faster tfmodisco-lite

[MuhammedHasan]

Hi @jmschrei,

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

• 381cf298ff7587fd2090641a6de50c0dbd952bdf 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.
• f7f5b94234f1ecf78cec6cdd2fb7ddbef2b7912a logging and progress bars added: Logging and progress bars are added. You can check how long each step is taking with improved logging. fixes https://github.com/jmschrei/tfmodisco-lite/issues/45
• c0f38c6b974865f5d6598dd9f8c1141175949ad4 multiprocessing for reporting: Multi-threading for reporting step which runs tomtom for each pattern
• 5e85b03b5081ceb446cc8e269364c35e96a7aef2 add support for calling only positive or negative patterns
• bd274ef6d77b0dca66a701e9bb8c93729be467a4 stranded modisco. fixes https://github.com/jmschrei/tfmodisco-lite/issues/69 and fixes https://github.com/jmschrei/tfmodisco-lite/pull/57
• 96e2ba4cd3d191a94ec195388e741342ba5e643a 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 https://github.com/jmschrei/tfmodisco-lite/pull/60#issuecomment-3224149495 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.