74 Commits

Author	SHA1	Message	Date
Samuel Sledzieski	52ea92959c	transition documentation theme and streamline	2025-12-04 15:55:13 -05:00
Daniel E. Schaffer	8ffe2906af	Update documentation	2025-09-08 23:37:36 +02:00
Daniel E. Schaffer	ba68c6ceb1	Update documentation w/ examples and links	2025-09-08 23:37:36 +02:00
Daniel E. Schaffer	8fdb4d4b2e	Update device argument to embed and predict_serial	2025-09-08 23:37:36 +02:00
Samuel Sledzieski	33f2d08600	downgrade to biotite 1.2.0 for gh actions consistency	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	b0b9ff1434	update documentation	2025-08-12 11:49:25 +02:00
Samuel Sledzieski	b45ce88db8	fix underlines	2025-08-12 11:35:11 +02:00
Samuel Sledzieski	80c034ae79	update api for new predict commands	2025-08-12 11:31:31 +02:00
Samuel Sledzieski	312407e7fd	update docs	2025-08-12 11:16:32 +02:00
Samuel Sledzieski	132291da55	added tests for bipartite prediction and fixed silent failure causing hanging	2025-07-22 11:10:42 -04:00
Daniel E. Schaffer	92f1582719	Extend CPU support to bipartite	2025-07-21 19:28:52 -04:00
Daniel E. Schaffer	f13926a718	Improve CPU mode	2025-07-21 18:58:51 -04:00
Samuel Sledzieski	2cd60a892b	edit to pass tests	2025-07-21 16:20:47 -04:00
Samuel Sledzieski	faad88d684	Merge branch 'main' into parallel	2025-07-21 14:52:13 -04:00
Samuel Sledzieski	8cbf288b86	massively increase test coverage and continuous integration	2025-07-21 14:21:48 -04:00
Daniel E. Schaffer	7ddbbea10c	Correct default model; move file check to main	2025-07-21 13:13:33 -04:00
Daniel E. Schaffer	875ff4af82	Change loading process defaults	2025-07-21 12:29:58 -04:00
Daniel Schaffer	abbce8c1fb	Update usage.rst	2025-07-21 10:39:27 -04:00
Daniel Schaffer	7f6c368151	Update usage.rst	2025-07-18 15:29:48 -04:00
Samuel Sledzieski	2f4c222717	Update documentation to explain hfh	2024-09-13 11:06:30 -04:00
samsledje	5cefd93122	Add tt3d pretrained model	2023-07-31 12:44:48 -04:00
samsledje	2dcf240101	add topsy turvy pretrained model to api and docs	2022-08-18 11:32:07 -04:00
Samuel Sledzieski	a49759174f	Delete docs/source/_build/html directory	2022-06-24 10:21:23 -04:00
samsledje	bec4b6fd0e	update command testing	2022-06-23 12:40:27 -04:00
samsledje	6000faccfb	fix training script	2022-06-23 12:03:39 -04:00
samsledje	ea41becbb6	update gitignore, logging, and docs	2022-06-23 11:38:08 -04:00
samsledje	e883489d03	update docs and citations	2022-06-23 10:19:16 -04:00
samsledje	78ca8aad61	clean up docs	2022-04-29 10:44:20 -04:00
samsledje	39848bb98c	rtd	2022-04-29 10:36:47 -04:00
samsledje	03781b3701	trying to fix rtd	2022-04-29 10:30:58 -04:00
samsledje	ceca25a2c2	update documentation	2022-04-29 10:15:04 -04:00
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
Samuel Sledzieski	30c3654f24	Update index.rst	2021-11-08 16:54:00 -05:00
samsledje	3fa7ea685f	v0.1.6 Fixed bug in data augmentation	2021-09-06 13:18:27 -04:00
Samuel Sledzieski	69bc09e8eb	updated link to preprint in docs	2021-04-23 10:08:24 -04:00
Samuel Sledzieski	9dc847fda7	added links to ecoli data to docs	2021-03-06 10:47:18 -05:00
Samuel Sledzieski	78cf91183c	removed duplicate pytorch requirement in docs	2021-02-17 10:09:37 -05:00
Samuel Sledzieski	7c2c473f5d	updated documentation for 0.1.3	2021-02-17 09:53:52 -05:00
Samuel Sledzieski	9d54338f09	Update installation.rst	2020-11-18 16:29:21 -05:00
Sam Sledzieski	25020a76b8	Clarify updated prediction usage	2020-11-18 15:25:30 -05:00
Sam Sledzieski	4aac90a4f8	Fixed linking typos	2020-11-18 15:19:34 -05:00
Sam Sledzieski	fe88711c61	Provided links to data and pre-trained models	2020-11-18 15:09:36 -05:00
Sam Sledzieski	8be2dca037	Updated installation	2020-11-18 14:50:21 -05:00
Sam Sledzieski	83fefb6cac	Merge branch 'main' of https://github.com/samsledje/D-SCRIPT into main	2020-11-18 14:42:29 -05:00
Sam Sledzieski	e4a0c80f83	Move prediction to be more prominent	2020-11-18 14:42:26 -05:00
Samuel Sledzieski	974230138f	Merge branch 'main' of github.com:samsledje/D-SCRIPT into main	2020-11-18 14:40:46 -05:00
Samuel Sledzieski	96a437ac5f	fixed typo in automodule	2020-11-18 14:40:34 -05:00