23 Commits

Author	SHA1	Message	Date
Samuel Sledzieski	c21dee6059	Ruff check and format	2025-08-12 14:05:49 +02:00
Samuel Sledzieski	103eab70b2	update to use biotite for version 0.3.1	2025-08-12 14:05:49 +02:00
Samuel Sledzieski	c7682041e2	update foldseek commands to use biotite interface	2025-08-12 14:05:49 +02:00
Samuel Sledzieski	92bff2b530	skip gpu tests if gpu not available	2025-07-22 11:27:35 -04:00
Samuel Sledzieski	349a4ae0ee	one day I will remember to lint	2025-07-22 11:18:00 -04:00
Samuel Sledzieski	132291da55	added tests for bipartite prediction and fixed silent failure causing hanging	2025-07-22 11:10:42 -04:00
Samuel Sledzieski	fa467edd40	formatting and cleaning device code	2025-07-22 10:00:20 -04:00
Samuel Sledzieski	0215215a1f	I forgot to run the linter	2025-07-21 17:03:40 -04:00
Samuel Sledzieski	6b2cbac3d6	slight update to testing to not run gpu test on gh actions	2025-07-21 16:59:38 -04:00
Samuel Sledzieski	9f21e01f0b	add broader device support	2025-07-21 16:53:25 -04:00
Samuel Sledzieski	2cd60a892b	edit to pass tests	2025-07-21 16:20:47 -04:00
Samuel Sledzieski	e80af9d123	formatting	2025-07-21 14:44:37 -04:00
Samuel Sledzieski	f7073f5c16	fix security issues	2025-07-21 14:40:26 -04:00
Samuel Sledzieski	8cbf288b86	massively increase test coverage and continuous integration	2025-07-21 14:21:48 -04:00
samsledje	5b95875b98	change language_model.py to use with h5py context	2022-08-26 14:56:34 -04:00
samsledje	988c1b35ff	update language model to fix issue #35	2022-08-18 12:10:32 -04:00
samsledje	2dcf240101	add topsy turvy pretrained model to api and docs	2022-08-18 11:32:07 -04:00
samsledje	f4b9b1f961	This file is tab separated, not comma separated. act like it.	2022-06-28 11:48:32 -04:00
samsledje	dfbc81829f	use biopython for fasta io	2022-06-23 13:36:06 -04:00
samsledje	bec4b6fd0e	update command testing	2022-06-23 12:40:27 -04:00
samsledje	bf688400f1	update testing	2022-06-23 12:18:45 -04:00
samsledje	1b63b008fd	testing embed, evaluate, predict	2022-06-23 11:58:23 -04:00
samsledje	b9e49336dc	fix issue relating to pretrained models and updated model arguments/parameters	2022-02-11 12:20:30 -05:00