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Reece Hart
@reece
hgvs 1.1.2 just released. See http://hgvs.readthedocs.io/en/1.1.2/changelog/1.1/1.1.2.html for details.
Reece Hart
@reece
I updated the slides from last night's SFPUG meeting. http://bit.ly/2De2Uy4
Reece Hart
@reece

Hi everyone who came to the SFPUG meeting last night. Here's a quick summary:

  • I'll keep gitter up and we can try that for communication. You're welcome to email as well.
  • Slides (http://bit.ly/2De2Uy4) are update with a link to the paper.
  • At the next project night, I'll go a little deeper on how variants are projected between aligned sequences. Until then, please...
  • Try installing hgvs. First, try with pip install hgvs just to get a feel for it. Then, fork the project, clone it, and run make devready in the directory. (You may have some dependencies to resolve first.) In particular, see biocommons/hgvs#523.
  • Look through issues for any that interest you. If you start working on any, please tag @yourself in the comments so that we don't have conflicts.
  • Be on the lookout for any repo changes that would make it easier for folks to get started: docs, better issue labels, etc.

Again, thanks for your willingness to contribute. This is going to be fun!

Aaron Slaff
@aaronslaff
Howdy ya'll,
I will be working on the documentation update. Please feel free to message me directly if you have input on how to make the docs well-rounded for biologists and programmers. All suggestions are welcome. Look forward to hearing from you!
Reece Hart
@reece
Yay! Thanks, @aaronslaff. When you do this, please treat it like a code contribution. That means: 1) fork the repo, 2) create a branch with git, 3) make changes, 4) push to the branch. I'll then be able to merge the changes (just like I would with code). Probably best to try a small case first, such as updating installation instructions. Again, thanks!
Aaron Slaff
@aaronslaff
Happy Thanksgiving everyone!!
Reece Hart
@reece
@aaronslaff : I've been monitoring your PR and made some comments a while back that are unresolved. So, if that's why I haven't merged. Are you getting those notifications?
Aaron Slaff
@aaronslaff
@reece my apologies. I had taken some time to focus on job search. Last night I submitted the changes you had proposed for the installation and example docs that I generated. Today I will be working on creating templates for UX of the docs site. I will message you when I have pushed them to my branch.
Reece Hart
@reece
:thumbsup:
Reece Hart
@reece
Hi Folks- I can't meet Thursday after all. Mon, Tue, Wed still work. Please answer here: https://doodle.com/poll/cgk7iyzufb2p3cci
Sandeep Narayanaswami
@sandeep-n
Hey team, I'm trying to understand the build failure in the hgvs project. Is there a good way for me to attempt to reproduce the build (without spamming bogus PRs to trigger builds)?
Reece Hart
@reece
The build is now fixed. The problem was that pytest introduced a change that broken one of their plugins. The answer to your question is that there really isn't a way for you to test other than to download the code and run tests locally. Travis-ci repo admins can trigger a rebuild.
Sandeep Narayanaswami
@sandeep-n
Reece: I'm thinking about working on a Windows build for hgvs. Do you think this would be a good use of time?
(I looked into a little bit, and it looks like the only blocker for a Windows build is the optional dependency on seqrepo)
Reece Hart
@reece
I don't think Windows support is a good use of time. I'm not aware of any demand for Windows builds from end users, which should probably be the primary measure of utility and use of time. You can run hgvs without seqrepo (and I'll make the dependency optional very soon), but it's apx 40x (!) slower because many operations require the reference sequence, and networks are slow relative to local disk access.
Sandeep Narayanaswami
@sandeep-n
Makes sense. Thanks!