Commit Graph

  • d1e3abe9d0 Update env structural_analysis_septop hannahbaumann 2026-06-02 12:15:58 +02:00
  • 62a34dcba2 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2026-06-02 09:34:23 +00:00
  • 53947857b7 fix mypy hannahbaumann 2026-06-02 11:33:50 +02:00
  • 850b1a5b9b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2026-06-02 09:12:14 +00:00
  • d9538480c2 Add tests for structural analysis hannahbaumann 2026-06-02 11:11:44 +02:00
  • 14ce7fd3ea Some updates hannahbaumann 2026-06-01 15:40:09 +02:00
  • 4f4f1a5a1e Merge branch 'membrane_charge_change' of https://github.com/OpenFreeEnergy/openfe into membrane_charge_change membrane_charge_change hannahbaumann 2026-06-01 10:18:24 +02:00
  • 2cb287af63 Address review comments hannahbaumann 2026-06-01 10:18:19 +02:00
  • e95adef8de DNM: testing pint maint/test_pint_0.25 Alyssa Travitz 2026-05-29 16:20:33 -07:00
  • e1c101ee73 Add ligand indices to test hannahbaumann 2026-05-29 14:53:30 +02:00
  • 54d4839253 Small fix hannahbaumann 2026-05-29 12:52:22 +02:00
  • 811a1b675a Fix complex alignment hannahbaumann 2026-05-29 12:42:02 +02:00
  • 14381f9abc Fix ligand indices mapping hannahbaumann 2026-05-29 09:43:22 +02:00
  • 18f2c72392 Merge branch 'main' into add/contributing add/contributing Alyssa Travitz 2026-05-28 08:14:26 -07:00
  • 00d3066752 Small fix hannahbaumann 2026-05-28 15:41:34 +02:00
  • 0ae11d9b7c Small fix hannahbaumann 2026-05-28 14:45:37 +02:00
  • b0538acead [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2026-05-28 10:06:16 +00:00
  • ea6e58a6ae First pass at adding structural analysis to the SepTop protocol hannahbaumann 2026-05-28 12:04:36 +02:00
  • cc48cbeaad Merge branch 'main' into membrane_charge_change Hannah Baumann 2026-05-22 18:10:44 +02:00
  • 9facb94274 add news item maint/remove_element_change_warning Alyssa Travitz 2026-05-22 08:38:07 -07:00
  • 7809d1e16b remove extraneous test Alyssa Travitz 2026-05-22 08:33:44 -07:00
  • a5e70f4986 Merge branch 'main' into maint/remove_element_change_warning Irfan Alibay 2026-05-21 19:57:57 +01:00
  • 53470827a4 Switch repeat id assignment from leg to repeat in AFE Protocols (#1948) main Irfan Alibay 2026-05-21 17:50:48 +01:00
  • f508d3442e [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2026-05-21 14:25:50 +00:00
  • 7f06c1cc54 Split of water and ion into separate functions hannahbaumann 2026-05-21 16:24:56 +02:00
  • f1ca989e92 Get ion parameters from ff if no ions present in system hannahbaumann 2026-05-21 15:47:39 +02:00
  • b32a57568f Merge branch 'main' into htf_speed htf_speed Josh Horton 2026-05-19 11:50:33 +01:00
  • 1c218a29ee [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2026-05-18 14:55:42 +00:00
  • 403d38e02f Initial test at what we may need to change to support charge changes for explicitly solvated systems hannahbaumann 2026-05-18 16:50:08 +02:00
  • cb10892e79 Updated CHANGELOG for 1.11.1 (#1973) v1.11.1 Alyssa Travitz 2026-05-01 19:32:51 -07:00
  • 311d821186 update example notebooks pin release/v1.11.0 Alyssa Travitz 2026-05-01 12:39:08 -07:00
  • 246c082353 docs: add blurb to release notes (#1970) Alyssa Travitz 2026-04-30 12:04:11 -07:00
  • fa74a35f02 speed up cli responsiveness (#1972) Alyssa Travitz 2026-04-30 11:33:13 -07:00
