faster modisco

[MuhammedHasan]

Hi @austintwang,

I created faster version of modisco with extra feature and we are using this version in our package: https://github.com/Genentech/decima.

Copying the original PR from modisco-lite repo: jmschrei/tfmodisco-lite#75

"""
Hi @jmschrei,

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

jmschrei/tfmodisco-lite@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.
jmschrei/tfmodisco-lite@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 jmschrei/tfmodisco-lite#45
jmschrei/tfmodisco-lite@c0f38c6 multiprocessing for reporting: Multi-threading for reporting step which runs tomtom for each pattern
jmschrei/tfmodisco-lite@5e85b03 add support for calling only positive or negative patterns
jmschrei/tfmodisco-lite@bd274ef stranded modisco. fixes jmschrei/tfmodisco-lite#69 and fixes jmschrei/tfmodisco-lite#57
jmschrei/tfmodisco-lite@96e2ba4 progressbar for numba functions steps with thread safe accumulator
Let me know if you have further comments.
"""

[austintwang]

Hi @MuhammedHasan, thanks for making all these improvements!

Reiterating @jmschrei's comments—it would be great to split this into multiple PRs given the scale of the changes. The unit tests and CLI refactor would be a good one to start with. Feel free to start multiple PRs in parallel too.

[MuhammedHasan]

See #126. Hoping that this smaller PRs more digestible for review.