f13b9b6212
[Doc] Scan the API docs and make many changes ( #2080 )
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* 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
debfd4bf78
Graph chapter, user guide ( #2078 )
2020-08-20 21:08:40 +08:00
ef78d675e9
Fix docs ( #2073 )
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* remove mxnet tutorial
* remove sse
* fix docs
2020-08-20 15:37:50 +08:00
9da1629c9d
[Distributed] Some small fixes on doc ( #2049 )
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* quick fix.
* update sparse optimizer.
* fix.
* fix
2020-08-18 21:13:19 -07:00
75ffc31f76
[Doc] Update the docstring of distributed APIs. ( #2025 )
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* 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
65866989c0
[NN] [Doc] Fix nn api doc ( #2047 )
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* fix mxnet nn doc and no note on chebconv
* change notes to note to highlight
2020-08-18 23:47:16 +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 )
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* add chebconv
* fix
* lint
* fix lint
* docs
2020-08-17 22:12:27 +08:00
5cb5759366
[Doc] split docs to multiple rst files ( #2037 )
2020-08-17 19:02:31 +08:00
a9c4df67b9
[Doc] Move image in dataset User guide to s3 server ( #2033 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
* update links using ref
* modify the link of save_graphs and load_graphs in dataset user guide
* move image to s3 server.
2020-08-17 15:33:41 +08:00
4f1da61b58
[Doc] fix inconsistencies in minibatch user guide ( #2032 )
2020-08-17 12:43:43 +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
62e69b67aa
[Doc] Modify the link of save_graphs and load_graphs in dataset user guide ( #2027 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
* update links using ref
* modify the link of save_graphs and load_graphs in dataset user guide
2020-08-15 09:21:08 +08:00
de2e608bb3
Update dgl.rst ( #2020 )
2020-08-14 18:18:45 +08:00
f4f78803cf
[Doc] Update links by :ref in dataset user guide ( #2024 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
* update links using ref
2020-08-14 17:28:54 +08:00
fe121c63f5
[Doc] Image in dataset user guide ( #2018 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
2020-08-14 12:26:38 +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
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
a753972826
[Doc] Data pipeline User guide fix links to classes ( #2006 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
2020-08-12 15:48:59 +08:00
af990989cf
[Doc] Data pipeline user guide remove chapter number ( #1997 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
2020-08-11 23:07:04 +08:00
f5eb80d221
[Feature] Edge DataLoader for edge classification & link prediction ( #1828 )
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* 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
d090ae865c
[Doc] Chapter 3 Graph data input pipeline in DGL ( #1995 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
2020-08-11 16:49:45 +08:00
e262e11083
[Doc] Message passing and NN User Guide ( #1991 )
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* add message passing user gude rst
* add nn user guide
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2020-08-11 16:20:16 +08:00
c2cd6eb22e
[Doc] Reorg doc ( #1989 )
2020-08-10 23:19:03 +08:00
18bfec24cf
[hotfix] Refactor edge softmax module ( #1967 )
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* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
2020-08-07 23:50:12 +08:00
3d8377062c
[Doc] Dataset api doc add save_info(), load_info() ( #1954 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* update doc
* Update data.rst
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-06 22:25:45 +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
a28bfa9f5f
[hotfix] Activate kernel unittest for tensorflow ( #1895 )
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* upd
* upd
* upd
* upd
* upd
* trigger
* simplify unittest
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-07-31 19:57:53 +08:00
05a4337901
[Doc] Introduce the relation of message passing APIs and operators in docstring. ( #1878 )
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* upd
* fix typo
* upd
2020-07-29 00:41:47 +08:00
2fa2b4534e
[Feature] Support higher order derivative for message passing. ( #1877 )
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* upd
