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Author SHA1 Message Date
Samuel Sledzieski
1a382651a6 update information on contribution workflow 2021-08-15 19:02:09 -05:00
Samuel Sledzieski
d597f67f5f Merge branch 'main' of github.com:samsledje/D-SCRIPT into dev 2021-08-12 10:36:22 -04:00
Samuel Sledzieski
054d4388c8 updated human training and test data 2021-08-12 10:35:58 -04:00
Samuel Sledzieski
f86605b3a0 rm old tests 2021-07-05 09:45:17 -04:00
Samuel Sledzieski
b3e7b691d2 moved test location and added test config 2021-07-05 09:44:50 -04:00
Samuel Sledzieski
27d5a138aa update pre-commit config 2021-07-05 09:39:39 -04:00
Samuel Sledzieski
7527d6c621 added test directory 2021-07-04 21:00:35 -04:00
Samuel Sledzieski
d2c76f3549 fixing precommit hooks 2021-07-04 17:48:02 -04:00
Samuel Sledzieski
e928480741 checking pre-commit hooks 2021-07-04 10:58:14 -04:00
Samuel Sledzieski
1aaceb2280 pre-commit 2021-07-04 10:55:54 -04:00
Samuel Sledzieski
5247099818 black formatting 2021-07-04 10:48:05 -04:00
Samuel Sledzieski
8f7c234583 remove ipynb checkpoints 2021-07-03 23:05:48 -04:00
Samuel Sledzieski
62fe3f035e pretrained uses download or local function 2021-07-03 23:04:53 -04:00
Samuel Sledzieski
580c023def move paired dataset to datamodules 2021-07-03 23:04:34 -04:00
Samuel Sledzieski
ce3b82e937 updated logging and imports in commands 2021-07-03 23:03:59 -04:00
Samuel Sledzieski
854349dc2a wrote datamodule for loading paired sequences from embeddings 2021-07-03 23:03:31 -04:00
Samuel Sledzieski
c736383143 Merge main into dev 2021-07-01 18:07:47 -04:00
Samuel Sledzieski
8a55490180 Use sensible defaults for epoch and epoch scale 
epoch: 100 -> 10
epoch_scale: 5 -> 1
v0.1.5 		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
7e773be9cb update changelog and init for 0.1.5 2021-06-23 20:45:37 -04:00
Samuel Sledzieski
1db0b84e5b fixed inconsistency in data augmentation 2021-06-23 20:45:23 -04:00
Samuel Sledzieski
9c2dc101a0 Updated CHANGELOG.md 2021-04-23 10:17:22 -04:00
Samuel Sledzieski
0f0065b3ea added changelog 2021-04-23 10:15:46 -04:00
Samuel Sledzieski
e66a95d768 updated package level imports 2021-04-23 10:09:04 -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
799781ec3a Added ecoli test pairs and sequences to /data 2021-03-06 10:44:27 -05:00
Samuel Sledzieski
7034c880a1 Bug fix issue #7 - typo in ContactModule.forward() v0.1.4 2021-03-05 10:14:17 -05:00
Samuel Sledzieski
894edfeaa5 fixed logging code to flush file and to not write # at beginning v0.1.3 2021-02-17 10:23:25 -05:00
Samuel Sledzieski
78cf91183c removed duplicate pytorch requirement in docs 2021-02-17 10:09:37 -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
7c2c473f5d updated documentation for 0.1.3 2021-02-17 09:53:52 -05:00
Samuel Sledzieski
8fb5ba266f fixed format string 2021-02-16 13:43:03 -05:00
Samuel Sledzieski
6e312bfa66 Merge branch 'main' of github.com:samsledje/D-SCRIPT into main 2021-02-16 13:24:57 -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
73eb5d250f Update README.md 2021-01-26 13:18:01 -05:00
Samuel Sledzieski
793035359b added dev branch 2020-11-30 21:42:50 -05:00
Samuel Sledzieski
dc04e373e3 put model in eval mode before making new predictions v0.1.2 2020-11-30 15:58:43 -05:00
Samuel Sledzieski
d2759bca5c Merge branch 'main' of github.com:samsledje/D-SCRIPT into main 2020-11-24 11:32:35 -05:00
Samuel Sledzieski
4ff927a06b updated versioning 2020-11-24 11:32:12 -05:00
Samuel Sledzieski
1a604d980b Update setup.py 2020-11-24 11:27:05 -05:00
Samuel Sledzieski
898a9aeef1 Update __init__.py 2020-11-24 11:26:42 -05:00
Samuel Sledzieski
9d54338f09 Update installation.rst 2020-11-18 16:29:21 -05:00
Samuel Sledzieski
1218ebf584 Update README.md 2020-11-18 16:17:29 -05:00
Samuel Sledzieski
4b35b52516 Update LICENSE 2020-11-18 16:16:08 -05:00
Samuel Sledzieski
ba2af3e796 Update README.md 2020-11-18 15:59:19 -05:00
Samuel Sledzieski
dd9a51aa70 Update README.md v0.1.1 2020-11-18 15:57:02 -05:00
Samuel Sledzieski
7c3d006070 Update README.md 2020-11-18 15:56:32 -05:00