7815fe8adc
[CUDA] Make sanity check optional for dgl.create_block. ( #7240 )
2024-03-26 10:14:03 +08:00
3d854a6b9b
[Misc] Correct docstrings in python/dgl/convert.py ( #7060 )
2024-02-04 11:39:43 +08:00
cf829dc38e
Fixing some unittest warnings. ( #6122 )
...
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
2023-08-10 11:53:20 +08:00
a9d6f77012
[Feature] Support heterogeneous graphs in the to_networkx method ( #5726 )
...
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-06-01 19:49:15 +08:00
8f9f2e2a4d
[Misc] Rename number_of_edges and number_of_nodes to num_edges and num_nodes. ( #5472 )
...
* core
* revert
---------
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
2023-03-29 08:57:47 +08:00
a566b60be4
auto-fix ( #5331 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
2023-02-21 01:25:16 +08:00
ab0c0ec68f
[API Deprecation] Deprecate candidates in convert module ( #4988 ) ( #5115 )
2023-01-06 14:45:52 +08:00
3132da2826
Deprecate ( #4864 )
...
rename DGLHeteroGraph to DGLGraph
2022-11-15 10:01:01 +08:00
9ae117d3cd
[Feature] Add to_cugraph and from_cugraph to DGL ( #4166 )
...
* Added to_cugraph and from_cugraph functionality
* fix from_cugraph example
* Addressed Reviews
* Fix linting
* Apply suggestions to docstrings from code review
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
* Add API docs and remove `from_cugraph` alias
* move cugraph tests to tests/cugraph/test_basics.py
* remove ununsed imports from test_basics.py
* remove pytest.importorskip as no longer needed
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-07-07 11:52:17 +08:00
da877df238
[CI] Migrate to pylint 2.6.0 ( #3698 )
...
* migrate to pylint 2.6.0
* fix
* fix?
* ???
* oops
2022-01-28 18:32:18 +08:00
acd21a6d60
[Feature] Support direct creation from CSR and CSC ( #3045 )
...
* csr and csc creation
* fix
* fix
* fixes to adj transpose
* fine
* raise error if indptr did not match number of nodes
* fix
* huh?
* oh
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-25 10:05:47 +08:00
2df4a95f3e
[Feature] Make to_heterogeneous(to_homogeneous(hg)) return hg ( #2958 )
...
* make to_heterogeneous and to_homogeneous invertible
* docstring
* oops
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-06-03 18:50:18 +08:00
657c220de7
[Feature] Python interface for adjacency matrix summation and multiplication ( #2893 )
...
* test commit
* fixes
* oops
* add docs
* lint
* why does it say I have a trailing whitespace
* oh ok
* fixes
* why there's an invalid argument error
* address comments
* fix
* address comments
2021-05-17 19:47:02 +08:00
bbebde4660
[Performance] Track sorted status of COO from creation ( #2645 )
...
* Add row/col sorted flags
* improve sorting paths
* Remove print statement
* Keep track of sorted matrices
* Remove sort check in to_block
* Improve CPU sorted COO->CSR
* Handle the zero edge case
* Remove omp default clause to work with MSVC
* Update comments on sorted COO->CSR cpu implementatoin
* Expose sorted to python interface
* Make check_sorted default to false for dgl.graph()
* remove check sorted; add utests
* remove check_sorted flag
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-16 10:30:07 +08:00
0576a33b7f
Update convert.py ( #2789 )
...
Co-authored-by: Zihao Ye <expye@outlook.com >
2021-03-28 20:59:52 +08:00
99751d4960
[Doc] Rename block to message flow graph ( #2702 )
...
* rename block to mfg
* revert
* rename
2021-02-25 18:26:19 +08:00
2288098ba6
[Feature] Converting a block to a graph and allow block construction ( #2555 )
...
* first commit
* more commit
* fix and docstring
* add to api reference
* address comments
* Update convert.py
2021-01-24 12:44:54 +08:00
d3c1645550
[Performance][Test] New low memory implementation for RGCN and related regression tests ( #2468 )
...
