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  • 36577435c8 separate train loss reporting (#96) tt3d_new focitti 2026-02-19 12:05:22 -08:00
  • 23cbb0fbbb Claude/expand test coverage (#95) main Samuel Sledzieski 2026-01-06 13:01:16 -05:00
  • 7c9dc61a8c add coverage text file claude/expand-test-coverage-01LESFRdKZ3cgtzyfhKfzto4 Samuel Sledzieski 2026-01-06 12:45:24 -05:00
  • 8a34c606de Add .coverage to .gitignore Claude 2026-01-06 17:29:51 +00:00
  • 5563d41e30 Add test coverage report for easy reference Claude 2026-01-06 17:28:59 +00:00
  • cf18d26875 Update model saved to W&B (#93) focitti 2025-12-22 13:48:07 -08:00
  • bf21437b13 add artifact for wandb and fix checkpoint loads Samuel Sledzieski 2025-12-17 15:07:34 -05:00
  • 9b1b12c1f2 update training to use wandb Samuel Sledzieski 2025-12-17 15:04:09 -05:00
  • 220ace1b2c first pass at updating training script to incorporate backbone (#88) focitti 2025-12-17 10:14:43 -08:00
  • 1bed6a048a Claude/expand test coverage (#91) Samuel Sledzieski 2025-12-16 10:24:04 -05:00
  • 2892c9dacc Merge remote-tracking branch 'origin' into claude/expand-test-coverage-01LESFRdKZ3cgtzyfhKfzto4 Samuel Sledzieski 2025-12-16 10:18:34 -05:00
  • 4bbb641a12 Update .github/workflows/autorun-tests.yml Samuel Sledzieski 2025-12-16 10:15:24 -05:00
  • 8ff7402c9a Update .github/workflows/autorun-tests.yml Samuel Sledzieski 2025-12-16 10:15:03 -05:00
  • 80cadd191f transition documentation theme and streamline Samuel Sledzieski 2025-12-04 15:55:13 -05:00
  • d9ab262851 adjust embedding for other files haozhaoyun 2025-12-13 21:45:34 -05:00
  • 6d96553b2f Remove new bash haozhaoyun 2025-12-01 14:20:59 -05:00
  • 43a4f69e45 format parallel file haozhaoyun 2025-11-29 14:31:28 -05:00
  • 29781fe70a parallel loading haozhaoyun 2025-11-29 14:20:22 -05:00
  • 0121884275 Update train.py to build embeddings haozhaoyun 2025-11-17 12:11:33 -05:00
  • 52ea92959c transition documentation theme and streamline update-documentation Samuel Sledzieski 2025-12-04 15:55:13 -05:00
  • 0b1d9e5007 fix failing tests Samuel Sledzieski 2025-12-04 15:13:52 -05:00
  • 09c2bea9b2 Rewrite test_language_model.py to use mocks instead of real model Claude 2025-12-04 13:59:35 +00:00
  • 38783e8628 Fix test_load_worker.py hanging issue in CI Claude 2025-12-04 13:52:12 +00:00
  • 680b44974a Fix linting issues and apply code formatting Claude 2025-12-03 20:37:10 +00:00
  • 701f217feb Add comprehensive tests for command modules and worker functions Claude 2025-12-02 22:15:16 +00:00
  • 4766b9684e Merge remote-tracking branch 'origin/main' into claude/expand-test-coverage-01LESFRdKZ3cgtzyfhKfzto4 Claude 2025-12-02 22:07:26 +00:00
  • 3a8b7eaab1 Rename CLAUDE.md to AGENTS.md Claude 2025-12-02 19:58:50 +00:00
  • 6275047aaf Add comprehensive CLAUDE.md development guide Claude 2025-12-02 19:48:38 +00:00
  • c79c9d63a9 Expand test coverage with comprehensive test suites Claude 2025-12-02 20:00:32 +00:00
  • ceed729243 remove duplicate sequence files Samuel Sledzieski 2025-10-24 09:23:42 -04:00
  • 0711b284a2 Update references Daniel Schaffer 2025-10-11 22:34:00 -04:00
  • bcf2ab083e satisfy ruff check Daniel E. Schaffer 2025-09-08 14:15:46 -04:00
