文件历史

58 次代码提交

作者 SHA1 备注 提交日期
Minjie Wang 597ac7f8b5 [Release] v0.1.3 (#288)
* 0.1.2 release

* oops

* more fixes on windows

* [Bugfix] fix download dir (#275)

* fix download dir

* add doc for the env var

* windows 7 -> 10

* doc update

* [Bugfix] Fix conversion from networkx (#286)

* fix from_nx when no edge id available

* add test cases

* more detailed tests

* more comments

* [Bugfix] Switch to sparse_coo_matrix for torch 1.0+ (#282)

* switch to sparse_coo_matrix for torch 1.0+

* fix bug when the version is 0.4.1.post2

* change to distutils
2018-12-11 01:30:47 -05:00
Minjie Wang 2194b7dfa6 [Bugfix] edge order is not preserved when converting from edge list (#262) 2018-12-05 17:41:26 -05:00
Minjie Wang 21255b6528 [Bugfix] tolist and dependencies in dgl.data (#239)
* change Index.tolist -> Index.tonumpy; fix bug in traversal; remove dependencies in data

* fix import

* fix __all__ and some docstring
2018-12-05 12:20:59 -05:00
Lingfan Yu 455ea48570 [Bugfix] Conversion between networkx and DGLGraph (#244)
* copy feature to networkx

* fix to_network for multi-graph

* test case for nx conversion

* iterate over Index returns plain int instead of numpy.int64

* fix from_network multi-edge bug
2018-12-04 16:19:11 -05:00
Lingfan Yu 52ed09a392 [Bug] Fix inplace update (#221)
* inplace write row op and executor

* update scheduler and graph to use inplace write

* fix

* fix bug

* test case for inplace

* fix bugs for inplace apply node/edge

* fix comments

* th.allclose -> U.allclose
2018-12-02 19:14:39 -05:00
Minjie Wang 524e656dd6 [Bugfix] enable SPMV for multi-dimension node feature (#178)
* Support multi-dimension node feature in SPMV

* fix as requested
2018-11-26 11:12:28 -05:00
Minjie Wang b1eeb93449 [Bugfix][Runtime] Zero degree behaviors (#177)
* fix recv nodes are all 0deg; fix hybriddict does not through keyerror properly

* fallback to apply_nodes when all nodes are 0deg; WIP on pull spmv 0deg

* new 0deg behavior

* new 0deg behavior

* update mx utest for pull-0deg

* fix mx

* fix mx

* get rid of unnecessary sort-n-unique
2018-11-25 22:33:08 -05:00
Minjie Wang 4dfe7547e8 Fix num_rows bug in batched_graph (#169) 2018-11-23 02:49:59 +08:00
Zihao Ye 23e2e83b5e [API] change the signature of node/edge filter (#166)
* change the signature of node/edge filter

* upd filter
2018-11-22 13:00:36 -05:00
Lingfan Yu deb653f8dc [Runtime] Scheduler and Executor (#140)
* executor api

* draft executor interface

* WIP

* revert changes to avoid conflict with api change

* core scheduling logic

* WIP: build graph adj

* incidence matrix for in edges

* support incidence matrix for partial recv nodes

* improve

* build adjmat in scheduler

* graph store

* get degree bucketing schedule

* connect to c++ degree bucketing

* conceptual executor creation code

* executor comments

* fix

* more executor comments

* WIP: full send_and_recv schedule

* most schedulers

* simplify scheduler

* executors

* runtime

* builtin function base class

* adj indices and shape

* completely refactor scheduler

* rename and move bundled out to function.py

* use_edge_feature in msg func

* rewrite scheduler

* node edge executor

* connect with graph api

* handle zero degree

* misc

* fix test cases

* fix a good many bugs...

