jdrusso/msm_we issues and pull requests

#44 - Fixes to mamba env building in Actions

Pull Request - State: closed - Opened by jdrusso about 1 year ago - 1 comment

#43 - Merge develop

Pull Request - State: closed - Opened by jdrusso about 1 year ago

#42 - Add function for coarsening and plotting coarse flux profile

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#41 - Detect overcorrection

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#40 - Switch from Workers to Actors

Pull Request - State: open - Opened by SHZ66 over 1 year ago - 1 comment

#39 - Restart bstate weighting

Pull Request - State: closed - Opened by jdrusso over 1 year ago

#38 - Minor Assertion bug fix

Pull Request - State: closed - Opened by SHZ66 over 1 year ago - 2 comments

#37 - Parallelism assumes direct `west.h5` file access

Issue - State: open - Opened by jdrusso over 1 year ago - 1 comment
Labels: enhancement

#36 - Don't assume west.cfg filename

Issue - State: open - Opened by jdrusso over 1 year ago

#35 - Handle exceptions from already-augmented segments

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#34 - Rich-style progress bars, some improvements to dimensionality reduction and plugin config

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 2 comments

#33 - Implement ray + joblib for accelerated sklearn

Issue - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#32 - Rewrite clustering using Ray Actors

Issue - State: open - Opened by jdrusso over 1 year ago - 5 comments
Labels: enhancement

#31 - Added tests for optimization

Pull Request - State: closed - Opened by jdrusso over 1 year ago

#30 - Allow different optimizations at different iterations

Issue - State: open - Opened by jdrusso over 1 year ago
Labels: Optimization

#29 - Allow optimization at custom intervals

Issue - State: open - Opened by jdrusso over 1 year ago
Labels: Optimization

#28 - Make optimization pcoord extension generic, not SynD specific

Issue - State: open - Opened by jdrusso over 1 year ago - 1 comment
Labels: enhancement, Optimization, High priority

#26 - iPCA hangs

Issue - State: open - Opened by jdrusso over 1 year ago - 2 comments
Labels: bug

#25 - Suppress `openmm` import warnings in code using MDAnalysis

Issue - State: closed - Opened by jdrusso over 1 year ago - 2 comments

#24 - Allow disabling validation models in haMSM plugin

Issue - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#23 - Allow haMSM plugin to use a pre-saved haMSM

Issue - State: open - Opened by jdrusso over 1 year ago
Labels: enhancement

#22 - Handling failed model building

Issue - State: open - Opened by jdrusso over 1 year ago - 2 comments
Labels: bug, enhancement

#21 - Progress bars rebased

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 2 comments

#20 - Progress bars

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#19 - Blend progress bars into rich live display

Issue - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#18 - HDF5 framework compatibility

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 2 comments

#17 - Remove all `aggregate` methods

Issue - State: open - Opened by jdrusso over 1 year ago
Labels: enhancement

#16 - Cache pcoord on restart

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#15 - Added coverage

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#14 - Updated msm_we tests with more recent models

Pull Request - State: closed - Opened by jdrusso over 1 year ago

#13 - Add WESTPA HDF5 framework support to augmentation plugin

Issue - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#12 - Substantial reorganization

Pull Request - State: closed - Opened by jdrusso over 1 year ago

#11 - Merge in new WESTPA plugins

Pull Request - State: closed - Opened by jdrusso over 1 year ago - 1 comment

#10 - Weighted KMeans, TICA+VAMP, and some performance improvements

Pull Request - State: closed - Opened by jdrusso almost 2 years ago

#9 - Support for multiple basis/target states

Issue - State: closed - Opened by jdrusso almost 2 years ago

#8 - Release/1.1

Pull Request - State: closed - Opened by jdrusso over 2 years ago

#7 - Improved CI workflow

Pull Request - State: closed - Opened by jdrusso over 2 years ago

#6 - Dimreduce none cluster fix

Pull Request - State: closed - Opened by jdrusso over 2 years ago

#5 - fixed dimreducemethod=none errors when using a subset of atoms

Pull Request - State: closed - Opened by jeremyleung521 over 2 years ago

#4 - Add Ray tests

Issue - State: open - Opened by jdrusso over 2 years ago
Labels: enhancement

#3 - Remove egregiously duplicated Ray code

Issue - State: closed - Opened by jdrusso over 2 years ago
Labels: enhancement

#2 - add choice for prmtop

Pull Request - State: closed - Opened by jeremyleung521 almost 3 years ago

#1 - Sort out dependencies

Issue - State: closed - Opened by jdrusso almost 3 years ago - 1 comment
Labels: enhancement

GitHub / jdrusso/msm_we issues and pull requests