MHCflurry 0.9 - Githubissues

openvax / mhcflurry

Peptide-MHC I binding affinity prediction

http://openvax.github.io/mhcflurry/

Apache License 2.0

193 stars 58 forks source link

MHCflurry 0.9 #86

Closed timodonnell closed 7 years ago

timodonnell commented 7 years ago

This is a rewrite of MHCflurry to support our new better-performing class1 single-allele architectures. It includes downloadable models using the new architectures. The code is much simpler and more compact than what we had before. I've updated the README and the example notebook to show the new interfaces. I've also written / verified docstrings for most methods.

Once this gets a bit of use (and perhaps we setup read the docs integreation with some autogenerated documentation), I think we can call it 1.0.

coveralls commented 7 years ago

Coverage decreased (-4.2%) to 75.628% when pulling 0d72da0586d1c14db3582627795df1edd7d5beb4 on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

coveralls commented 7 years ago

Coverage decreased (-4.1%) to 75.689% when pulling e5a7ee9453588bd92660d71ae7e9d841dcf3a3a0 on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

coveralls commented 7 years ago

Coverage decreased (-4.09%) to 75.702% when pulling 04c85f27d0710e2ff60d7e759e908fa8b4cf4c5c on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

coveralls commented 7 years ago

Coverage decreased (-4.03%) to 75.763% when pulling 6b1e94d5b741de2b2575753e0bc56fa699f55cb6 on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

coveralls commented 7 years ago

Coverage decreased (-4.03%) to 75.763% when pulling 6b1e94d5b741de2b2575753e0bc56fa699f55cb6 on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

coveralls commented 7 years ago

Coverage decreased (-4.03%) to 75.763% when pulling 6b1e94d5b741de2b2575753e0bc56fa699f55cb6 on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

coveralls commented 7 years ago

Coverage decreased (-4.2%) to 75.55% when pulling 62794808d64fe09580fee3ee30577d5bbc8f1587 on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.

timodonnell commented 7 years ago

@iskandr and I did an in person code review

Also noting:

Fixes #78 - no more imputation
Fixes #76 - new index encoding implementation
Fixes #72
Fixes #70 - now works with both keras backends
Fixes #66
Fixes #61 - switched to mhcnames
Fixes #58
Fixes #44 - much simpler set of fit methods, which are documented
Fixes #6 - full data + qualitative data using a simple transformation strategy worked best, which is what we do now

Also just added a commit to make the change suggested in PR #79 for windows compatibility

coveralls commented 7 years ago

Coverage decreased (-4.3%) to 75.458% when pulling 503c84924c1dfe939139b7520513c92374e8c44c on rewrite1 into f8d13fc0c439ee390229abf08f9a7c7e24e232f9 on master.