51ba662169
Fix GINDT and #2087 ( #2103 )
...
* fix gindt
* ff
* fix
* minor fix
* fix
2020-08-26 15:53:45 +08:00
2ce426d956
[Bug] add_edges() crashes if the input tensor is empty ( #2100 )
...
* [Bug] add_edges() crashes if the input tensor is empty
* lint
* fix
2020-08-24 16:04:41 +08:00
bcff14ccde
[Dco] Remove preface in guide ( #2096 )
...
* fix
* fix
2020-08-23 10:27:15 +08:00
7ead28c315
[Doc] [NN] Fix message and nn user guide link ( #2090 )
...
* fix user guide link
* some fix on tensorflow
2020-08-22 00:18:22 +08:00
cd204a4ac9
[Distributed] Use barrier instead of sleep in DistDataloader ( #2086 )
...
* use barrier instead of sleep
* lint
2020-08-21 18:01:09 +08:00
ad8530a4dc
[Readme] 0.5.0 release and bump to new prerelease versions ( #2082 )
...
* [Readme] 0.5.0 release and bump to new prerelease versions
* bump version
2020-08-21 12:29:17 +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
35e25914ad
Update version check of PyTorch to 1.5 ( #2079 )
2020-08-20 21:33:29 +08:00
ef976be1e9
[Bug][Doc] Fix NodeDataLoader docstrings and code ( #2063 )
2020-08-19 21:59:02 +08:00
83654fdc4e
fix tu dataset ( #2064 )
2020-08-19 18:25:56 +08:00
3af0e91c0e
[Frame] Fix for Column Index Device ( #2055 )
...
* Update frame.py
* add unit test
* fix test
* fix
* fix
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-19 16:10:52 +08:00
a4a7e02f5f
[BugFix] Fix a small bug on kvstore ( #2058 )
...
* small fix
* update
2020-08-19 14:57:45 +08:00
75e89a153f
remove debug information ( #2056 )
2020-08-19 13:19:41 +08:00
9da1629c9d
[Distributed] Some small fixes on doc ( #2049 )
...
* quick fix.
* update sparse optimizer.
* fix.
* fix
2020-08-18 21:13:19 -07:00
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
75ffc31f76
[Doc] Update the docstring of distributed APIs. ( #2025 )
...
* add doc.
* update DistGraph.
* add DistTensor.
* update DistEmbedding.
* add partition.py
* add sampling.
* fix.
* add graph partition book and create a base class.
* fix test.
* add rst.
* update doc rst.
* update.
* fix.
* fix docs
* update distributed tensor and embeddings.
* add checks.
* update DistGraph.
* update initialization.
* fix graph partition book.
* update graph partition book.
* update partition.
* update partition.
* fix.
* add example code.
* update DistGraph
* Update python/dgl/distributed/dist_context.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* Update python/dgl/distributed/dist_context.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* Update python/dgl/distributed/dist_dataloader.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* Update python/dgl/distributed/dist_dataloader.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* Update python/dgl/distributed/dist_dataloader.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* update initialize.
* update dataloader.
* update distgraph.
* update DistGraph.
* update DistTensor.
* update.
* more updates.
* fix lint.
* add num_nodes and num_edges
Co-authored-by: Chao Ma <mctt90@gmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-18 11:53:45 -07:00
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
65866989c0
[NN] [Doc] Fix nn api doc ( #2047 )
...
* fix mxnet nn doc and no note on chebconv
* change notes to note to highlight
2020-08-18 23:47:16 +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
9088c63592
[Feature] Change the Default Value of transpose in DGLGraph.adj ( #2046 )
...
* Update adj
* Fix
2020-08-18 22:45:46 +08:00
edfbee2ca8
[Feature] Make sample_neighbors copy features on demand ( #2042 )
...
* fix
* fix
* lint
* fix
* test
* fix
* fix
2020-08-18 22:25:19 +08:00
aa19df1bbb
[Bugfix] Fix batching isolated node types ( #2035 )
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* [Bugfix] Fix batching isolated ntypes
* fix test
* remove test.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-18 09:29:05 +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
0afc3cf8e1
[NN] Add ChebConv for Tensorflow ( #2038 )
...
