63 Commits

Author	SHA1	Message	Date
samsledje	e3428d1613	Resolve merge	2022-08-18 12:27:49 -04:00
Mert Erden	e4adc459a3	enhancement: added typing documentation & automatic retrying for corrupted models	2022-06-29 14:09:44 -04:00
samsledje	f588d257fa	merge main into dev -- there is still clean up to do for sure	2022-06-24 20:32:07 -04:00
Samuel Sledzieski	1b598e4762	Update glider-thresh argument help string ... "threshold beyond which GLIDER scores treated as positive edges (0 < gt < 1) (default: 0.925)"	2022-06-24 19:33:56 -04:00
samsledje	e148390f7f	load embeddings in parallel	2022-06-23 16:06:22 -04:00
samsledje	dfbc81829f	use biopython for fasta io	2022-06-23 13:36:06 -04:00
samsledje	6000faccfb	fix training script	2022-06-23 12:03:39 -04:00
samsledje	1b63b008fd	testing embed, evaluate, predict	2022-06-23 11:58:23 -04:00
samsledje	ea41becbb6	update gitignore, logging, and docs	2022-06-23 11:38:08 -04:00
samsledje	78ca8aad61	clean up docs	2022-04-29 10:44:20 -04:00
samsledje	ceca25a2c2	update documentation	2022-04-29 10:15:04 -04:00
samsledje	aa855550b8	Merge master into topsy turvy	2022-04-29 09:58:13 -04:00
Samuel Sledzieski	970e909f3a	Update evaluate.py	2022-04-12 18:06:22 -04:00
samsledje	431946f19f	Merge remote-tracking branch 'origin/main' into topsyturvy	2022-03-07 17:44:14 -05:00
samsledje	57bc2fa4d4	fixed how cpu mapping works	2022-03-07 15:17:35 -05:00
samsledje	2caf7712f5	tt cleaning	2022-03-07 14:51:44 -05:00
samsledje	f2429adeaa	initial topsy turvy port	2022-03-07 13:42:10 -05:00
samsledje	b052dbe30e	fix issue relating to pretrained models and updated model arguments/parameters	2022-02-11 11:55:55 -05:00
samsledje	71f9e52ff5	pull main into dev	2022-02-08 13:02:15 -05:00
samsledje	a82dd7d6b8	code style updated with black	2022-02-08 12:00:11 -05:00
samsledje	65ebd2381e	training seems to be fixed, require a few more cleaning passes and tests before publishing	2022-02-07 12:56:32 -05:00
samsledje	45d693bc2d	updated docstrings from legacy code	2021-12-07 12:18:38 -05:00
samsledje	df4e1bf729	0.1.7-dev7 -- training fixed but code extremely messy	2021-12-07 11:46:13 -05:00
samsledje	f186227bd3	saving	2021-10-18 16:02:44 -04:00
samsledje	3fa7ea685f	v0.1.6 Fixed bug in data augmentation	2021-09-06 13:18:27 -04:00
samsledje	12316914bf	update code	2021-09-06 12:47:35 -04:00
Samuel Sledzieski	5666ff6e54	add preload functionality to evaluate and predict	2021-09-01 19:40:40 -05:00
Samuel Sledzieski	8a82e329a7	update missed import	2021-09-01 18:37:49 -05:00
Samuel Sledzieski	c5851d1173	update logging and commands	2021-09-01 18:29:04 -05:00
Samuel Sledzieski	3872f70b60	update print statments to log statements	2021-08-15 20:14:19 -05:00
Samuel Sledzieski	f8c59cf694	begin to migrate data to lightning	2021-08-15 20:12:18 -05:00
Samuel Sledzieski	31e04375b5	updating tests and beginning lightning transition	2021-08-15 20:07:38 -04:00
Samuel Sledzieski	d2c76f3549	fixing precommit hooks	2021-07-04 17:48:02 -04:00
Samuel Sledzieski	5247099818	black formatting	2021-07-04 10:48:05 -04:00
Samuel Sledzieski	ce3b82e937	updated logging and imports in commands	2021-07-03 23:03:59 -04:00
Samuel Sledzieski	8a55490180	Use sensible defaults for epoch and epoch scale ... epoch: 100 -> 10 epoch_scale: 5 -> 1	2021-06-24 13:49:33 -04:00
Samuel Sledzieski	1fd94ed7c4	fixed issue #12, not fully tested but should work	2021-06-23 21:48:47 -04:00
Samuel Sledzieski	1db0b84e5b	fixed inconsistency in data augmentation	2021-06-23 20:45:23 -04:00
Samuel Sledzieski	e66a95d768	updated package level imports	2021-04-23 10:09:04 -04:00
Samuel Sledzieski	894edfeaa5	fixed logging code to flush file and to not write # at beginning	2021-02-17 10:23:25 -05:00
Samuel Sledzieski	6918c98239	added logging functionality and use it to report skips in predict.py	2021-02-17 10:02:08 -05:00
Samuel Sledzieski	e59ef6c78f	updated arguments to be internally consistent	2021-02-17 10:01:20 -05:00
Samuel Sledzieski	8fb5ba266f	fixed format string	2021-02-16 13:43:03 -05:00
Samuel Sledzieski	f58763efa4	if pair is too large that leads to runtime error, skip and report error instead of breaking	2021-02-16 13:24:24 -05:00
Samuel Sledzieski	2bce0cdbb4	fixed wrong variable name in loading from sequence file	2021-02-03 10:26:00 -05:00
Samuel Sledzieski	dc04e373e3	put model in eval mode before making new predictions	2020-11-30 15:58:43 -05:00
Sam Sledzieski	25020a76b8	Clarify updated prediction usage	2020-11-18 15:25:30 -05:00
Samuel Sledzieski	c253373788	updated prediction and evaluation bugs, pretrained model loading	2020-11-18 14:31:22 -05:00
Samuel Sledzieski	3328f3bf0c	update prediction module to save cmaps	2020-11-17 12:11:22 -05:00
Samuel Sledzieski	e365a6a74d	updated installation instructions, bug fixing on commands	2020-11-17 11:46:19 -05:00