33a8bb93bf
[Feature] Basic utils to handle raw data features ( #2102 )
...
* add feature utils and add test for feature norm
* Add docstring and test
* upd
* dis able some test
* Update
* update doc string
* update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
2020-08-27 11:36:39 +08:00
51ba662169
Fix GINDT and #2087 ( #2103 )
...
* fix gindt
* ff
* fix
* minor fix
* fix
2020-08-26 15:53:45 +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
83654fdc4e
fix tu dataset ( #2064 )
2020-08-19 18:25:56 +08:00
4edde000a4
Fix tree lstm ( #2052 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-63-129.ec2.internal >
2020-08-19 10:44:10 +08:00
3d65484323
Fix mxnet gin ( #2048 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-19 00:05:15 +08:00
be444e52d9
[Doc/Feature] Refactor, doc update and behavior fix for graphs ( #1983 )
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* 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
b35388020d
[Bugfix] fix vocab not saved bug in SSTDataset ( #2036 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update tree.py
2020-08-17 21:59:14 +08:00
c113a5a0d7
Update dgl_dataset.py ( #2021 )
2020-08-14 16:17:37 +08:00
5362908236
Fix save/load for old version files ( #1994 )
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* load hetero
* fix
* more error message
* add warning
* add alias to dgl namespace
* fix tests
2020-08-12 23:45:21 +08:00
e4b4fcffc2
hotfix ( #1987 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-10 22:06:25 +08:00
e75157738b
hotfix ( #1980 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal >
2020-08-09 11:25:13 +08:00
264d96cdf5
[bugfix] Fix a bunch of examples to be compatible with dgl 0.5 ( #1957 )
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* upd
* upd
* upd
* upd
* upd
* upd
* fix pinsage also
* upd
* upd
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-29-3.us-east-2.compute.internal >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-08 01:31:23 +08:00
22167f7203
[Refactor] Enable new kernel in all message passing APIs ( #1953 )
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* WIP: frame refactor
* new frame
* simple update_all builtin
* move all subgraph routines into the same file
* sddmm & spmm schedule; node & edge udf
* degree bucketing
* some tricky 0deg corner cases
* bug in frame append
* merge test_hetero_basics and test_basics
* some code rearange
* fix test_heterograph
* add mean spmm
* enable all builtin combinations
* pass gpu test
* pass pytorch tests
* wip
* fix some pt debugging codes
* fix bug in mxnet backward
* pass all mxnet utests
* passed tf tests
* docstring
* lint
* lint
* fix broadcasting bugs
* add warning and clamp for mean reducer
* add test for zero-degree mean
* address comments
* lint
* small fix
2020-08-07 15:40:25 +08:00
5d5436ba18
[Dataset] RedditDataset change data.train_mask to numpy array ( #1961 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update reddit.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-07 15:22:13 +08:00
78651016f4
[Hot fix][Dataset] knowledge graph dataset statistics output ( #1952 )
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* Hot fix
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-06 20:20:20 +08:00
13ea9ddb06
[Doc] Fix some format issues in dataset api doc ( #1951 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* update doc
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-06 16:51:46 +08:00
967ecb8064
[Dataset] Fix the docstring format for dgl.data section ( #1941 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* update data rst
* update data doc and docstring
* API doc rst for dataset
* docstring
* update api doc
* add url format
* update docstring
* update citation graph
* update knowledge graph
* update gc datasets
* fix index
* Rst fix (#3 )
* Fix syntax
* syntax
* update docstring
* update doc (#4 )
* final update
* fix rdflib
* fix rdf
Co-authored-by: HuXiangkun <huxk_hit@qq.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-06 14:47:49 +08:00
451ed6d836
[Dataset] SBMMixtureDataset ( #1920 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* SBMMixture dataset
* Update sbm.py
* fix example
* Update sbm.py
* Revert "Update sbm.py"
This reverts commit 066db5c89bd5e159981ae7cad1bfb883ea5db71d.
* Update sbm.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-04 15:06:53 +08:00
2c141229d5
[Dataset] RedditDataset ( #1914 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* RedditDataset
* Update reddit.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 23:49:22 +08:00
37aa99c510
[Dataset] GNNBenchmarkDataset ( #1912 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* gnn benchmark dataset
* Update gnn_benckmark.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 23:28:58 +08:00
001d793711
[Dataset] SSTDataset ( #1918 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* SSTDataset
* Update tree.py
2020-08-03 19:15:28 +08:00
73b9c6f18c
[Dataset] GDELTDataset ( #1911 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* gdelt dataset
* Update gdelt.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 17:43:50 +08:00
06ea03d0f8
[Dataset] ICEWS18Dataset ( #1913 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* ICEWS18Dataset
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 17:07:02 +08:00
b5be4f4bbf
[Dataset] Update dataset hash with deterministic function ( #1919 )
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* update hash with deterministic function
* update docstring
* add test on determination
2020-08-03 16:17:00 +08:00
39ed096630
[Dataset] Builtin LegacyTUDataset and TUDataset ( #1891 )
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* add LegacyTUDataset and TUDataset
* update docstrings and url
* update docstrings
* add hash to fix save/load
* update docstring and use hash
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 14:40:36 +08:00
22485e58d3
[Dataset] BitcoinOTCDataset ( #1910 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* bitcoinotc dataset
* Update bitcoinotc.py
2020-08-03 12:15:04 +08:00
d22f96feb4
[Dataset] QM7bDataset ( #1915 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* QM7bDataset
* Update qm7b.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 11:58:31 +08:00
9bcce7bead
[Dataset] PPIDataset ( #1906 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Revert "Revert "PPIDataset""
This reverts commit 6938a4cbe3ac6e38d3e0188b5699e5c952a6102e.
