What's Changed
- Fix sing file installer by @mikemhenry in #667
- Protocol to run plain MD simulations by @hannahbaumann in #516
- Set cache to expire after a day by @mikemhenry in #676
- Remove flatten torsions from HTF by @IAlibay in #684
- Expand water virtual site tests by @IAlibay in #680
- Fix barostat frequency passing by @IAlibay in #669
- Properly set the cutoff distance in HTF nonbonded forces by @IAlibay in #675
- Add cookbook entry for user charges by @IAlibay in #687
- Tokenizable atom mappers by @richardjgowers in #690
- Add devtools for json results generation + replace old ones by @IAlibay in #691
- updates to some code & tests following upstream changes by @richardjgowers in #696
- Adding LambdaSettings object for AFE by @hannahbaumann in #681
- Fix typo in README by @mattwthompson in #698
- Renaming and moving some of the protocol settings by @hannahbaumann in #689
- Solvation settings prep by @IAlibay in #695
- Switch settings input to protocol units to creating protocol itself. by @IAlibay in #700
- consequences of gufe #260 change by @richardjgowers in #666
- Fix devtools for #666 changes by @IAlibay in #707
- Add base partial charge setting things by @IAlibay in #706
- Fix checkpointing by @IAlibay in #719
- Add try/except for forward_backward analysis by @hannahbaumann in #721
- fixup scope of try/except around forward/backwards analysis by @richardjgowers in #724
- Add charge backends by @IAlibay in #598
- Doc drive 2 by @richardjgowers in #725
- Changelog automation by @mikemhenry in #728
- Change some MD settings by @hannahbaumann in #729
- Add MD equilibration for AFE calculations by @IAlibay in #720
- Create OutputSettings baseclass by @hannahbaumann in #732
- Change default settings lambda_restraints by @hannahbaumann in #735
- Document cli settings by @richardjgowers in #736
- Codecov and pre-commit ci config by @mikemhenry in #738
- Issue 592 alt radial options by @richardjgowers in #737
- Just don't install espaloma charge by @IAlibay in #763
- Fix Issue 683 by @mikemhenry in #767
- Change changelog title name by @IAlibay in #764
- Fixing API settings things by @IAlibay in #766
- docs: update badge on front page by @richardjgowers in #755
- Add warnings & docs for forward and reverse analysis getters by @IAlibay in #749
- Fix ahfe integration tests - missing restraints lamdas by @IAlibay in #750
- Add
NonTransformationto top level__init__.pyby @IAlibay in #754 - Checkpoint itnterval by @IAlibay in #773
- Some docstring fixes by @IAlibay in #775
- Docs userguide by @richardjgowers in #760
- Update fetch results by @richardjgowers in #779
- update LomapAtomMapper default settings to established best practices by @richardjgowers in #730
- Add an MD tutorial by @hannahbaumann in #731
- Clean up tutorials by @IAlibay in #782
- docs ligand networks by @RiesBen in #780
- Update CLI help docs by @IAlibay in #797
- docs: working with individual results page by @richardjgowers in #783
- docs setup intro page changes by @hannahbaumann in #812
- Issue 801 execution quickrun by @richardjgowers in #814
- Add alchemical network creation userguide page by @IAlibay in #808
- docs: fix links from top of each notebook by @richardjgowers in #822
- including comments from #793 by @RiesBen in #815
- FIx overlap matrix label issue by @IAlibay in #811
- fix to Protocol keys after off v2.1.1 bump in gufe base settings by @richardjgowers in #823
- Docs protocol cycles results by @richardjgowers in #787
- Add protocol details (hybrid topology, etc) to docs by @hannahbaumann in #776
- docs: chemical system theory by @richardjgowers in #785
- Don't dump all results to std out by @mikemhenry in #824
- added min hardware specs to install doc by @mikemhenry in #821
- added note about the GUFE package by @mikemhenry in #828
- don't test openfecli, it is flaky for some reason by @mikemhenry in #831
- docs: refresh docs landing page by @richardjgowers in #832
- docs: clarify long tests slightly by @richardjgowers in #834
- docs: first pass at working with networks page by @richardjgowers in #830
New Contributors
- @mattwthompson made their first contribution in #698
Full Changelog: v0.15.0...v1.0.0