Bioconda Contribution Fest: 2-3 November #2277

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bgruening opened this Issue Sep 4, 2016 · 53 comments

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@bgruening
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bgruening commented Sep 4, 2016 edited

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:

  • more tests: #2276
  • improving documentation
  • getting more packages to build under OSX
  • interest in setting up Windows builds?
  • betting travis testing - fail early! #1860
  • perl/R packages should be migrated into a subdir
  • convert all packages from git_url to url
  • transition generic packages (ex. scala, generic pypi packages) from bioconda to conda-forge
  • Implement security enhancements (e.g. #2327)
  • 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?

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

PreHack preparation:

@tomkinsc
Contributor
tomkinsc commented Sep 4, 2016

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

@jmchilton
Contributor

I'd participate in some capacity.

@daler
Member
daler commented Sep 4, 2016

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

@bgruening
Contributor

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

@brwnj
Contributor
brwnj commented Sep 4, 2016

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
Contributor

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

@eggzilla
Member
eggzilla commented Sep 4, 2016

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

@dkoppstein
Member

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
#1860 sounds
interesting for me :-)


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@leobiscassi
Contributor

Hi all, I'm in! 😃

@nturaga
Contributor
nturaga commented Sep 4, 2016

I will try participate too.

@tiagoantao
Member

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

@tiagoantao
Member

Idea:

#2282 (age of packages)

@jerowe
Contributor
jerowe commented Sep 5, 2016

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 #2282 (age of
packages)


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@cbrueffer
Member

Same here; interested but depends on date/time.

@johanneskoester
Contributor

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

@mdehollander
Contributor

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

@jrderuiter
Contributor

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
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zachcp commented Sep 6, 2016

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
Contributor
endrebak commented Sep 6, 2016

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
Contributor
abretaud commented Sep 6, 2016

I'll try to join if I have time!

@lucapinello

This is a great idea!

@olgabot
olgabot commented Sep 7, 2016

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
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tseemann commented Sep 8, 2016

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
Contributor
roryk commented Sep 8, 2016

Down for helping with this!

@yesimon
Contributor
yesimon commented Sep 8, 2016

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

@bgruening
Contributor

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

@leobiscassi
Contributor

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
Contributor

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

@souravsingh
Member

I am really looking forward to this!

@bgruening
Contributor

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

@johanneskoester
Contributor

Works for me!

@jerowe
Contributor
jerowe commented Sep 23, 2016 edited

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
Member

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

@bgruening
Contributor

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

@bgruening bgruening changed the title from Interested in a bioconda Contribution Fest? to Bioconda Contribution Fest: 2-3 November Sep 24, 2016
@tseemann
Contributor

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

@bgruening
Contributor

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

@tomkinsc
Contributor
tomkinsc commented Sep 26, 2016 edited

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
Contributor

@tomkinsc please add it to the top post.

@dkoppstein
Member

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

@kyleabeauchamp
Contributor

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
Contributor

@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
Contributor

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:

  • source_url_https <package_name> — changes urls http:// -> https:// for hostnames known to support TLS (github, etc.)
  • list_sources_without_hash <package_name> [--update_recipe] — lists packages that include url: but no md5:/sha1:/sha257:/etc, perhaps with an optional argument to automatically populate hash values: download each source for a package, calculate hashes, and add to the recipe)
  • validate_recipe <package_name> — a validation function, including bioconda/bioconda-utils#19 and checks of our own: that the license field is populated, that https is used for known TLS hostnames, etc.
  • attempt_version_update <package_name> [--leave_on_build_failture] — A function to update a recipe and try to build it, where possible. For packages sourced from GitHub, this is a matter of comparing the current version with the most recent release/tag, with an optional function to convert the GitHub tag to the version used by conda (i.e. strip the preceding v from v1.x). Not sure how feasible this would be for sourceforge packages. This is in response to #2282. If the build fails after the automated update attempt, the recipe could be rolled back, or left as-is for manual fixes.

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

@bgruening
Contributor

I plan to go over all PR in the next days and label them. For example see this one: #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
Contributor

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

@bgruening
Contributor

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
Contributor

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
Member

I'm in!

@vodkatad
Contributor

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

@bgruening
Contributor

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

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?

@bgruening
Contributor

There will be a bunch of people from all over the world my hope/guess is that 24h someone will be available ... :-)

@bgruening bgruening referenced this issue Nov 1, 2016
Merged

Exparna #2673

2 of 4 tasks complete
@bgruening
Contributor

@bioconda/all just a few our and we will start our first bioconda hackathon. Please prepare yourself with our PreHack list:

PreHack preparation:

Moreover, we have tagged Issues that seems to be suitable for a Hackathon, please see:
https://github.com/bioconda/bioconda-recipes/labels/hackathon

See you all on gitter: https://gitter.im/bioconda/Lobby

@claresloggett
claresloggett commented Nov 1, 2016 edited

Ah sorry, my feed had not updated with the Gitter link. I see it now!

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