Upgrade infrastructure: Python 3.6, Travis CI, compression, and tag ordering

greenelab / pubtator

Retrieve and process PubTator annotations

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Upgrade infrastructure: Python 3.6, Travis CI, compression, and tag ordering #10

Closed dhimmel closed 7 years ago

dhimmel commented 7 years ago

Switch to Python 3.6

Some usabilty / bug fixes. See individual commits.

Add Travis CI.

Sorry this PR is so large, I just kind of got rolling.

Still a work in progress. Will assign reviewers when complete.

dhimmel commented 7 years ago

Added a script (execute.sh) to run download and process the entire pubtator in 6862a91.

dhimmel commented 7 years ago

@danich1 this PR is now ready for you to review. I'd suggest looking through each commit and making sure you understand why I made the changes. If not just leave a comment.

Once this is approved, I suggest we make a merge commit rather than a squash commit, since these commits are quite diverse.

And sorry for grouping so many things together... this is not an ideal PR!