* remove old scheduler

* push and pull

* fix send recv

* c++ lint

* fix batched send recv

* hot fix for mxnet

* typo

* write back executor

* apply node edge

* clean up, doc string

* fix as requested

* refactor

* fix

* WIP

* WIP

* ir draft

* more on ir

* WIP: spmv schedule

* WIP

* recv schedule

* refactor

* WIP

* snr degree bucketing

* snr scheduler

* move prog to graph.py; rename

* unittest for send/recv

* remove some legacy codes

* WIP: update_all

* pass test_basics

* passed all current utests

* more utests; fix mx utest

* WIP: fixing zero deg initial value

* some tests

* fix 0deg problem

* fix mx

* fix mx

* some notes

* fix as requested
2018-11-22 12:15:50 -05:00
Minjie Wang 0ec1a492b3 [Frame] change num rows behavior (#163)
* move initializer to column scheme; change num rows behavior

* poke mx ci

* fix mx utest in append

* fix bug in add edges

* utest for updating partial rows

* fix bug in from_networkx and from_scipy_matrix

* revert per-col initializer change

* fix pickle utest
2018-11-21 11:50:46 -05:00
Gan Quan e515f5311b [Frame] supporting partial row on first column and individual column initializers (#160)
addresses issue #156
2018-11-19 18:18:36 -05:00
Gan Quan 79a510252b Pickling support (#155)
* pickling support

* resorting to suggested way of pickling

* custom attribute pickling check

* working around a weird pytorch pickling bug

* including partial frame case

* pickling everything now

* fix as requested
2018-11-16 17:19:20 -05:00
Gan Quan 05f464f824 [Bugfix] fix args with incontiguous node and edge tensor (#153) 2018-11-15 10:55:15 -05:00
Minjie Wang 048f6d7a30 [GraphIndex] refactor graph caching (#150)
* refactor graph caching

* fix mx test

* fix typo
2018-11-13 22:12:38 -05:00
Minjie Wang a95459e3a2 [CI] Improved CI (#141)
* change ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* update ci

* nx package

* update ci

* update ci

* update ci

* fix

* mx dockerfile by zhengda

* python3.6->3.5

* update ci image

* add tutorial test

* fix ci

* fix ssl problem

* minor change

* small fix on traversal utest

* fix syntax

* add matplotlib in image

* fix

* update ci

* update ci
2018-11-12 01:06:05 -05:00
Gan Quan 7cbb83db9f better bfs edge test (#142) 2018-11-11 23:09:39 -05:00
Gan Quan d6c80e0cf7 [API] bfs with edges (#132)
* bfs with edges

* dfs toy test case

* clean up

* style fix

* bugfix

* updating docs for bfs_edges and readouts
2018-11-11 17:19:55 -05:00
Minjie Wang 66676a548d [Bugfix] Fix bug in bfs and topo (#135)
* Fix bug in bfs and topo

* remove legacy codes
2018-11-10 20:34:17 -05:00
Gan Quan 40ca5de450 [API] Readout interfaces (#124)
* fixing builtin src*edge shape mismatch

* bundled function refactor (?)

* fixing names

* readout prototype

* oops

* more fixes

* removing readout prototype

* sum_on() with SPMV, fixing batching with 0 edges

* readouts with segmented sum

* typo (??????)

* fixes NLTK dependency (#125)

* misc fixes including #126 (pushing again)

* sanity check for mxnet

* fixes NLTK dependency (#125) and #126

* reverting to sum_nodes/edges
2018-11-10 11:35:34 -05:00
Minjie Wang 8ea359d125 [API] Message propagation APIs (#127)
* add examples in traversal.py

* message propagate methods

* use the new message propagation for tree-lstm

* update to the new name

* update propagate API doc

* update doc

* add propagate utest
2018-11-09 15:04:57 -05:00
Gan Quan 72efb42718 [Bugfix] fixes NLTK dependency (#125) and #126 (#131) 2018-11-09 14:16:52 -05:00
Minjie Wang 3e43d7b8d2 [Test] Lower allclose precision (#129) 2018-11-08 22:52:22 -05:00
GaiYu0 2319167444 [API] Graph traversal (#103)
* bfs, dfs and topological traversal

* dfs and test cases

* Conflicts:
	python/dgl/graph.py
	src/graph/graph.cc
	src/graph/graph_op.cc

* documentation

* requested changes

* Conflicts:
	Jenkinsfile
	examples/pytorch/gcn/gcn.py
	examples/pytorch/gcn/gcn_spmv.py
	python/dgl/graph.py
	python/dgl/graph_index.py
	src/graph/graph.cc
	src/graph/graph_op.cc