* WIP
* finish lowmem impl; benchmarking
* wip
* wip
* fix benchmarks
* fix bug in searchsorted
* update readme
* update
* lint and ogb dependency
* add flags to to_homogeneous
* fix docstring
* address comments
2021-01-04 22:23:59 +08:00
edb978772c
[Doc, UG, Tutorial] Misc Fix ( #2376 )
...
* Update
* Update
* Update
* Update
* Update
2020-11-30 13:40:10 +08:00
f13b9b6212
[Doc] Scan the API docs and make many changes ( #2080 )
...
* WIP: api
* dgl.sampling, dgl.data
* dgl.sampling; dgl.dataloading
* sampling packages
* convert
* subgraph
* deprecate
* subgraph APIs
* All docstrings for convert/subgraph/transform
* almost all funcs under dgl namespace
* WIP: DGLGraph
* done graph query
* message passing functions
* lint
* fix merge error
* fix test
* lint
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-20 23:26:49 +08:00
dacc7afeb2
[Convert] Reserve node/edge IDs in to_heterogeneous ( #2045 )
...
* Fix
* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-18 23:16:33 +08:00
be444e52d9
[Doc/Feature] Refactor, doc update and behavior fix for graphs ( #1983 )
...
* Update graph
* Fix for dgl.graph
* from_scipy
* Replace canonical_etypes with relations
* from_networkx
* Update for hetero_from_relations
* Roll back the change of canonical_etypes to relations
* heterograph
* bipartite
* Update doc
* Fix lint
* Fix lint
* Fix test cases
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Fix test
* Fix
* Update
* Use DGLError
* Update
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* rewrite sanity checks
* delete unnecessary checks
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Fix
* Update
* Fix
* Update
* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-18 04:26:29 +08:00
d2ccd218cf
[hotfix] Allow creating graph from edges with restrict formats excluding coo. ( #1926 )
...
* upd
* upd
* upd
* upd
2020-08-04 00:33:36 +08:00
f4608c2227
[CUDA][Kernel] A bunch of int64 kernels for COO and CSR ( #1883 )
...
* COO sort
* COOToCSR
* CSR2COO
* CSRSort; CSRTranspose
* pass all CSR tests
* lint
* remove int32 conversion
* fix tensorflow nn tests
* turn on CI
* fix
* addreess comments
2020-07-30 21:02:07 +08:00
40950629b2
[Feature] Shared memory utilities ( #1807 )
...
* update
* update
* update
* update
* fix
* update
* fix
* update
* update
* win32
* update
* fix
* update
* update
* update
* updat
* update
* update
* fix
* update
* update
* update
* update
* update
* fix
* TODO
* 111
* fix
* minor fix
* minor fix
* fox
* Update shared_mem_manager.cc
* update
* update
* update
* update metis
* update metis
* update
Co-authored-by: VoVAllen <jz1749@nyu.edu >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-07-28 15:26:15 +08:00
44089c8b4d
[Refactor][Graph] Merge DGLGraph and DGLHeteroGraph ( #1862 )
...
* 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 >
2020-07-28 14:30:41 +08:00
85e660cb6b
[hotfix] Fix #1682 ( #1683 )
...
* upd
* upd to_hetero
2020-06-23 15:59:02 +08:00
c2e61ce10b
[Refactor] Restrict sparse format for DGLHeteroGraph ( #1474 )
...
* upd
* simplify
* further simplify
* lint
* doc
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* lint
* rename format
* upd
* lint
* upd
* upd
* upd
* udp
* debug
* upd
* upd
* upd
* upd
* upd
* 无可厚非吧
* 中三边肥
* 你一定要喊吗
* lint
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* Update unit_graph.h
Co-authored-by: Zihao Ye <yzh119@192.168 .0.110>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2020-05-14 22:11:12 +08:00
e5b10b10ee
[Performance] fixing performance on heterogeneous graph creation in specific cases ( #1506 )
...
* [Performance] fixing performance on heterogeneous graph creation in specific cases
* fix for mxnet
2020-05-13 17:15:06 +08:00
dc8ca88e58
[Refactor] Explicit dtype for HeteroGraph ( #1467 )
...
