bugfix: 0 read fasta raised an error instead of continue

[amnona]

following move to scikit-bio, when encountering a 0 read file (after msa), deblur raised an error instead of continuing with a warning. fixed to write a warning and continue (so samples with 1 read will not stop the deblurring)

[mortonjt]

Looks like there is a failing test

[amnona]

oops. forgot to fix the unittest. should work now (test warn instead of raise)

[coveralls]

Coverage increased (+0.08%) to 89.412% when pulling dc9ce06e68ba12bfafd44012c949bc0fe771d915 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.

[amnona]

ok, now passes all checks :)

[amnona]

Also, can we push this change to the pip install (and bump up the version :) )

[mortonjt]

I'd hold off on the pip install - it gets confusing if there are too many releases. Looks like the change is rather small - so I'd suggest waiting until a whole bunch of patches are made to shoot off another release.

And the dev version is still pip installable via

pip install git+https://github.com/biocore/deblur.git

So it won't be a problem pip installing the dev version. This can be added to the readme if necessary.

[mortonjt]

good to merge once comments are addressed

[mortonjt]

Forgot to mention.

Now we are post alpha release, it is advantageous to start squashing commits. It'll simplify the process of debugging using tools such as git bisect.

You can do this by

git rebase -i 675f7fb
# rebase all commits except the first commit with `squash`
git push -f

Note that this is optional, but it will clean up the commit history.

[wasade]

Can a change log mention be added please?

[amnona]

Fixed (except specific warn msg text testing in unit_test) tried to squash (not sure it worked)

[amnona]

Since this is a BUGFIX, i think we should immediately update the pip (since the version is already out). Don't see any advantage in waiting?

[coveralls]

Coverage increased (+0.1%) to 89.437% when pulling 53922d50998ee7cc8c3a597ed8de98c20b573e33 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.

[wasade]

@amnona, do you perceive this as impacting most users or just a small percent? If the latter, then we might want to hold off another few days to see if any other bugs pop up which we should fix immediately.

[coveralls]

Coverage increased (+0.1%) to 89.437% when pulling 4585d7bac3c9a6f9ee0939858cd270ed831f3631 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.

[coveralls]

Coverage increased (+0.1%) to 89.437% when pulling 102f99bd637fdf324317bf4b0085651478473731 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.

[coveralls]

Coverage increased (+0.1%) to 89.437% when pulling 102f99bd637fdf324317bf4b0085651478473731 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.

[amnona]

ready for merge :)

[coveralls]

Coverage increased (+0.1%) to 89.437% when pulling f20fee3c7f98cfd45c3403833cec40417bfb4d66 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.

[coveralls]

Coverage increased (+0.1%) to 89.437% when pulling bcfeb2b27c4719d7f3c4dc778641d34f5db698a9 on amnona:develop into 675f7fbbbd5a79b319ae8264d4c5fb6986fb676c on biocore:master.