GitLab

Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Make column double indices lazy

* Copy indices to proper contexts

* Fix initialization

* Add unit test

* Fix unit test for tensorflow

* Remove unused member
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Merge

* [Graph][CUDA] Graph on GPU and many refactoring (#1791)

* change edge_ids behavior and C++ impl

* fix unittests; remove utils.Index in edge_id

* pass mx and th tests

* pass tf test

* add aten::Scatter_

* Add nonzero; impl CSRGetDataAndIndices/CSRSliceMatrix

* CSRGetData and CSRGetDataAndIndices passed tests

* CSRSliceMatrix basic tests

* fix bug in empty slice

* CUDA CSRHasDuplicate

* has_node; has_edge_between

* predecessors, successors

* deprecate send/recv; fix send_and_recv

* deprecate send/recv; fix send_and_recv

* in_edges; out_edges; all_edges; apply_edges

* in deg/out deg

* subgraph/edge_subgraph

* adj

* in_subgraph/out_subgraph

* sample neighbors

* set/get_n/e_repr

* wip: working on refactoring all idtypes

* pass ndata/edata tests on gpu

* fix

* stash

* workaround nonzero issue

* stash

* nx conversion

* test_hetero_basics except update routines

* test_update_routines

* test_hetero_basics for pytorch

* more fixes

* WIP: flatten graph

* wip: flatten

* test_flatten

* test_to_device

* fix bug in to_homo

* fix bug in CSRSliceMatrix

* pass subgraph test

* fix send_and_recv

* fix filter

* test_heterograph

* passed all pytorch tests

* fix mx unittest

* fix pytorch test_nn

* fix all unittests for PyTorch

* passed all mxnet tests

* lint

* fix tf nn test

* pass all tf tests

* lint

* lint

* change deprecation

* try fix compile

* lint

* update METIDS

* fix utest

* fix

* fix utests

* try debug

* revert

* small fix

* fix utests

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [kernel] Use heterograph index instead of unitgraph index (#1813)

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [Graph] Mutation for Heterograph (#1818)

* mutation add_nodes and add_edges

* Add support for remove_edges, remove_nodes, add_selfloop, remove_selfloop

* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* upd

* upd

* upd

* fix

* [Transfom] Mutable transform (#1833)

* add nodesy

* All three

* Fix

* lint

* Add some test case

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* fix

* triger

* Fix

* fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* [Graph] Migrate Batch & Readout module to heterograph (#1836)

* dgl.batch

* unbatch

* fix to device

* reduce readout; segment reduce

* change batch_num_nodes|edges to function

* reduce readout/ softmax

* broadcast

* topk

* fix

* fix tf and mx

* fix some ci

* fix batch but unbatch differently

* new checkk

* upd

* upd

* upd

* idtype behavior; code reorg

* idtype behavior; code reorg

* wip: test_basics

* pass test_basics

* WIP: from nx/ to nx

* missing files

* upd

* pass test_basics:test_nx_conversion

* Fix test

* Fix inplace update

* WIP: fixing tests

* upd

* pass test_transform cpu

* pass gpu test_transform

* pass test_batched_graph

* GPU graph auto cast to int32

* missing file

* stash

* WIP: rgcn-hetero

* Fix two datasety

* upd

* weird

* Fix capsuley

* fuck you

* fuck matthias

* Fix dgmg

* fix bug in block degrees; pass rgcn-hetero

* rgcn

* gat and diffpool fix
also fix ppi and tu dataset

* Tree LSTM

* pointcloud

* rrn; wip: sgc

* resolve conflicts

* upd

* sgc and reddit dataset

* upd

* Fix deepwalk, gindt and gcn

* fix datasets and sign

* optimization

* optimization

* upd

* upd

* Fix GIN

* fix bug in add_nodes add_edges; tagcn

* adaptive sampling and gcmc

* upd

* upd

* fix geometric

* fix

* metapath2vec

* fix agnn

* fix pickling problem of block

* fix utests

* miss file

* linegraph

* upd

* upd

* upd

* graphsage

* stgcn_wave

* fix hgt

* on unittests

* Fix transformer

* Fix HAN

* passed pytorch unittests

* lint

* fix

* Fix cluster gcn

* cluster-gcn is ready

* on fixing block related codes

* 2nd order derivative

* Revert "2nd order derivative"

This reverts commit 523bf6c249bee61b51b1ad1babf42aad4167f206.

* passed torch utests again

* fix all mxnet unittests

* delete some useless tests

* pass all tf cpu tests

* disable

* disable distributed unittest

* fix

* fix

* lint

* fix

* fix

* fix script

* fix tutorial

* fix apply edges bug

* fix 2 basics

* fix tutorial
Co-authored-by: yzh119 <expye@outlook.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-7-42.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal>

* add clone function to frame

* add utest

* replace all local_var with local_scope

* fix utest

* avoid creating canonical types in __getitem__

* lint

* try another utest  appraoch for mx

* utest

* add bool to F.data_type_dict

* add utest

* skip bool test for mx

* change ci image

* fix

* force bash

* fix

* fix python version

* fix

* fix

* fix

* update gpu

* cuda

* jenkins

* fix build sh

* fix

* Revert "fix"

This reverts commit 6b091914b3ef6b4300fa662ee375aa4b27944f5c.