  • 9e58dad665 ruff format Daniel E. Schaffer 2025-09-08 14:12:55 -04:00
  • 8ffe2906af Update documentation Daniel E. Schaffer 2025-09-08 14:10:25 -04:00
  • 0eec268d79 Add utility scripts from BMPI benchmarking Daniel E. Schaffer 2025-09-05 21:10:07 -04:00
  • ba68c6ceb1 Update documentation w/ examples and links Daniel E. Schaffer 2025-09-05 20:32:04 -04:00
  • 8fdb4d4b2e Update device argument to embed and predict_serial Daniel E. Schaffer 2025-09-05 20:04:40 -04:00
  • 0b3f7363b7 update and add pre-commits v0.3.1 Samuel Sledzieski 2025-08-12 08:00:48 -04:00
  • c21dee6059 Ruff check and format Samuel Sledzieski 2025-08-12 07:56:57 -04:00
  • 33f2d08600 downgrade to biotite 1.2.0 for gh actions consistency Samuel Sledzieski 2025-08-12 07:54:55 -04:00
  • 103eab70b2 update to use biotite for version 0.3.1 Samuel Sledzieski 2025-08-12 07:47:32 -04:00
  • c7682041e2 update foldseek commands to use biotite interface Samuel Sledzieski 2025-08-12 07:13:10 -04:00
  • c92b333928 update and add pre-commits biotite-foldseek Samuel Sledzieski 2025-08-12 08:00:48 -04:00
  • 4032d7adbf Ruff check and format Samuel Sledzieski 2025-08-12 07:56:57 -04:00
  • ef77296335 downgrade to biotite 1.2.0 for gh actions consistency Samuel Sledzieski 2025-08-12 07:54:55 -04:00
  • d987f23750 update to use biotite for version 0.3.1 Samuel Sledzieski 2025-08-12 07:47:32 -04:00
  • 642068f1d8 update foldseek commands to use biotite interface Samuel Sledzieski 2025-08-12 07:13:10 -04:00
  • 36c735113d Merge pull request #79 from samsledje/update-documentation Samuel Sledzieski 2025-08-12 12:15:11 +02:00
  • 10587a4249 fix documentation Samuel Sledzieski 2025-08-12 06:10:15 -04:00
  • c0a4c1a84b fix glider docstring Samuel Sledzieski 2025-08-12 11:53:32 +02:00
  • b0b9ff1434 update documentation Samuel Sledzieski 2025-08-12 11:49:25 +02:00
  • b45ce88db8 fix underlines Samuel Sledzieski 2025-08-12 11:35:11 +02:00
  • 80c034ae79 update api for new predict commands Samuel Sledzieski 2025-08-12 11:31:31 +02:00
  • 40af63c2ff use newer version of artifact upload Samuel Sledzieski 2025-08-12 11:25:18 +02:00
  • 7d4693aa82 Update doc building and testing Samuel Sledzieski 2025-08-12 11:23:45 +02:00
  • 312407e7fd update docs Samuel Sledzieski 2025-08-12 11:16:32 +02:00
  • da5e37dd27 Update requirements.txt Samuel Sledzieski 2025-08-12 11:09:16 +02:00
  • 09515c17e9 Update .readthedocs.yml Samuel Sledzieski 2025-08-12 11:05:13 +02:00
  • 3ed5a17236 Update .readthedocs.yml Samuel Sledzieski 2025-08-12 11:00:50 +02:00
  • b1957f109b Delete .flake8 v0.3.0 Samuel Sledzieski 2025-07-22 11:44:48 -04:00
  • 482642f5c5 Update README.md Samuel Sledzieski 2025-07-22 11:42:49 -04:00
  • b982d04d4b Merge pull request #75 from schafferde/parallel Samuel Sledzieski 2025-07-22 11:34:27 -04:00
  • 92bff2b530 skip gpu tests if gpu not available Samuel Sledzieski 2025-07-22 11:27:35 -04:00
  • 349a4ae0ee one day I will remember to lint Samuel Sledzieski 2025-07-22 11:18:00 -04:00
  • ca3453a604 Merge pull request #78 from samsledje/readme-badges Samuel Sledzieski 2025-07-22 11:13:27 -04:00
  • 132291da55 added tests for bipartite prediction and fixed silent failure causing hanging Samuel Sledzieski 2025-07-22 11:10:42 -04:00