  • 3c83972143 fix typo in installation docs (#1971) Alyssa Travitz 2026-04-30 10:17:34 -07:00
  • d60fb8e5fe update installation restrictions (#1969) Alyssa Travitz 2026-04-29 14:04:21 -07:00
  • d911b11ea4 Merge branch 'main' into htf_speed Josh Horton 2026-04-29 11:40:39 +01:00
  • db379890b2 release prep for v1.11.0 (#1967) v1.11.0 Alyssa Travitz 2026-04-28 11:10:16 -07:00
  • dcebd36928 update comment in env Alyssa Travitz 2026-04-28 10:19:32 -07:00
  • e0a6c4b161 update example notebook tag Alyssa Travitz 2026-04-28 09:45:06 -07:00
  • cde06d42e1 Updated CHANGELOG for 1.11.0 Alyssa Travitz 2026-04-28 09:32:30 -07:00
  • 6f2154cb1d fix code formatting Alyssa Travitz 2026-04-27 14:16:07 -07:00
  • 7b6117e738 update release prep template Alyssa Travitz 2026-04-27 12:47:23 -07:00
  • 8828e13f0b add PR links Alyssa Travitz 2026-04-27 12:40:16 -07:00
  • 8601822716 Updated CHANGELOG for 1.11.0 Alyssa Travitz 2026-04-27 12:33:17 -07:00
  • 42562cbab7 Merge branch 'main' into htf_speed Josh Horton 2026-04-28 15:11:03 +01:00
  • 1acb1eb14d Merge branch 'main' into maint/remove_element_change_warning Hannah Baumann 2026-04-28 16:07:16 +02:00
  • 7bc31e1df5 Fix 1-4 interpolation for core-dummy interactions (#1856) Josh Horton 2026-04-28 15:05:48 +01:00
  • e599f413d0 Merge branch 'main' into maint/remove_element_change_warning Hannah Baumann 2026-04-28 09:37:06 +02:00
  • 82558ea7cd update changelog for perses deprecation planned in v1.12 (#1966) Alyssa Travitz 2026-04-27 12:29:20 -07:00
  • 403ecbd794 Add CLI septop gather tests for current SepTop AnalysisUnit behaviour (#1960) Irfan Alibay 2026-04-27 19:19:57 +01:00
  • 301cc71386 remove warning for element changes Alyssa Travitz 2026-04-27 11:08:59 -07:00
  • 8d229cffe3 membrane CLI support (#1896) Alyssa Travitz 2026-04-27 09:05:43 -07:00
  • dd7b9febbc Switch multistate data to use a specific version's DOI (#1959) Irfan Alibay 2026-04-27 17:01:24 +01:00
  • 909d29ad25 Plain MD restart support (#1884) Josh Horton 2026-04-27 16:04:28 +01:00
  • be6cd88414 Add resume support to SepTop (#1949) Irfan Alibay 2026-04-24 14:55:18 +01:00
  • fc6689eaf1 User guide updates membrane (#1933) Hannah Baumann 2026-04-24 14:03:06 +02:00
  • 90846148c9 update systems and components docs for completeness (#1954) Alyssa Travitz 2026-04-24 04:17:31 -07:00
  • e6dd981b11 Update resume data zenodo hash (#1957) Irfan Alibay 2026-04-24 11:33:08 +01:00
  • c81d27cf0d Add Analysis unit for Septop (#1937) Irfan Alibay 2026-04-24 10:00:06 +01:00
  • 7959cc6e74 Only warn if forces mismatch in hash check (#1914) Irfan Alibay 2026-04-22 18:21:59 +01:00
  • 8c088e7ada Rename Ashley Mitchell in CITATION.cff (#1951) Ashley Mitchell 2026-04-21 15:58:32 +10:00
  • f0a407497c Merge branch 'main' into htf_speed Hannah Baumann 2026-04-20 11:23:48 +02:00
  • 18a6f0ae1a update version update_authors Alyssa Travitz 2026-04-17 09:21:19 -07:00
  • 12f4210aec update authors in CITATION.cff Alyssa Travitz 2026-04-17 09:20:05 -07:00
  • ed1a016b3d Merge branch 'main' into remove_perses remove_perses Alyssa Travitz 2026-04-17 09:52:54 -05:00
  • b501e2ed3c Add validate method for SepTop (#1946) Irfan Alibay 2026-04-17 15:45:33 +01:00
  • 8cc206b937 remove perses atommapper and scorer Alyssa Travitz 2026-04-16 16:16:59 -07:00
  • 528a59764f Septop move files (#1932) Irfan Alibay 2026-04-16 21:06:27 +01:00
