Minor fixes: added 2 spaces and QuartetNetwork docstring #135
Conversation
crsl4
commented
Aug 3, 2020
crsl4
commented
- Adding 2 spaces that were removed by emacs in this commit
- Created the docstring for QuartetNetwork
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This is unrelated to the docstring, but it would be good to include a formal test for the changes to By the way, the chunk of code repeated in |
Codecov Report
@@ Coverage Diff @@
## master #135 +/- ##
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+ Coverage 84.35% 84.56% +0.21%
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Files 28 28
Lines 10311 10770 +459
==========================================
+ Hits 8698 9108 +410
- Misses 1613 1662 +49
Continue to review full report at Codecov.
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yes, I agree! There is a lot of things that I want to re-write on this checkRoot situation. It is in my to-do list, but it needs some time to sit down and focus that I have not had. I will put my notes on an issue. |
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just to see how coverage had decreased after adding the two chunks to check that root is admissible: on codecov |
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To get more detail on code that was added but is not covered during testing: see in I need to fix a bug in the function that direct edges, because that function should return an error if the network is not a DAG. I would like to work from a clean |
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We also need to take care of the DataStructure update (PR #137). I would love for this PR to be finished, and make progress on the other things. |
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Sorry Cecile! I was waiting for you to merge the pull request. I got lost whether there was something missing here. By reading again, are we mainly missing the |
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Yes we should include them in this PR. Otherwise, we will never do it. We should also fix the documentation errors (Travis says "it's all good" in its summary, but when we look at what happened, there were errors.) I'm working on fixing the doc errors right now. |
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It looks like the random number generator has changed, in julia v1.4 vs v1.5... causing more errors in the doc. and probably a lot more in the tests... |
- stick to 80-character lines in markdown docstring - example using random seeds modified (julia v1.5) - tests & doc build under julia v1.5 and Documenter v0.25 - doc fix in coefficient outputs, to match format by GLM v1.3.10
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ok! to make sure I am on the same page: we need a test for the new |
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both ideally. I see that the tests are broken with julia v1.5, see starting here (including a conflict between our own |
limit what LinearAlgebra is brough into scope, because of its rotate! in v1.5 fixed tests based on RNG
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ahh.. the tests that were affected by the change in the RNG pass on julia v1.5 but break on julia v1.4, or vice versa. So we can't ask Travis to test both under julia v1.4 and v1.5 successfully. I would like to cancel the tests that are currently running (for commit e60f7f6) but I don't have permission. |
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sorry that you do not have permission to cancel them! I think we tried before to give you these permissions, but I cannot find the option in travis. sorry also that I am getting a bit lost (and slow) in this PR! I will pull your changes, and add the new tests. Please let me know if I am missing something |
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@cecileane how do I know if the coverage increased with these two new commits? I added the tests and tested locally on julia 1.5. But I do not know how to check the coverage. |
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After all the tests are done, you can go over to coveralls for PhyloNetworks, say, then pick a commit that was tested, follow the link to know more about coverage and coverage change due to this commit like here, then click on any file (like readwrite)to see the changes to this file, and what's covered or not. Codecov has another report, which I find a little easier to use. Like here for the current pull request. (click on Files then browse to see coverage for each file). |
