hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
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Require Python 3 #208

Closed tavinathanson closed 7 years ago

tavinathanson commented 7 years ago

No longer support Python 2, including:

Also update 2016 to 2017 in files.

I figured we should go all out and not allow Python 2 usage at all if we're no longer testing with Python 2. Otherwise, issues like str vs. unicode resulting in the wrong number of patients in the Cohort will be highly likely.

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-0.4%) to 56.907% when pulling 0c5addc88163ffce221c364c87fcf31d6159085f on drop_py2 into d61000550096002a6aed9b7aef475f0c53feb199 on master.

tavinathanson commented 7 years ago

@jburos I think I addressed your comments, lmk!

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-0.4%) to 56.907% when pulling 1c2b64a059b6aea25d4ae9aa8fe28157d7796945 on drop_py2 into d61000550096002a6aed9b7aef475f0c53feb199 on master.

tavinathanson commented 7 years ago

@jburos turns out pysam 0.9.0, which we conda install in Travis (https://github.com/hammerlab/cohorts/pull/49#issuecomment-225646603), requires 3.4.

So, instead, I made it >= 0.9.0 and also added pysam to our requirements.txt (since we do directly use it now). I also removed 3.3 from Travis, since no current version of pysam on Conda appears to support 3.3.

Hopefully that'll all work.

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-0.4%) to 56.907% when pulling 5dbb485aff0f755d61c08ded7721d991bc9d5621 on drop_py2 into d61000550096002a6aed9b7aef475f0c53feb199 on master.

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-0.4%) to 56.907% when pulling 5dbb485aff0f755d61c08ded7721d991bc9d5621 on drop_py2 into d61000550096002a6aed9b7aef475f0c53feb199 on master.