reorganizing commandline interface to resemble mhctools and other hammerlab Python tools - Githubissues

openvax / topiary

Predict mutated T-cell epitopes from sequencing data

Apache License 2.0

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reorganizing commandline interface to resemble mhctools and other hammerlab Python tools #76

Closed iskandr closed 6 years ago

iskandr commented 6 years ago

In preparation for making other more substantive changes to Topiary (e.g. allowing use of Isovar) I wanted to first reorganize Topiary to resemble the same structure as our other Python libraries (e.g. mhctools).

commandline_args renamed to cli
Instead of topiary Python script, it's now a console entry point contained in topiary.cli.script
from __future__ import print_function, division, absolute_import at top of each module
Getting rid of copyright years since they're a pain to keep updating
Moved predict_epitopes_from_args to cli. Any functions that deal with args objects should be in cli.

This change is

coveralls commented 6 years ago

Coverage decreased (-4.3%) to 87.273% when pulling f4072ab76aa021f49f59cd394b7d443b001f20b2 on refactor-cli-to-match-other-python-repos into a39d835e1b0b7aceee8df103a258ebcdd7c8afc0 on master.

coveralls commented 6 years ago

Coverage decreased (-4.3%) to 87.273% when pulling f4072ab76aa021f49f59cd394b7d443b001f20b2 on refactor-cli-to-match-other-python-repos into a39d835e1b0b7aceee8df103a258ebcdd7c8afc0 on master.

coveralls commented 6 years ago

Coverage decreased (-4.3%) to 87.273% when pulling f4072ab76aa021f49f59cd394b7d443b001f20b2 on refactor-cli-to-match-other-python-repos into a39d835e1b0b7aceee8df103a258ebcdd7c8afc0 on master.

coveralls commented 6 years ago

Coverage decreased (-4.3%) to 87.273% when pulling f4072ab76aa021f49f59cd394b7d443b001f20b2 on refactor-cli-to-match-other-python-repos into a39d835e1b0b7aceee8df103a258ebcdd7c8afc0 on master.

coveralls commented 6 years ago

Coverage decreased (-4.3%) to 87.273% when pulling d0ccc3c3cd54a8dab0a614c152bfd4d613d1e24f on refactor-cli-to-match-other-python-repos into a39d835e1b0b7aceee8df103a258ebcdd7c8afc0 on master.