  • 0af4cab4ed Add membrane support to OpenFE Protocols (#1561) Hannah Baumann 2026-04-16 20:06:11 +02:00
  • 0978b4dd07 Mark espaloma test as xfail for issue #1940 (#1941) Irfan Alibay 2026-04-16 17:59:57 +01:00
  • c60db0685a SepTop: slightly refactor _execute calls (#1930) Irfan Alibay 2026-04-09 11:21:39 +01:00
  • fab07ca639 fix prepare message for RFE (#1915) Irfan Alibay 2026-04-08 21:04:15 +01:00
  • 7654820009 Add ahfe resume test to be integration (#1931) Irfan Alibay 2026-04-08 20:22:40 +01:00
  • 41f1684706 bump openmm to v8.4 (#1909) Alyssa Travitz 2026-04-07 14:26:54 -07:00
  • 5544db53f9 [pre-commit.ci] pre-commit autoupdate (#1916) pre-commit-ci[bot] 2026-04-07 09:09:50 -07:00
  • dd2ee4bbd2 Simplify how to install correct cuda-version (#1910) septop-resume Mike Henry 2026-04-01 10:27:26 -07:00
  • c2297d5a44 update links in PR templates (#1907) Alyssa Travitz 2026-03-31 07:42:38 -07:00
  • 09d629a199 ruff format code in docstrings (#1908) Alyssa Travitz 2026-03-31 07:27:22 -07:00
  • adb19162b5 Release v1.10.0 (#1902) v1.10.0 Alyssa Travitz 2026-03-30 16:07:38 -07:00
  • 8fcd47b4df Update the userguide CLI docs to mention resuming (#1878) Irfan Alibay 2026-03-30 22:47:02 +01:00
  • 2f2aa9e26d Fix typo in quickrun execution error message. (#1906) Irfan Alibay 2026-03-30 15:53:07 +01:00
  • ec0a1131ce CI: add feedstock build test (#1905) Alyssa Travitz 2026-03-30 07:33:00 -07:00
  • 456e9c40c1 unify CI runner naming conventions (#1904) Alyssa Travitz 2026-03-27 13:05:05 -07:00
  • a1e2273360 update feedstock CI test for v1 (#1900) Alyssa Travitz 2026-03-26 15:59:46 -07:00
  • a15edcc441 Modify quickrun to allow resuming (#1848) Irfan Alibay 2026-03-26 16:37:25 +00:00
  • 421c9a0aa7 min pin interchange (#1901) Alyssa Travitz 2026-03-26 07:09:26 -07:00
  • ad1033fe32 quickrun testing: check default filename creation (#1898) Alyssa Travitz 2026-03-25 14:33:13 -07:00
  • cd17b547b6 tests: migrate from using deprecated tmpdir to preferred tmp_path (#1873) Alyssa Travitz 2026-03-24 07:10:21 -07:00
  • 461bf6017e Fixing various typos (#1882) Irfan Alibay 2026-03-20 01:11:03 +00:00
  • c5a27ae226 update abfe test data (#1862) Alyssa Travitz 2026-03-19 14:41:10 -07:00
  • 81da72f393 Don't use the CUDA platform by default in tests (#1881) Irfan Alibay 2026-03-19 20:52:14 +00:00
  • ee5a558fbc Add resuming support in AFE Protocols (#1808) Irfan Alibay 2026-03-17 12:41:34 +00:00
  • d69baa614b Use GitHub API to fetch latest release/version (#1870) Mike Henry 2026-03-10 14:52:07 -07:00
  • 1055bd08dc Merge branch 'main' into htf_speed Alyssa Travitz 2026-03-10 08:45:01 -07:00
  • a72e1354bf [pre-commit.ci] auto fixes from pre-commit.com hooks v1.9.1dev0 pre-commit-ci[bot] 2026-03-09 18:28:13 +00:00
  • 028e4425b9 Merge branch 'main' into membrane_prototype Alyssa Travitz 2026-03-09 11:26:47 -07:00
  • 031e13ccd1 Add resume support to HybridTop simulation unit (#1774) Irfan Alibay 2026-03-09 16:12:35 +00:00
  • 375e26b61c Merge branch 'main' into membrane_prototype Irfan Alibay 2026-03-09 10:43:15 +00:00
  • 6c0ea0fdef small typing fix to make mypy happy (#1865) Alyssa Travitz 2026-03-06 11:49:39 -08:00
  • c2a6467548 Adapt gather RFE membrane component types hannahbaumann 2026-03-06 10:25:50 +01:00