* Conflicts:
	Jenkinsfile
	python/dgl/graph_index.py

* fix lint errors

* fix lint errors

* fix lint errors

* fix test cases

* requested changes

* traversal interface

* [Bug] fixed a typo that caused syntax error (#120)

* WIP

* bfs nodes generator works

* topological traversal

* WIP: dfs_edges

* dfs edges

* dfs labeled edges

* utest for traversal

* fix lint

* fix utest

* code clean

* changes as requested
2018-11-08 10:14:19 -05:00
Minjie Wang b355d1eddf [API] Apply nodes & apply edges (#117) 2018-11-04 01:22:53 -04:00
Minjie Wang 68ec624782 [API][Doc] API change & basic tutorials (#113)
* Add SH tutorials

* setup sphinx-gallery; work on graph tutorial

* draft dglgraph tutorial

* update readme to include document url

* rm obsolete file

* Draft the message passing tutorial

* Capsule code (#102)

* add capsule example

* clean code

* better naming

* better naming

* [GCN]tutorial scaffold

* fix capsule example code

* remove previous capsule example code

* graph struc edit

* modified:   2_graph.py

* update doc of capsule

* update capsule docs

* update capsule docs

* add msg passing prime

* GCN-GAT tutorial Section 1 and 2

* comment for API improvement

* section 3

* Tutorial API change (#115)

* change the API as discusses; toy example

* enable the new set/get syntax

* fixed pytorch utest

* fixed gcn example

* fixed gat example

* fixed mx utests

* fix mx utest

* delete apply edges; add utest for update_edges

* small change on toy example

* fix utest

* fix out in degrees bug

* update pagerank example and add it to CI

* add delitem for dataview

* make edges() return form that is compatible with send/update_edges etc

* fix index bug when the given data is one-int-tensor

* fix doc
2018-11-02 17:19:14 -04:00
Gan Quan 2ecd2b23ec [Frame] Support slice type indexing; optimize dgl.batch (#110)
* 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

* remove comment

* forgot the find edges interface

* subclassing namedtuple
2018-11-01 00:03:06 -04:00
Mufei Li 9827e48176 Support for adding nodes/edges after setting representations (#114)
* Fix

1. Fix two typos in gcn.py and gcn_spmv.py
2. Update README

* Fix GCN module

1. Update the outdated graph convolution layer class
2. Fix a bug in the code where dropout never works. Modules like dropout/batch norm depend on whether we are in the training stage or inference stage.

* Fix a bug in dropout

1. dropout depends on nn.Module.training

* Update GCN module

* Fix README

* Fix dropout & remove self.msg_field

* Fix

* Align with TF implementation

* Make g an argument for forward

* Remove features from the argument of GraphConv layer

* Support for create nodes/edges after setting representations

* Remove redundant commit

* Delete test_init_repr.py

* Test case for dynamic addition

* Base 'add_rows' upon 'append'

* Move test function

* Fix

* test by assertion

* changed add_rows to adding blank rows only; adding convert_to to backend

* moving test to basics

* oops mxnet
2018-10-29 23:33:54 -04:00
Minjie Wang 3e76bcc052 remove anonymous repr 2018-10-18 21:43:40 -04:00
Da Zheng 4af3f8bcc8 update the MXNet backend. (#89)
* update mxnet.

* add get_tvmtype.

* remove undefined test.
2018-10-18 12:49:13 -07:00
Minjie Wang 6cbdf37c37 Merge branch 'master' into cpp 2018-10-18 15:29:20 -04:00
Minjie Wang b9631912db [Frame] Refactor frame. (#85)
* refactor frame codes

* fix unit test

* fix gcn example

* minor doc/message changes

* raise errors for non-exist columns in FrameRef; sanity check when append

* fix unittest; change error msg

* Add warning for none initializer

* fix unittest

* use warnings package
2018-10-18 15:08:21 -04:00
Minjie Wang 66261aee03 [Hotfix] Revert part of the send logic; disable the send twice test case; GCN on GPU works again. (#88) 2018-10-18 14:20:44 -04:00
Gan Quan bc3f852dab [GRAPHINDEX] Multigraph support (#79)
* multigraph support on graph index

