. What time (and timezone) are you planning to start the Hangout / Gitter?