GitLab

* Update prerequisites of README

* dependencies for pytorch models

* dependencies for mxnet models

* minor

* cherry picking optimization from jtnn

* adding official code.  TODO: fix DGLMolTree

* updating to current api.  vae test still failing

* reverting to list stacking

* reverting to list stacking

* cleaning x flags (stupid windows)

* cleaning x flags (stupid windows)

* adding stats

* optimization

* updating dgl stats

* update again

* more optimization

* looks like computation is faster

* removing profiling code

* cleaning obsolete code

* remove comparison warning

* readme update

* official implementation got a lot faster

* minor fixes

* unbatch by slicing frames

* working around unbatch

* reduce pack

* oops

* support frame read/write with slices

* reverting back to readout as unbatch-by-slicing slows down backward

* reverting to unbatch by splitting; slicing is unfriendly to backward

* replacing lru cache with static object factory

* cherry picking optimization from jtnn

* unbatch by slicing frames

* reduce pack

* oops

* support frame read/write with slices

* reverting to unbatch by splitting; slicing is unfriendly to backward

* replacing lru cache with static object factory

* replacing Scheme object with namedtuple

* forgot the find edges interface

* subclassing namedtuple

* updating to the latest api spec

* bugfix

* bfs with edges

* dfs toy test case

* clean up

* style fix

* bugfix

* update to latest api; include traversal

* replacing with readout

* simplify decoder

* oops

* cleanup

* reducing number of sets

* more speed up

* profile results

* random fixes

* fixing tvmarray handling incontiguous dlpack input

* fancier dataloader

* fix a potential context mismatch

* todo: support pickling or using scipy in multiprocessing load

* pickling support

* resorting to suggested way of pickling

* custom attribute pickling check

* working around a weird pytorch pickling bug

* including partial frame case

* enabling multiprocessing dataloader

* pickling everything now

* really works

* oops

* updated profiling results

* cleanup

* fix as requested

* cleaning random blank lines

* removing profiler outputs

* starting decoding

* testing, WIP

* tree decoding

* graph decoding, WIP

* graph decoding works

* oops

* fixing legacy apis

* trimming number of candidate structures

* sampling cleanups

* removing comparison test

* updated description

* junction tree vae example

* added README and moved data to dropbox

* auto download; some fix in python3