* add chebconv
* fix
* lint
* fix lint
* docs
2020-08-17 22:12:27 +08:00
b35388020d
[Bugfix] fix vocab not saved bug in SSTDataset ( #2036 )
...
* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update tree.py
2020-08-17 21:59:14 +08:00
a8b27b475c
disable batching blocks ( #2034 )
2020-08-17 16:45:57 +08:00
b1e69105d4
[Doc] API Doc update for mxnet and tf, remove some degree check ( #2028 )
...
* mx tf relconv
* use method instead of private attr
* src and dst have different fc for gat
* update edgeconv
* change sage and sgconv
* no degree check on gin
* add remainding API doc
* fix pylint
* infer fc_src and fc_dst, only one tensor for block
* fix pytest
2020-08-17 13:23:44 +08:00
4f1da61b58
[Doc] fix inconsistencies in minibatch user guide ( #2032 )
2020-08-17 12:43:43 +08:00
e291f503f2
[Fix] Update libinfo.py ( #1830 )
...
* Update libinfo.py
fix `if search_path is list` error, and improve the code.
* change string format for compatibility with py35
change string format
* Update libinfo.py
* Update libinfo.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2020-08-17 10:52:11 +08:00
1f7b219594
[Doc] User guide section 5 and 6 ( #2029 )
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* [Doc] User guide section 5 and 6
* oops
* fix
2020-08-17 09:47:01 +08:00
2fc280ba65
only filling zeros for min/max reducer ( #2026 )
2020-08-15 12:43:36 +08:00
63e2ba23c6
[WIP][Kernel] Set the built-in reduce result of zero-degree nodes to 0 in C ( #2017 )
...
* test idea
* cuda kernels
* lint and fixes
* lint
* change to another strategy
* use infinity
* fix
Co-authored-by: Zihao Ye <expye@outlook.com >
2020-08-14 22:59:24 +08:00
2fa7f71ad5
[Doc] new nn api doc ( #2019 )
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* Add dotproduct attention
* [Feature] Add dotproduct attention
* [Feature] Add dotproduct attention
* [Feature] Add dotproduct attention
* [New] Update landing page
* [New] Update landing page
* [New] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Improvement] use dgl build-in in dotgatconv
* [Doc] review API doc string bottom up
* [Doc] Add doc of input and output features
* [Doc] Update doc string for pooling and transformer.
* [Doc] Reformat doc string and change some wordings.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-14 18:00:38 +08:00
c113a5a0d7
Update dgl_dataset.py ( #2021 )
2020-08-14 16:17:37 +08:00
efa95d8673
[Distributed] Fix bugs ( #2009 )
...
* fix.
* add tests.
* fix.
* fix.
2020-08-13 23:51:11 -07:00
1ad46fd015
[Distributed] support distributed sampling in NodeDataLoader ( #2012 )
...
* fix.
* doesn't support EdgeDataLoader
* add test.
* fix.
* fix test.
* catch errors in the test.
* fix.
* fix error message
* add print.
* join the server processes.
* update test.
* fix test.