  • e2a4792091 minor cleanup Samuel Sledzieski 2025-07-22 10:10:41 -04:00
  • fa467edd40 formatting and cleaning device code Samuel Sledzieski 2025-07-22 10:00:20 -04:00
  • f3734661df Update autorun-tests.yml readme-badges Samuel Sledzieski 2025-07-22 09:52:39 -04:00
  • da38469bf7 Update README.md Samuel Sledzieski 2025-07-22 09:51:53 -04:00
  • 92f1582719 Extend CPU support to bipartite Daniel E. Schaffer 2025-07-21 19:26:33 -04:00
  • f13926a718 Improve CPU mode Daniel E. Schaffer 2025-07-21 18:58:51 -04:00
  • cd10a97607 Update minimum pytorch version Daniel E. Schaffer 2025-07-21 18:20:11 -04:00
  • 0215215a1f I forgot to run the linter Samuel Sledzieski 2025-07-21 17:03:40 -04:00
  • 6b2cbac3d6 slight update to testing to not run gpu test on gh actions Samuel Sledzieski 2025-07-21 16:59:38 -04:00
  • 3fe16083f4 Merge Samuel Sledzieski 2025-07-21 16:58:16 -04:00
  • 9f21e01f0b add broader device support Samuel Sledzieski 2025-07-21 16:53:25 -04:00
  • 854985b787 try/except for local model loading Daniel E. Schaffer 2025-07-21 16:52:49 -04:00
  • 2cd60a892b edit to pass tests Samuel Sledzieski 2025-07-21 16:20:47 -04:00
  • 50f3d9750e ruff formatting and linting Samuel Sledzieski 2025-07-21 15:09:08 -04:00
  • faad88d684 Merge branch 'main' into parallel Samuel Sledzieski 2025-07-21 14:52:13 -04:00
  • 58cd401b1c Merge pull request #77 from samsledje/modernization Samuel Sledzieski 2025-07-21 14:47:49 -04:00
  • e80af9d123 formatting Samuel Sledzieski 2025-07-21 14:44:37 -04:00
  • f7073f5c16 fix security issues Samuel Sledzieski 2025-07-21 14:40:26 -04:00
  • 777aeff58f update coverage Samuel Sledzieski 2025-07-21 14:34:45 -04:00
  • 5b9e836fa7 update default model to load from huggingfce for predict or eval Samuel Sledzieski 2025-07-21 14:33:17 -04:00
  • f4bfcd824f migrate to loguru while maintaining lecacy interface Samuel Sledzieski 2025-07-21 14:31:12 -04:00
  • 8cbf288b86 massively increase test coverage and continuous integration Samuel Sledzieski 2025-07-21 14:21:48 -04:00
  • a1f4af2e65 Refactor csv Daniel E. Schaffer 2025-07-21 13:21:11 -04:00
  • ff72bc3fb8 Restore two lines (incorrectly deleted) Daniel E. Schaffer 2025-07-21 13:14:36 -04:00
  • 7ddbbea10c Correct default model; move file check to main Daniel E. Schaffer 2025-07-21 13:13:33 -04:00
  • 875ff4af82 Change loading process defaults Daniel E. Schaffer 2025-07-21 12:29:58 -04:00
  • 6ecae4ed8f Change loading process defaults Daniel E. Schaffer 2025-07-21 12:25:15 -04:00
  • de7707d3f8 Remove log file from GPU process Daniel E. Schaffer 2025-07-21 12:21:36 -04:00
  • 4b83b3a205 Create python-publish.yml Samuel Sledzieski 2025-07-21 11:11:22 -04:00
  • 00bf586858 Update README.md Samuel Sledzieski 2025-07-21 10:50:55 -04:00
  • f3c592396f Merge pull request #76 from samsledje/weights_only_loading Samuel Sledzieski 2025-07-21 10:44:21 -04:00
  • 01125ef013 Update predict.py weights_only_loading Samuel Sledzieski 2025-07-21 10:39:38 -04:00
  • abbce8c1fb Update usage.rst Daniel Schaffer 2025-07-21 10:39:27 -04:00
  • c1b88c909f Update evaluate.py Samuel Sledzieski 2025-07-21 10:38:35 -04:00