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• 4c7cdd414f Merge branch 'membrane_prototype' of https://github.com/OpenFreeEnergy/openfe into membrane_prototype hannahbaumann 2025-11-12 14:56:24 +01:00
• 4d7da119e7 Add tests for system creation hannahbaumann 2025-11-12 14:56:17 +01:00
• 3e6b0631fa Apply suggestion from @hannahbaumann Hannah Baumann 2025-11-12 13:33:39 +01:00
• 5d5bc8e721 Some fixes in SepTop to fix tests hannahbaumann 2025-11-12 13:15:06 +01:00
• 19761df2e8 Revert box changes hannahbaumann 2025-11-12 11:07:11 +01:00
• 1f408fc8f0 Remove some prints hannahbaumann 2025-11-12 11:06:19 +01:00
• e67ecd2c9b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-11-12 10:01:49 +00:00
• e53512b250 Merge branch 'main' into membrane_prototype Hannah Baumann 2025-11-12 11:01:07 +01:00
• 741e44c0cb First pass at ABFE membrane prototype hannahbaumann 2025-11-12 10:57:22 +01:00
• 8780ddcf4d add TODOs ruff/unused-variables Alyssa Travitz 2025-11-11 17:12:41 -07:00
• 36481541e9 add ruff formatting commits to git-blame-ignore-revs (#1669) Alyssa Travitz 2025-11-11 16:32:33 -07:00
• 5a5df90060 addressing unused variables Alyssa Travitz 2025-11-11 16:04:12 -07:00
• b693d37c8a ruff: address pycodestyle changes (#1668) Alyssa Travitz 2025-11-11 11:34:29 -07:00
• 18f211db97 ruff linting: f-strings and whitespace (#1667) Alyssa Travitz 2025-11-10 17:19:12 -07:00
• 588f552ca9 add ruff isort linting rule (#1665) Alyssa Travitz 2025-11-10 14:58:30 -07:00
• 339a9edbaf Test box vectors SepTop more hannahbaumann 2025-11-10 17:06:29 +01:00
• 6e4023d072 Change box vector units for handling membrane barostat hannahbaumann 2025-11-10 11:15:35 +01:00
• 12e1f9d531 Test example notebooks on demand (#1613) Mike Henry 2025-11-09 18:16:05 -07:00
• aa83a6194e Update conda pkg test + test to see if it catches missing files (#1630) Mike Henry 2025-11-09 15:20:37 -07:00
• d46db57e32 expose the septop and abfe analysis tutorials (#1664) Irfan Alibay 2025-11-07 15:25:27 +00:00
• c27bfa599d refactor: rename to WarehouseBaseClass (#1660) Ethan Holz 2025-11-06 16:37:05 -07:00
• 44e3545fe6 Add membrane test septop hannahbaumann 2025-11-06 16:05:21 +01:00
• 7a640ce6bc [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-11-06 13:49:38 +00:00
• a33d882b95 Merge branch 'main' into membrane_prototype Hannah Baumann 2025-11-06 14:41:05 +01:00
• 508fa62818 Some small fixes hannahbaumann 2025-11-06 13:19:57 +01:00
• 27d15f7b0c Move changes in solvent validation to validate_solvent hannahbaumann 2025-11-06 13:14:13 +01:00
• 872c914312 Change validation solvent hannahbaumann 2025-11-06 10:51:49 +01:00
• bf51b0c02e First pass membrane support for SepTop protocol hannahbaumann 2025-11-06 10:16:52 +01:00
• 9be9f877bd gzip the 6CZJ (#1659) Irfan Alibay 2025-11-05 00:00:37 +01:00
• 1e707ba74e Merge branch 'main' into membrane_prototype Hannah Baumann 2025-11-04 13:31:37 +01:00
• 728a6810b3 Create Pooch Cache (#1647) Mike Henry 2025-11-03 09:12:08 -07:00
• e12164b442 refactor: remove result_server references in favor of gufe ExternalStorage (#1632) Ethan Holz 2025-11-03 08:56:53 -07:00