* try fix

* fix

* Revert "fix"

This reverts commit e42c3035fa4974c6b197aaba0748f7b45113ddaa.

* try fix

* fix

* fix

* fix

* fix

* fix

* fix

* fix tests

* try fix

* fix

* fix

* fix

* fix

* fix

* fix

* fix ctx problem

* fix many tests

* fix typo

* add backend

* move to pytorch folder

* fix?

* fix ci

* try skip

* try false

* try?

* try?

* Revert to 7d9a52f

* fix various

* fix lint

* Revert Jenkinsfile

* revert env

* revert env

* address comment

* remove file

* [Kernel] Minigun integration and fused kernel support (#519)

* kernel interface

* add minigun

* Add cuda build

* functors

* working on binary elewise

* binary reduce

* change kernel interface

* WIP

* wip

* fix minigun

* compile

* binary reduce kernels

* compile

* simple test passed

* more reducers

* fix thrust problem

* fix cmake

* fix cmake; add proper guard for atomic

* WIP: bcast

* WIP

* bcast kernels

* update to new minigun pass-by-value practice

* broadcasting dim

* add copy src and copy edge

* fix linking

* fix none array problem

* fix copy edge

* add device_type and device_id to backend operator

* cache csr adj, remove cache for adjmat and incmat

* custom ops in backend and pytorch impl

* change dgl-mg kernel python interface

* add id_mapping var

* clean up plus v2e spmv schedule

* spmv schedule & clean up fall back

* symbolic message and reduce func...

* test basics

* batched graph & filter, mxnet filter fix

* frame and function; bugfix

* test graph adj and inc matrices

* fixing start = 0 for mxnet

* test index

* inplace update & line graph

* multi send recv

* more tests

* oops

* more tests

* removing old test files; readonly graphs for mxnet still kept

* modifying test scripts

* adding a placeholder for pytorch to reserve directory

* torch 0.4.1 compat fixes

* moving backend out of compute to avoid nose detection

* tests guide

* mx sparse-to-dense/sparse-to-numpy is buggy

* oops

* contribution guide for unit tests

* printing incmat

* printing dlpack

* small push

* typo

* fixing duplicate entries that causes undefined behavior

* move equal comparison to backend

* fix lint for graph_index.py

* pylint for base.py

* pylint for batched_graph.py

* pylint for frame.py; simplify and fix bugs in frame when index is slice type

* pylint for graph.py

* pylint for immutable_graph_index.py

* pylint for init.py

* pylint for rest files in root package

* pylint for _ffi package

* pylint for function package

* pylint for runtime package

* pylint for runtime.ir package

* add pylint to ci

* fix mx tests

* fix lint errors

* fix ci

* fix as requested

* fix lint

* change Index.tolist -> Index.tonumpy; fix bug in traversal; remove dependencies in data

* fix import

* fix __all__ and some docstring

* 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

addresses issue #156

* 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

* 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

* 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

* subgraph copy from

* WIP

* cached members

* Change all usage of id tensor to the new Index object; remove set device in DGLGraph;

* subgraph merge API tested

* add dict type reduced msg test

* subgraph

* more test cases

* WIP

* new FrameRef and test

* separate nx init code

* WIP

* subgraph code and test

* line graph code and test

* adding new test for adding new features on line graphs

* no backtracking line graph

* fix inplace relabel

* batch message_func, reduce_func and update_func

Conflicts:
	python/dgl/backend/pytorch.py

* test cases for batching

Conflicts:
	python/dgl/graph.py

* resolve conflicts

* setter/getter

Conflicts:
	python/dgl/graph.py

* test setter/getter

Conflicts:
	python/dgl/graph.py

* merge DGLGraph and DGLBGraph

Conflicts:
	python/dgl/graph.py

Conflicts:
	python/dgl/graph.py

* batchability test

Conflicts:
	python/dgl/graph.py

Conflicts:
	python/dgl/graph.py

* New interface (draft)

Conflicts:
	_reference/gat_mx.py
	_reference/molecular-gcn.py
	_reference/molecular-gcn_mx.py
	_reference/multi-gcn.py
	_reference/multi-gcn_mx.py
	_reference/mx.py
	python/dgl/graph.py

* Batch operations on graph

Conflicts:
	.gitignore
	python/dgl/backend/__init__.py
	python/dgl/backend/numpy.py
	python/dgl/graph.py

* sendto

* storage

* NodeDict

* DGLFrame/DGLArray

* scaffold code for graph.py

* clean up files; initial frame code

* basic frame tests using pytorch

* frame autograd test passed

* fix non-batched tests

* initial code for cached graph; tested

* batch sendto

* batch recv

* update routines

* update all

* anonymous repr batching

* specialize test

* igraph dep

* fix

* fix

* fix

* fix

* fix

* clean some files

* batch setter and getter

* fix utests