* more tests

* multigraph flag, bugfix on clear & copy

* networkx interfaces

* including graph index tests in Jenkins

* node subgraph test

* edge subgraphs

* removing duplicates in pred/succ

* more explicit test and doc

* query source and destination from edge id

* subgraphindex

* renaming has_edge to has_edge_between, apply_edges adding eid

* send_on and send_and_recv_on

* DGLGraph edge subgraph

* merged send_on and send_and_recv_on

* change request

* removing hashmap

* creating multigraph by flag; mingw support

* changes per request

* reverting networkx auto multigraph discovery

* notes on send/send_and_recv on multigraphs

* changing test reducer from sum to max

* added a fixme note in spmv scheduler
2018-10-17 21:46:10 -04:00
Gan Quan b2c1c4facd node/edge filtering (#80)
* node/edge filtering

* changing to tensor operations (what did i do???)

* ???
2018-10-16 21:37:43 -04:00
GaiYu0 e7679cf2e6 implement requested changes 2018-10-13 14:24:46 +08:00
Minjie Wang 7603b8c351 Fix dlpack bug; zero copy between dgl.ndarray and user tensor enabled 2018-10-09 11:37:59 -04:00
Lingfan Yu cdf7334cc6 Dockerfile and CI (#74)
* Test CPP branch CI (#2)

* Fix batching node-only graphs (#62)

* fixing batching with graphs with no edges

* oops forgot test

* fix readme

* Docker and Jenkins (#1)

* docker ci cpu

* install python packages

* docker ci gpu

* add readme

* use dgl cpu image

* run command in container as root

* use python3

* fix test case

* remove nose from docker file

* docker folder readme

* parallelize cpu and gpu

* top level stages

* comment out python2 related installation

* fix

* remove igraph

* building for cpp

* change building order

* export env in test stage

* withEnv

* run docker container as root

* fix test cases

* fix test cases

* minor

* remove old build
2018-10-07 19:18:43 -04:00
Minjie Wang 72f6345515 Fix for subgraph test and some docs 2018-10-05 23:58:42 -04:00
Da Zheng b0e02e5b52 Update the subgraph (#73)
* update subgraph.

* update subgraph API.

* keep node embedding.
2018-10-05 22:17:33 -04:00
Minjie Wang 1b06998465 doc for batched graph 2018-10-05 15:07:42 -04:00
Minjie Wang fde4f581d2 gcn runnable 2018-10-03 21:05:19 -04:00
Minjie Wang 2be55fb50a graph batch and unbatch 2018-10-03 17:07:41 -04:00
Minjie Wang 7d04c8c9f3 remove nonbatchable mode 2018-10-03 12:20:12 -04:00
Minjie Wang 7b5d4c5886 pass specialization test 2018-09-20 18:22:46 -04:00
Minjie Wang b2e4bdc03f passed basic test batching 2018-09-20 14:44:06 -04:00
Gan Quan f26ecb4909 Fix batching node-only graphs (#62)
* fixing batching with graphs with no edges

* oops forgot test
2018-09-20 10:36:35 -04:00
Lingfan Yu 9b0a01db41 Support list of msg or reduce func for update_all and send_and_recv (#58)
* support multiple fields in spmv

* finishing SPMV executor

* non-spmv case

* refactor code to give single mfunc rfunc a shortcut

* two test cases to test multiple msg/red func

* catching cases where msg uses anonymous field

* default ALL for update edge

* more corner case test

* print failed test

* delete print

* fix builtin max reducer
2018-09-19 20:49:29 -04:00
Minjie Wang 61fa3c6cf5 Builtin function and API changes (#53)
* WIP: API renaming

* API rewrite and node function refactor

* builtin functions

* builtin functions tested

* fix test

* send and recv spmv test

* WIP: fix examples

* Fix examples using new APIs
2018-09-01 13:38:01 -04:00
Gan Quan b7eb16595f Fix 0deg update_to and Tree-LSTM model (#51)
* WIP

* WIP

* treelstm dataloader

* Main training loop.

* trainable treelstm script

* fix dependency

* cuda training

* Add tensorized topological traversal

* allowing update_to() with no incoming messages

* fixing partial cases
2018-08-28 11:57:08 -04:00