* fix typo
2020-07-28 23:11:06 +08:00
2b8eb5be6f
[refactor] Move spmm and sddmm operators to operator module ( #1873 )
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* upd
* upd
* upd
* upd
2020-07-28 18:39:12 +08:00
bc209bff94
[bugfix] Fix the deterministic of kernel test and add documentation. ( #1799 )
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* upd
* upd
* upd
* relax
* relax too
* upd
2020-07-14 04:22:31 +08:00
168a88e570
[Sampling] NodeDataLoader for node classification ( #1635 )
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* neighbor sampler data loader first commit
* more commit
* nodedataloader
* fix
* update RGCN example
* update OGB
* fixes
* fix minibatch RGCN crashing with self loop
* reverting gatconv test code
* fix
* change to new solution that doesn't require tf dataloader
* fix
* lint
* fix
* fixes
* change doc
* fix docstring
* docstring fixes
* return seeds and input nodes from data loader
* fixes
* fix test
* fix windows build problem
* add pytorch wrapper
* fixes
* add pytorch wrapper
* add unit test
* add -1 support to sample_neighbors & fix docstrings
* docstring fix
* lint
* add minibatch rgcn evaluations
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Tong He <hetong007@gmail.com >
2020-07-02 16:31:05 +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
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
cc07bd44e4
[Readme] Add cuda 10.2 to docs ( #1560 )
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* add cuda 10.2
* type
2020-05-25 16:24:30 +08:00
7ba9cbc63e
[Docs] Fix docstrings and documentations ( #1420 )
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* fix docs of to_block
* fix
* oops
* more fixes
2020-05-19 13:04:55 +08:00
c2e61ce10b
[Refactor] Restrict sparse format for DGLHeteroGraph ( #1474 )
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* 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
8d20c24928
[Docs] Fix typos in env vars docs ( #1429 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-04-09 12:33:06 +08:00
d3560b7155
[DGL-LifeSci] Documentation ( #1414 )
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* Update
* Update
* Update
2020-04-02 21:19:07 +08:00
7e0893e697
[Docs] Fix doc build doesn't work for nn.tensorflow and nn.mxnet ( #1413 )
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* fix
* lint
* fix
2020-04-02 20:31:07 +08:00
e9440acb06
[TF] TF backend fix and new logic to choose backend ( #1393 )
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* TF backend fix and new logic to choose backend
* fix
* fix
* fix
* fix
* fix backend
* fix
* dlpack alignment
* add flag
* flag
* lint
* lint
* remove unused
* several fixes
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-30 18:45:17 +08:00
08fcda325b
[Doc] Fix link to backends docs ( #1376 )
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Co-authored-by: Tong He <hetong007@gmail.com >
2020-03-25 18:20:09 +08:00
166275754c
Update instructions for building from source ( #1363 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-16 19:38:36 +08:00
7ee77f72ae
Fix submodule has submodules ( #1332 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-60-78.ec2.internal >
2020-03-09 02:40:10 +08:00
09ade2f265
upd ( #1321 )
2020-03-06 14:17:48 +08:00
93ac29ce34
[Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph ( #1216 )
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* upd
* upd
* upd
* lint
* fix
* fix test
* fix
* fix
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd tutorial
* upd
* upd
* fix kg
* upd doc organization
* refresh test
* upd
* refactor doc
* fix lint
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2020-03-05 18:03:57 +08:00
5967d81782
[Doc] Re-organize API docs and tutorials ( #1222 )
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* reorg tutorials and api docs
* fix
2020-01-26 21:26:34 +08:00
f1a8f926a4
[Feature] Add environment variable to switch on/off MXNet set_np_shape ( #1207 )
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* add env var
* Trigger CI
* simplification
* add doc
2020-01-20 13:54:14 +08:00
a00636a02b
[Tensorflow] Several nn & example ( #1191 )
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* several nn example
* appnp
* fix lint
* lint
* add dgi
* fix
* fix
* fix
* fff
* docs
* 111
* fix
* change init
* change result
* tiaocan+1
* fix
* fix lint
* fix
* fix
2020-01-19 22:48:40 +08:00
Minjie Wang