• 8888b5d88f Merge branch 'main' into feat/vendor-perses-atom-mapper feat/vendor-perses-atom-mapper Mike Henry 2025-10-31 11:43:54 -07:00
• e654a4dfb1 Merge branch 'main' into membrane_prototype Hannah Baumann 2025-10-31 13:39:17 +01:00
• fcf0229c89 allow ci to run on all branches, not just main (#1649) Alyssa Travitz 2025-10-30 16:43:51 -07:00
• a7c68fdfc3 add workflow_dispatch event trigger for cleaning up cache by branch (#1644) Alyssa Travitz 2025-10-30 11:31:22 -07:00
• 0873b26591 Merge branch 'main' into fix/pytest-warnings fix/pytest-warnings Alyssa Travitz 2025-10-30 08:12:28 -07:00
• 2913994ccb support membrane in gather hannahbaumann 2025-10-30 10:01:56 +01:00
• 932f9f0b8b Fix import error from pr# 1640 (#1642) Mike Henry 2025-10-29 17:13:08 -07:00
• 2c03c8933d [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-10-29 23:03:29 +00:00
• 386fafee5a fmt Mike Henry 2025-10-29 15:59:08 -07:00
• a804f3bcf4 Merge branch 'main' into feat/vendor-perses-atom-mapper Mike Henry 2025-10-29 14:49:20 -07:00
• 0a5265fa65 Switch to using skip_if_missing (#1640) Mike Henry 2025-10-29 14:48:51 -07:00
• 31eac86677 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-10-29 17:52:40 +00:00
• a30b32bb88 Forgot to commit these extra files Mike Henry 2025-10-29 10:52:10 -07:00
• fa721aa932 Merge remote-tracking branch 'refs/remotes/origin/feat/vendor-perses-atom-mapper' into feat/vendor-perses-atom-mapper Mike Henry 2025-10-29 10:51:32 -07:00
• 87b020773a make it clear the copyright of the file Mike Henry 2025-10-29 10:51:25 -07:00
• 09defb1da9 Merge branch 'main' into feat/vendor-perses-atom-mapper Mike Henry 2025-10-29 10:39:11 -07:00
• 5bfe636cb4 use requires_oe_module since we don't need perses anymore Mike Henry 2025-10-29 10:38:43 -07:00
• 7f28a0d837 make vendor code and classes a private namespace Mike Henry 2025-10-29 09:57:53 -07:00
• e1f30757f3 add bit to news blurb this is an internal change Mike Henry 2025-10-29 09:56:56 -07:00
• 2c1dd42338 Revert "format and rename" refactor/septop-gather Alyssa Travitz 2025-10-29 09:54:34 -07:00
• 6595689c04 MBAR uncertainty Alyssa Travitz 2025-10-29 08:41:21 -07:00
• 0fc8de7b20 update docstring Alyssa Travitz 2025-10-28 18:41:49 -07:00
• 0e97297aad format and rename Alyssa Travitz 2025-10-28 18:14:39 -07:00
• 25b8b3c84c Revert "MBAR uncertainty" Alyssa Travitz 2025-10-29 09:46:39 -07:00
• c094241f8f Merge branch 'main' into feat/cli-septop-gather Alyssa Travitz 2025-10-29 08:42:09 -07:00
• a346ad65df remove planning stub Alyssa Travitz 2025-10-29 08:41:51 -07:00
• bf32aa3c6e MBAR uncertainty Alyssa Travitz 2025-10-29 08:41:21 -07:00
• b492de0114 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-10-29 09:53:01 +00:00
• 48a78445a0 Small fixes hannahbaumann 2025-10-29 10:10:09 +01:00
• 080d93e45a Temporarily use branches for openmmtools and openmmforcefield hannahbaumann 2025-10-29 10:05:08 +01:00
• 9dce0e0fe6 Merge conflicts hannahbaumann 2025-10-29 09:47:19 +01:00
• 5c313b1956 Small fix hannahbaumann 2025-10-29 09:44:48 +01:00
• c53fd6046a Merge branch 'main' into membrane_prototype Hannah Baumann 2025-10-29 09:44:10 +01:00
