Simplealign

[yinjun111]

Hi, Chris,

This is my implementation of Bio::SimpleAlign. I have a detailed report describing the improvement to the code, and explaining the failed tests using t/Align/SimpleAlign.t. If you need any help, please just let me know.

Cheers,
Jun

[hyphaltip]

Oops - comments from me not a student in my class...

So this currently fails in the travis build -- can someone comment about what it will take to fix it.
Where is the detailed report on what was added Jun - is it in the code or in a mail to the mailing list?

[yinjun111]

I have send the update log to Chris Fields, who was my mentor during my coding project in Google summer of code. I think I can put the update log in the BioPerl wiki, so everybody can see it. If you pull the new SimpleAlign code, you will expect some failed tests from t/Align/SimpleAlign.t, you will see the explanation in the report.

[yinjun111]

See the wiki page for details of the updates:
http://www.bioperl.org/wiki/SimpleAlign_Updates#Abstract

[jhannah]

Without objection I'll be reviewing and merging the 3 open github pull requests this week.

[yinjun111]

Hi, Jay,

I notice that there is no revision on the SimpleAlign code for the last few months. So this implementation should work without problem using the SimpleAlign2.t provided. Let me know if you need any clarification.

Cheers,
Jun

[cjfields]

We have failing Travis-CI at the moment, so hold off on a merge. We're planning on a new point release of BioPerl 1.6.x in about 1 month, we might want to wait before merging this one in.

[cjfields]

Jun, after a long long wait I'm finally getting around to reviewing these. I've pulled them into a separate branch from master and will merge back in after checking tests.

[yinjun111]

Hi, Chris,

You will have some errors from the old t/Align/SimpleAlign.t. You can try t/Align/SimpleAlign2.t, which is edited to test the new Bio::SimpleAlign

[cjfields]

I saw the errors. Do you recall whether these are failing b/c the implementation details changed, or where the tests erroneous to begin with?

[yinjun111]

These are mainly caused by different implementation of several methods. The changes are listed in the BioPerl wiki.
http://www.bioperl.org/wiki/SimpleAlign_Updates#Abstract

[mohawk2]

Is there any appetite for me to rebase this and submit as a new PR?

[yinjun111]

Thank you for looking into this PR. This project was done almost 14 years ago. There may not be any real value in merging it into the main repo. But let me know if you are still interested. Jun

…

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[cjfields]

@mohawk2 @yinjun111 despite the age it's still completely feasible to merge this in since tests exist. My recommendation would be to work off either a new branch or the original one, rebase to the current master, then make sure any changes are in place for at least some minimal supported version of perl.

In addition, if the original SimpleAlign tests are breaking we need to consider renaming the newer module something else since it would be a breaking API change for the original SimpleAlign and anyone using it (which is stunningly quite a bit of code out there). That shouldn't be too hard, and we could in effect work towards deprecating the original module in place of this one.