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Author SHA1 Message Date
richard gowers
987009e607 fixup manifest for new test files v0.11.0 2023-07-06 09:29:37 +01:00
richard gowers
23cb438fa7 rfe_protocol execute forbids oechem backend 2023-07-06 08:40:43 +01:00
richard gowers
fa8730826b add without_oechem_backend 2023-07-06 08:40:43 +01:00
richard gowers
516a3aeb55 allow gathering of legacy results 2023-07-05 18:22:21 +01:00
richard gowers
916695fa87 fix gather entry order 
also sort leg types in gather
 2023-07-03 10:52:40 +01:00
richard gowers
8c99d03941 remove a debug line 2023-07-03 10:52:40 +01:00
richard gowers
1ad3e41143 add tyk2 tutorial tests 2023-07-03 10:52:40 +01:00
richard gowers
8af9335f32 add tyk2 test files 2023-07-03 10:52:40 +01:00
richard gowers
2632760e75 fixes gather command 2023-07-03 10:52:40 +01:00
Mike Henry
d01856d244 added CoC 2023-06-30 16:40:20 +01:00
richard gowers
6bce2f4d8a silence a warning about types 2023-06-27 17:50:54 +01:00
richard gowers
98f761116c fixup warning about element changes 2023-06-27 17:50:54 +01:00
IAlibay
ddc4d55d5a fix up a few things 2023-06-27 17:50:54 +01:00
IAlibay
ae831f2910 Handle trajectories, now with unit cells 2023-06-27 17:50:54 +01:00
IAlibay
2d81dbfe7d switch to mdtraj for writing out the PDB file 2023-06-27 17:50:54 +01:00
IAlibay
83e347a82c a bit more coverage 2023-06-27 17:50:54 +01:00
IAlibay
4ef455fbd9 Add test for subsample topology 2023-06-27 17:50:54 +01:00
IAlibay
8e1083c04a typo 2023-06-27 17:50:54 +01:00
IAlibay
1c43086b8a some people like continue 2023-06-27 17:50:54 +01:00
IAlibay
4b90dbd223 Remove passing chainid to addChain 2023-06-27 17:50:54 +01:00
IAlibay
c4438a1b4b Update token 2023-06-27 17:50:54 +01:00
IAlibay
4c5493d678 Add extra vacuum tests 2023-06-27 17:50:54 +01:00
IAlibay
d0306ca114 Fix omm_topology writing, fix mdtraj_topology creation, some refactoring 2023-06-27 17:50:54 +01:00
IAlibay
eb80f8283e list to set to just sets 2023-06-27 17:50:54 +01:00
IAlibay
d1e53ff0d4 Add PDB serialization 2023-06-27 17:50:54 +01:00
David W.H. Swenson
a8c0c92058 Reconfigure stdout to be line-buffered in quickrun 2023-06-26 11:36:07 +01:00
David W.H. Swenson
23e3a2be71 Sort while running gather 
It seems that the order things get listed in gather is arbitrary,
making it very annoying compare results from two users. Sorting
will fix.
 2023-06-26 11:16:05 +01:00
David W.H. Swenson
2a67e35e5b Merge pull request #471 from slochower/typo 
Fix minor typo
 2023-06-23 13:19:38 -05:00
David Slochower
9e6766ee78 Fix minor typo 2023-06-23 10:48:05 -07:00
richard gowers
0c9703f086 use -C for cofactors input 
allow multiple cofactor files
 2023-06-22 13:00:32 +01:00
richard gowers
2bb19f0ad3 exclude slow test from coverage 2023-06-22 13:00:32 +01:00
richard gowers
87ccf5757b strip out most of the eg5 ligands 
speeds up cli tests
 2023-06-22 13:00:32 +01:00
richard gowers
b052d22c34 fix mypy complaints 2023-06-22 13:00:32 +01:00
richard gowers
c7a291a51e fixup slow test 2023-06-22 13:00:32 +01:00
richard gowers
bf14794ebe add test for cofactor containing system through cli 2023-06-22 13:00:32 +01:00
richard gowers
c87e53fdac add eg5 moist test 2023-06-22 13:00:32 +01:00
richard gowers
ff513e484a add eg5 test files 2023-06-22 13:00:32 +01:00
richard gowers
69b8bd947a mypy type annotations 2023-06-22 13:00:32 +01:00
richard gowers
588b80554c make cofactors optional in builder functions 2023-06-22 13:00:32 +01:00
richard gowers
65e527dcb4 RANPlanner: fixup tests around planning 2023-06-22 13:00:32 +01:00
richard gowers
da229b5757 RANPlanner: fixup calls to EasyChemicalSystemGenerator 
must include (possibly no) cofactors
 2023-06-22 13:00:32 +01:00
richard gowers
f5435cf0fd RANPlanner: remove red herring in abstract method 2023-06-22 13:00:32 +01:00
richard gowers
3abaf55849 plumb in cofactors to rbfe cli 2023-06-22 13:00:32 +01:00
richard gowers
be3b512364 add COFACTORS to cli parameters 2023-06-22 13:00:32 +01:00
richard gowers
620210cb0f WIP adding cofactors to CLI 2023-06-22 13:00:32 +01:00
David W.H. Swenson
a38a06e6cc CodeCov only on PR 2023-06-21 20:11:20 +01:00
David W.H. Swenson
2991e0f77f Actually fix silence_root_logging (#467) 2023-06-21 07:26:31 -07:00
Irfan Alibay
a49a2d8e1a Merge pull request #466 from OpenFreeEnergy/pin_units 
Pin units - same thing as in gufe
 2023-06-20 12:10:00 +01:00
Irfan Alibay
768bd58ed3 Update environment.yml 2023-06-20 11:50:23 +01:00
Mike Henry
a19b64b523 also update docker to python 3.10 2023-06-20 05:59:22 +01:00