• e48d6410c4 store 6CZJ.pdb in git repo (#1634) Alyssa Travitz 2025-10-28 18:16:41 -07:00
• 433b23b5aa condense code a bit Alyssa Travitz 2025-10-28 18:07:49 -07:00
• dd9bd2c5ac pull more error handling into septop Alyssa Travitz 2025-10-28 17:20:10 -07:00
• f36ab6657f don't need perses anymore Mike Henry 2025-10-28 16:57:07 -07:00
• 7a52d95a57 fix imports and logging Mike Henry 2025-10-28 16:56:51 -07:00
• e438ef11f7 tests pass for dg cli/add_septop_support Alyssa Travitz 2025-10-28 16:55:41 -07:00
• d6db0f2834 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-10-28 23:53:47 +00:00
• 690deb4abd test passes for ddg Alyssa Travitz 2025-10-28 16:48:05 -07:00
• cbcfa63609 add missing import Mike Henry 2025-10-28 16:52:34 -07:00
• fe04d9c31b add news entry Mike Henry 2025-10-28 16:51:02 -07:00
• 9c737f27ed update to f-string syntax Mike Henry 2025-10-28 16:45:23 -07:00
• 27a41469a3 use vendored perses atom mapper and scorer Mike Henry 2025-10-28 16:44:40 -07:00
• 36146370e9 update docs for what needs to be installed for the perses atom mapper Mike Henry 2025-10-28 16:40:51 -07:00
• f9d446b1cb Add atom_mapping.py, still need to wire it in Mike Henry 2025-10-28 16:38:41 -07:00
• 940092122c test passes for gather raw Alyssa Travitz 2025-10-28 16:30:25 -07:00
• eff57ab31d fix type hints in gather.py Alyssa Travitz 2025-10-28 16:20:20 -07:00
• 77665aaa70 clean up imports Alyssa Travitz 2025-10-28 16:16:09 -07:00
• 53c16a884f pin openmm to <8.3 (#1633) Alyssa Travitz 2025-10-28 16:03:59 -07:00
• d52b01bd37 add cli tmp Alyssa Travitz 2025-10-28 16:03:22 -07:00
• da5e03a07f comment out secondary tests Alyssa Travitz 2025-10-28 15:36:52 -07:00
• d426d1ffae add failing tests Alyssa Travitz 2025-10-28 14:18:00 -07:00
• bd548a19e0 format Alyssa Travitz 2025-10-28 13:54:18 -07:00
• f493f8f7d9 add plan and test Alyssa Travitz 2025-10-15 08:37:06 -07:00
• 7986a4f39c add todos Alyssa Travitz 2025-10-15 08:36:52 -07:00
• 584008e3f1 copy septop analysis notebook over Alyssa Travitz 2025-10-15 07:48:35 -07:00
• 7b585fec5d add yaml syntax check precommit hooks (#1567) Alyssa Travitz 2025-10-28 08:08:50 -07:00
• 1152edd752 Only run itergration tests on AWS GPU and CPU runners (#1538) Mike Henry 2025-10-27 11:36:07 -07:00
• fdea483f1c pin to python < 3.14 in pyproject.toml maint/upper_pin_python Alyssa Travitz 2025-10-27 10:19:26 -07:00
• fe2d11c479 add git-blame-ignore-revs for large formatting PRs (#1609) Alyssa Travitz 2025-10-27 08:59:12 -07:00
• d55d90cd8b Try to make this work properly net_charge_abfe IAlibay 2025-10-26 20:23:15 +00:00
• fddad37cec Merge branch 'net_charge_abfe' of github.com:OpenFreeEnergy/openfe into net_charge_abfe IAlibay 2025-10-25 23:46:25 +01:00
• 2631f721d0 Add custom restraint defn IAlibay 2025-10-25 23:46:00 +01:00
• 4866ba3b78 Merge branch 'main' into net_charge_abfe Irfan Alibay 2025-10-25 17:29:27 +01:00
• 036869ae81 Ci/add ruff format part4 - the final format! (#1623) Alyssa Travitz 2025-10-24 16:50:52 -07:00
• d7196d119e Ci/add ruff format part3 (#1622) Alyssa Travitz 2025-10-24 14:44:21 -07:00