* 111
* 111
* lint
* lint
* lint
* lint
* fix
* lint
* try
* fix
* lint
* lint
* test
* fix
* ttt
* test
* fix
* fix
* fix
* mxnet
* 111
* fix 64bits computation
* pylint
* roll back
* fix
* lint
* fix hetero_from_relations
* remove index_dtype in to_homo and to_hetero
* fix
* fix
* fix
* fix
* remove default
* fix
* lint
* fix
* fix error message
* fix error
* lint
* macro dispatch
* try
* lint
* remove nbits
* error message
* fix
* fix
* lint
* lint
* lint
* fix
* lint
* fix
* fix random walk
* lint
* lint
* fix
* fix
* fix
* lint
* fix
* lint
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-05-08 14:26:28 +08:00
f25bc176d0
[Hetero] Improve speed of several Hetero APIs ( #1486 )
...
* 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
2020-05-01 15:21:33 +08:00
67cb7a43a0
[Feature] Deprecate multigraph ( #1389 )
...
* Deprecate multi-graph
* Handle heterograph and edge_ids
* lint
* Fix
* Remove multigraph in C++ end
* Fix lint
* Add some test and fix something
* Fix
* Fix
* upd
* Fix some test case
* Fix
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-28 21:31:24 +08:00
0f40c6e49c
[Hetero] Replace card with num_nodes
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-20 16:56:53 +08:00
a9520f71ce
[Model][Sampler] GraphSAGE model, bipartite graph conversion & remove edges API ( #1297 )
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* remove edge and to bipartite and graphsage with sampling
* fixes
* fixes
* fixes
* reenable multigpu training
* fixes
* compatibility in DGLGraph
* rename to compact_as_bipartite
* bugfix
* lint
* add offline inference
* skip GPU tests
* fix
* addresses comments
* fix
* fix
* fix
* more tests
* more docs and unit tests
* workaround for empty slice on empty data
2020-03-08 02:38:29 +08:00
ce6e19f233
[Bugfix] Allows node types with no inbound/outbound edges ( #1323 )
...
* add num nodes in ctors
* fix
* lint
* addresses comments
* replace with constexpr
* remove function with rvalue reference
* address comments
2020-03-08 01:11:44 +08:00
1c4bfb62bb
[Performance] Replace np.array with np.asarray ( #1301 )
...
* replace np.array with np.asarray
* fix
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2020-03-03 20:45:41 +08:00
c3a33407fe
[Feature] PinSAGE sampler ( #1249 )
...
* [WIP] PinSAGE operators
* moved the edge remapping mess into C
* some docstrings
* lint
* lint x2
* lint x3
* skip gpu test on topk
* extend pinsage to any metapath
* lint x4
* addresses #1265
* add always_preserve (fixes #1266 ) and fix a silly bug
* disable gpu test on compaction
* lint
* fix a horrible bug and add more tests
* lint
* addresses comments
* lint
* bugfix
* addresses comments
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2020-02-28 20:46:13 +08:00
eeeb52f464
[Feature] Preference to COO for "hypersparse" unit graphs & graph compaction ( #1238 )
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* unit graph that prefers coo queries
* auto detect coo preference
* forgot some functions
* disable lint on detect_prefer_coo
* reorg
* change comment
* lint
* fix
* move array_utils.h to src
* compact graph impl
* fix redundant copying in idhashmap
* docstring
* moving preference detection to C
* lint
* fix unit test & address comments
* hypersparse autorestrict
* docstring & fix
* revert copyto and asnumbits
* fix stupid bug
* lint
* leave a TODO for sorted COO
* fixing same node type mapping to different id in different graphs
* addresses comments
* made induced nodes a feautre column
* lint?
2020-02-04 22:39:28 +08:00
31a7d50964
[Bug Fix] Add boundary check for heterograph build with card as input ( #1192 )
...
* Add boundary check for heterograph build with card as input
* Fix when u or v is empty
* fix test_kernel.py error print
* Revert "fix test_kernel.py error print"
This reverts commit a71c20292549c0ac62a5326c30669ca4bde8febc.
