faster tfmodisco-lite

[MuhammedHasan]

Hi @jmschrei,

See the number of features implemented for faster modisco-lite where each commit implements one feature:

• 381cf29 unit tested and cli refactored with click: See the unit-test which check results are exactly same with original. You can rerun this test-case in each downstream commits to confirm results are exactly same.
• f7f5b94 logging and progress bars added: Logging and progress bars are added. You can check how long each step is taking with improved logging. fixes --verbose is still rather taciturn #45
• c0f38c6 multiprocessing for reporting: Multi-threading for reporting step which runs tomtom for each pattern
• 5e85b03 add support for calling only positive or negative patterns
• bd274ef stranded modisco. fixes This isn't a bug....its a feature request.....can one turn off the reverse complement #69 and fixes Make reverse complementing optional #57
• 96e2ba4 progressbar for numba functions steps with thread safe accumulator

Let me know if you have further comments.

[jmschrei]

Hi @MuhammedHasan. Thanks for taking the time to re-organize this. When I said breaking the PR into smaller chunks what I meant is breaking it into smaller PRs that can be individually merged. This significantly reduces reviewing burden.

[MuhammedHasan]

@jmschrei no problem, I will send each commit as PR. Let's start with #76.

[caenrigen]

@MuhammedHasan I just noticed your changes incorporated also the fix in #60 that you might have forgotten to mention. See my suggestion in #60 (comment) regarding fixing the default argument value too to preserve the previous behaviour.

[austintwang]

Hi @MuhammedHasan, tfmodisco-lite has been merged into the official TF-MoDISco repository. We encourage you to re-open your PR there.