2020-08-13 22:49:21 -07:00
15e3ff878c
[Distributed] Fix memory leak in kvstore ( #2016 )
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* Fix memory leak
* update
* update
* update
* update
* update
* update
* update
2020-08-13 17:17:24 +08:00
4672c022a8
[hotfix] no in-degree check on sage ( #2014 )
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* no degre check on sage
* fix pytest
* no in degree check for heteroconv
2020-08-13 13:11:55 +08:00
cd48435206
[Transform] Docstring and subframes ( #1962 )
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* update knn graph docs
* more docs
* [Doc] transform module docstrings
* remove copy_ndata and copy_edata
* fix
* lint
* fix
* fix
* fix
* clean up docstrings
* fix docstring
* dtype specifications
* addresses comments
* fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-13 10:41:43 +08:00
6294677f8a
[hotfix] Set reduce results to all zero for nodes with zero in-degrees. ( #2011 )
2020-08-13 01:20:56 +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
69f5869f3b
[Doc] NN doc refactor Conv Layers ( #1672 )
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* go through gcn, relgcn
* fix tagconv formula
* fix doc in sageconv
* fix sgconv doc
* replace hat with tilde
* more comments on gmmconv
* fix agnnconv chebconv doc
* modify nnconv doc
* remove &
* add nn conv examples
* Rebase master
* More merge conflicts
* check homo
* add back self loop for some convs, check homo in tranform
* add example for denseconv
* add example and doc for dotgat and cfconv
* check in-degree for graphconv
* add language fix
* gconv address all comments
* another round of change based on api template
* change agnn
* go through agnn, appnp, atomic, cf, cheb, dense, gat, sage modules
* finish pytorch part of nn conv
* mxnet graphconv done
* tensorflow graphconv works
* add new modules into doc
* add comments to not split code
* refine doc
* resr
* more comments
* more fix
* finish conv and dense conv part api
* pylint fix
* fix pylink
* fix pylint
* more fix
* fix
* fix test fail because zere in degree
* fix test fail
* sage is not update for mxnet tf
Co-authored-by: Ubuntu <ubuntu@ip-172-31-0-81.us-east-2.compute.internal >
2020-08-12 18:47:19 +08:00
5e34ca8bb5
[Feature] Lazy copy ndata, edata to device ( #1986 )
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* Lazy to device
* remove print
* lint
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* lint
* Fix
* Revert "Fix"
This reverts commit 615c9b8f80f5f6ee2ab43c849a22f0083deedf3b.
* Add test for frame lazy update
* disable tensorflow
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-08-12 13:04:47 +08:00
d1cf5c383e
[Distributed] adjust various APIs. ( #1993 )
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* rename get_data_size.
* remove g from DistTensor.
* remove g from DistEmbedding.
* clean up API of graph partition book.
* fix DistGraph
* fix lint.
* collect all part policies.
* fix.
* fix.
* support distributed sampler.
* remove partition.py
2020-08-11 20:22:00 -07:00
4efa332044
[Distributed] Move server start code to initialize. ( #2002 )
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* move server start code to initialize.
* fix.
* fix lint.
* fix examples.
* add more checks.
2020-08-11 16:58:18 -07:00
0f56575938
[feature] Allow copy_e + udf reduce function ( #1996 )
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* up
* pylint
2020-08-11 18:47:40 +08:00
f5eb80d221
[Feature] Edge DataLoader for edge classification & link prediction ( #1828 )
...
* clean commit
* oops forgot the most important files
* use einsum
* copy feature from frontier to block
* Revert "copy feature from frontier to block"
This reverts commit 5224ec963eb6a3ef1b6ab74d8ecbd44e4e42f285.
* temp fix
* unit test
* fix
* revert jtnn
* lint
* fix win64
* docstring fixes and doc indexing
* revert einsum in sparse bidecoder
* fix some examples
* lint
* fix due to some tediousness in remove_edges
* addresses comments
* fix
* more jtnn fixes
* fix
2020-08-11 18:00:58 +08:00
d340ea3aa8
[Distributed] Remove server_count from ip_config.txt ( #1985 )
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* remove server_count from ip_config.txt
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* Update dist_context.py
* fix lint.
* make it work for multiple spaces.
* update ip_config.txt.
* fix examples.
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* udpate
* update
* update
* update
* update
* update
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-08-11 17:41:48 +08:00
71f4230a8b
[Fix] OpenMP compatibility issues ( #1992 )
...
* fix OpenMP compatibility issues
* typo
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-11 14:26:34 +08:00
a089b91fdf
Remove stale partition code and fix #1949 ( #1984 )
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* remove unused code
* fix litn
* fix
2020-08-11 10:51:07 +08:00
Jinjing Zhou