* update doc string
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-03 00:30:01 +08:00
743c38401c
[Dataset] KarateClubDataset ( #1897 )
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* karateclub dataset
* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update karate.py
* doc string
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-02 22:39:11 +08:00
cb2c4ec17b
Fix ( #1909 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-02 14:53:21 +08:00
303e42367d
Hot Fix docstring ( #1907 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-01 23:24:24 +08:00
b347590a37
[Dataset] Citation graph ( #1902 )
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* citation graph
* GCN example use new citatoin dataset
* mxnet gat
* triger
* Fix
* Fix gat
* fix
* Fix tensorflow dgi
* Fix appnp, graphsage for mxnet
* fix monet and sgc for mxnet
* Fix tagcn
* update sgc, appnp
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-01 19:25:50 +08:00
18c960a1b5
[Dataset] Builtin MiniGCDataset ( #1890 )
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* add minigc
* fix
* update docstrings
* update docstring
* add hash to fix save/load
* update hash
2020-07-31 17:40:02 +08:00
f05bd4971c
[Dataset] Builtin GINDataset ( #1889 )
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* update GINDataset
* update
* update docstring
* update
* update docstrings
* add hash to fix save/load
* fix some stupid bugs
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-07-31 17:12:14 +08:00
fb02aa2d85
[Dataset] Add hash function to distinguish instances from the same dataset class ( #1894 )
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* add hash function in base data classes
* update doc
2020-07-31 15:53:32 +08:00
dbb028acc8
[Dataset] Builtin knowledge graph dataset ( #1881 )
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* buildin knowledge graph dataset
* upd
* docstring
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Tong He <hetong007@gmail.com >
2020-07-30 23:37:33 +08:00
444becf00a
[Misc] Move many deprecated codes to the deprecate folder ( #1893 )
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* some file movements
* move some codes to deprecated
* more deprecation
* lint
* remove useless test
2020-07-30 18:17:33 +08:00
faa1dc56fc
hot fix ( #1888 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-30 12:02:49 +08:00
aee1067941
[Dataset] RDF dataset with DGL-Dataset template ( #1869 )
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* update rdf builtin dataset
* Fix
* use new dataset
* fix
* rdf dataset using new framework
* tf work
* Fix mxnet
* Fix tensorflow
* Fix mxnet
* Update
* upd
* update some docstring
* clean some dead code
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-30 09:12:00 +08:00
44089c8b4d
[Refactor][Graph] Merge DGLGraph and DGLHeteroGraph ( #1862 )
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* 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
41b905da71
Fix #1826 ( #1835 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-21 16:32:54 +08:00
64557819d9
Basic class for dgl datasetyy ( #1809 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-20 13:12:36 +08:00
8a183e3fcb
[BugFix] Fix #1779 ( #1781 )
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* Fix bug #1779
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-07-10 17:35:23 +08:00
cc73c60cbc
[Bug Fix] Fix Heterogenous graph save crash when some edge type names are identical. ( #1751 )
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* Fix hetero serialize
* Add test case
y
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-07-04 21:44:53 +08:00
18a26fcfb1
[Data] Support HeteroGraph save/load ( #1526 )
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* 111
* add history version test
* fix
* 111
* save
* ``
* fix1
* 111
* add save heterograph
* lint
* lint
* add tests
* minor fix
* fix
* docs
* add format tets
* use unique_ptr
* fix
* fix interface
* 111
* 111
* fix
* lint
* fix
* add support to s3
* fix
* fix
* fix leak
* fix
* fix docs
* fix
* linlt
* fix
* fix
* fix
* address comment
* address comment
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-06-30 13:34:50 +08:00
57d111f9e5
[Bug] Fix broken initialization in Reddit ( #1634 )
2020-06-14 03:08:40 +08:00
36c7b77167
[LifeSci] Move to Independent Repo ( #1592 )
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* Move LifeSci
* Remove doc
2020-06-05 21:28:24 +08:00
2b9d06b6e2
[Data] Retry downloading once if dataset initialization fails ( #1520 )
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* dataloader guard
* more fixes
* sets overwrite to true by default
* Update utils.py
* fix
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2020-06-03 17:21:05 +08:00
90d2118da5
[Dataset] Change Cora Split ( #1583 )
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* Use new version of Cora
* Fix import
2020-06-03 15:45:38 +08:00
xiang song(charlie.song)