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biocore / gneiss

compositional data analysis toolbox
https://biocore.github.io/gneiss/
BSD 3-Clause "New" or "Revised" License
55 stars 28 forks source link

Sparse utils #253

Closed mortonjt closed 6 years ago

mortonjt commented 6 years ago

This adds support for sparse data manipulation, namely

Depends on #250

mortonjt commented 6 years ago

There are some really weird errors going on with nose, making it difficult to get this functionality in.
@antgonza , @ElDeveloper any idea what is going on? I'm able to produce this on my laptop, but not sure why nose is behaving this way.

ElDeveloper commented 6 years ago

From the looks of the travis output, the problem does not seem to be coming from nose, it seems to becoming from the coverage tool. It appears to be interpreting that --with-doctest is an argument for setup.py. Later on setup.py errors as that's not an available option. I would try changing the makefile to enclose nose --with-doctest in single-quotes or use a double-hyphen to separate the positional arguments i.e ..... setup.py -- nose --with-doctest. If that doesn't work then I don't have any other ideas. ¯\_(ツ)_/¯

coveralls commented 6 years ago

Coverage Status

Coverage decreased (-0.4%) to 96.193% when pulling 7798aa17974543bb07a3a55d8d0390d0f60c8fc3 on mortonjt:sparse-utils into 52edad92f511b0f020b4df53df43cf941b465fef on biocore:master.

mortonjt commented 6 years ago

Alright - it looks like the tests are passing. If there aren't any issues with this PR, I'll be merging this in over the next few days.

What do you think @antgonza ?

antgonza commented 6 years ago

Wanna add test so the coverage doesn't decrease?

mortonjt commented 6 years ago

@antgonza thanks for catching that -- there were actually a couple of nasty bugs that would have slipped through if it weren't for that test. It should be ok now.

antgonza commented 6 years ago

Kewl, any idea why coveralls didn't run this time?

mortonjt commented 6 years ago

That's strange. Let's restart it

On Thu, Jun 7, 2018, 6:12 PM Antonio Gonzalez notifications@github.com wrote:

Kewl, any idea why coveralls didn't run this time?

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