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DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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Initial cleanups #351

Closed bredelings closed 3 years ago

bredelings commented 3 years ago

Hi Joe,

This branch has the 5 initial cleanups that we discussed.

-BenRI

coveralls commented 3 years ago

Pull Request Test Coverage Report for Build 1240

Totals Coverage Status
Change from base Build 1209: -90.0%
Covered Lines: 0
Relevant Lines: 0
💛 - Coveralls
shajoezhu commented 3 years ago

Hi @bredelings , would you mind take a look at this please https://travis-ci.org/github/DEploid-dev/DEploid/jobs/763695356#L554

bredelings commented 3 years ago

Hi Joe,

This is because the travis build (but not the github-actions build) is using an old version of gcc that does not support c++17.  Gcc 5 was released in 2015, and the current version is version 10, which was released in 2020.

We could fix the travis script, but instead it might be easier to move entirely to github actions.  I could probably move the remaining bits from travis to github actions.  Then we could decomission travis.  (Also, I think travis is getting worse -- github actions seems much better.  I have switch to github actions in my other projects.).

-BenRI

On 3/20/21 7:11 AM, Joe Zhu wrote:

Hi @bredelings https://urldefense.com/v3/__https://github.com/bredelings__;!!OToaGQ!--VC9fM3H65kEllMEOwR4yWJb0Uc85kJJGiCTeycdYaZY7RNNFSDhBAt7-A3XTkZSvvqB5A$ , would you mind take a look at this please https://travis-ci.org/github/DEploid-dev/DEploid/jobs/763695356#L554 https://urldefense.com/v3/__https://travis-ci.org/github/DEploid-dev/DEploid/jobs/763695356*L554__;Iw!!OToaGQ!--VC9fM3H65kEllMEOwR4yWJb0Uc85kJJGiCTeycdYaZY7RNNFSDhBAt7-A3XTkZ-g5fang$

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shajoezhu commented 3 years ago

Hi Ben, yes, I agree. Sometimes updating travis yml was a bit painful. I am happy to shift things towards github action. I have a few more things like checking coverage will depend on travis, let me explore how to move those as well. and the for the circleci's i am happy to drop 14.04. though some of the computing labs still have old machines and setup... let me do some checking as well. let me get back to you

shajoezhu commented 3 years ago

Many thanks! @bredelings