* Turn op validation check on graph and bipartite by default
* upd
* udp
* upd
* update test
2020-01-18 17:18:40 +08:00
28a24414c8
[BUG] Fix empty heterograph creation with list & tuple ( #1188 )
...
* [BUG] Fix empty heterograph creation with list & tuple
* more fix
2020-01-09 22:40:27 +08:00
870857cfba
udp ( #1083 )
2019-12-09 14:52:20 +08:00
fa0ee46a01
[hotfix] node id validity check ( #1073 )
...
* fix
* improve
* fix lint
* upd
* fix
* upd
2019-12-06 01:36:41 +08:00
ead64de98e
[Hetero] Batching/Unbatching DGLHeteroGraph ( #1017 )
...
* Update
* Update
* Update
* Fix
* CI style fix
* CI fix style
* Fix
* Try CI
* Fix test
* Update
* Update
* Update
* Update
2019-11-26 14:40:50 +08:00
f1542b9dfa
Fix ( #1019 )
2019-11-20 15:14:40 +08:00
e2b7f745ca
[Hetero] Doc ( #892 )
...
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* style fixes & undefined name fix
* transpose=False in test
2019-10-06 20:17:40 +08:00
33b8700b7d
[Bugfix][Hetero] Fix typo ( #891 )
...
Don't know why it passed the merging test...
2019-09-30 17:05:58 +08:00
0ca52bfc88
[Hetero] Create heterograph from dictionary of edge lists ( #882 )
...
* [Hetero] Create heterograph from dictionary of edge lists
* rename
* address comments
2019-09-30 15:41:41 +08:00
02fe316d7c
[Bugfix][Hetero] fix to_hetero when metagraph is given ( #873 )
...
* fix to_hetero when metagraph is given
* minor fix
* add more check
2019-09-22 11:41:49 -04:00
f9c0217d27
[Bugfix] Fix number of nodes mismatch in to_homo() conversion ( #874 )
2019-09-22 19:30:24 +08:00
9b4d60799a
[Hetero] New syntax ( #824 )
...
* WIP. remove graph arg in NodeBatch and EdgeBatch
* refactor: use graph adapter for scheduler
* WIP: recv
* draft impl
* stuck at bipartite
* bipartite->unitgraph; support dsttype == srctype
* pass test_query
* pass test_query
* pass test_view
* test apply
* pass udf message passing tests
* pass quan's test using builtins
* WIP: wildcard slicing
* new construct methods
* broken
* good
* add stack cross reducer
* fix bug; fix mx
* fix bug in csrmm2 when the CSR is not square
* lint
* removed FlattenedHeteroGraph class
* WIP
* prop nodes, prop edges, filter nodes/edges
* add DGLGraph tests to heterograph. Fix several bugs
* finish nx<->hetero graph conversion
* create bipartite from nx
* more spec on hetero/homo conversion
* silly fixes
* check node and edge types
* repr
* to api
* adj APIs
* inc
* fix some lints and bugs
* fix some lints
* hetero/homo conversion
* fix flatten test
* more spec in hetero_from_homo and test
* flatten using concat names
* WIP: creators
* rewrite hetero_from_homo in a more efficient way
* remove useless variables
* fix lint
* subgraphs and typed subgraphs
* lint & removed heterosubgraph class
* lint x2
* disable heterograph mutation test
* docstring update
* add edge id for nx graph test
* fix mx unittests
* fix bug
* try fix
* fix unittest when cross_reducer is stack
* fix ci
* fix nx bipartite bug; docstring
* fix scipy creation bug
* lint
* fix bug when converting heterograph from homograph
* fix bug in hetero_from_homo about ntype order
* trailing white
* docstring fixes for add_foo and data views
* docstring for relation slice
* to_hetero and to_homo with feature support
* lint
* lint
* DGLGraph compatibility
* incidence matrix & docstring fixes
* example string fixes
* feature in hetero_from_relations
* deduplication of edge types in to_hetero
* fix lint
* fix
2019-09-17 15:41:57 -04:00
Muhammed Fatih BALIN