GitLab

* [BugFix] fix unexpected exception when agg_type is GCN and bias is disabled

* Update sageconv.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Adding tarfile member sanitization to extractall()

* Update utils.py
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>

* overwrite default_collate_fn

* Update dataloader.py

* Update dataloader.py

* Update dataloader.py

* Update dataloader.py

* Update test_dataloader.py

* revert the test code being reverted in #4956

* Optimize bias term in sageconv

* fix lint

* Remove bias sharing

* Update sageconv.py
Co-authored-by: Bartlomiej Gawrych <barlomiej.gawrych@intel.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Update

* Update

* Update

* lint

* lint

* Update

* CI

* Update diag_matrix.py

* Update sparse_matrix.py

* Update sparse_matrix.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>

* fix fp16 in nn modules

* fix lint

* remove the example
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* update

* Update

* Update

* Update

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* Add SpatialEncoder and SpatialEncoder3d

* Optimize the code execution efficiency

* Fixed certain problems according to Dongyu's suggestions.

* Fix an error about probability of division by zero in PathEcoder; Change certain designs in SpatialEncoder

* Fix a typo

* polish the docstring

* fix doc

* lint
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Co-authored-by: rudongyu <ru_dongyu@outlook.com>

* update

* lint

* lint

* comments
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* new print func

* lintrunner

* pass gcn

* example tests

* pass gcnii, hgnn, sgc, sign

* black

* test file

* add torchmetrics

* migrate appnp, c_and_s, twirls

* fix style

* minor fix

* fix hypergraphatt and twirls

* pass gat

* fix torchmetric

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

* [Sparse] Support BSpMM and BSDDMM

* Update SpMM and SDDMM error messages

* Use TORCH_CHECK

* Update error string

* add coalesce() and has_duplicate()

* Add duplicate check in spspmm

* black

* fix

* clang-format

* lintrunner

* minor fix

* fix

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* Update

* update

* Update

* Update

* Update

* format

* Update

* lint

* Update

* lint

* CI

* CI

* Update

* address comments
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* rename

* next time i should use lintrunner

* [Sparse] Add SpSpMM

* Update matmul interface

* address comments

* fix test utils to generate only coalesced matrices

* fix linter

* fix ut

* fix

* rm print
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* initial commit

* lint

* rename

* address comments

* add doctests

* address comments

* remove additional test

* add description

* lint

* lint

* lint

* Update test_reduction.py
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>

* [Sparse] Support SpMM and SDDMM

* Add SDDMMAutoGrad

* Rename SpMMImpl and SDDMMImpl and move them to dgl_sparse/src/matmul.h

* Update comments

* Update

* Minor fix

[Sparse] Add Two Sparse Matrices with Different Sparsity, DiagMatrix.dense, Add SparseMatrix and DiagMatrix (#5044)

* Update

* undo wrong edit

* lint

* fix import

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* replace LooseVersion with packaging.version

* import packaging from setuptools

* import packaging.version in dgl.utils

* format

* revert changes to apps/kg

* revert changes to _dataloading

* Update

* Update

* lint

* CI

* Update
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* Update from master (#4584)

* [Example][Refactor] Refactor graphsage multigpu and full-graph example (#4430)

* Add refactors for multi-gpu and full-graph example

* Fix format

* Update

* Update

* Update

* [Cleanup] Remove async_transferer (#4505)

* Remove async_transferer

* remove test

* Remove AsyncTransferer
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>

* [Cleanup] Remove duplicate entries of CUB submodule   (issue# 4395) (#4499)

* remove third_part/cub

* remove from third_party
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>

* [Bug] Enable turn on/off libxsmm at runtime (#4455)

* enable turn on/off libxsmm at runtime by adding a global config and related API
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>

* [Feature] Unify the cuda stream used in core library (#4480)

* Use an internal cuda stream for CopyDataFromTo

* small fix white space

* Fix to compile

* Make stream optional in copydata for compile

* fix lint issue

* Update cub functions to use internal stream

* Lint check

* Update CopyTo/CopyFrom/CopyFromTo to use internal stream

* Address comments

* Fix backward CUDA stream

* Avoid overloading CopyFromTo()

* Minor comment update

* Overload copydatafromto in cuda device api
Co-authored-by: xiny <xiny@nvidia.com>

* [Feature] Added exclude_self and output_batch to knn graph construction (Issues #4323 #4316) (#4389)

* * Added "exclude_self" and "output_batch" options to knn_graph and segmented_knn_graph
* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information

* * Changed defaults on new knn_graph and segmented_knn_graph function parameters, for compatibility; pytorch/test_geometry.py was failing

* * Added test to ensure dgl.remove_self_loop function correctly updates batch information

* * Added new knn_graph and segmented_knn_graph parameters to dgl.nn.KNNGraph and dgl.nn.SegmentedKNNGraph

* * Formatting

* * Oops, I missed the one in segmented_knn_graph when I fixed the similar thing in knn_graph

* * Fixed edge case handling when invalid k specified, since it still needs to be handled consistently for tests to pass
* Fixed context of batch info, since it must match the context of the input position data for remove_self_loop to succeed

* * Fixed batch info resulting from knn_graph when output_batch is true, for case of 3D input tensor, representing multiple segments

* * Added testing of new exclude_self and output_batch parameters on knn_graph and segmented_knn_graph, and their wrappers, KNNGraph and SegmentedKNNGraph, into the test_knn_cuda test

* * Added doc comments for new parameters

* * Added correct handling for uncommon case of k or more coincident points when excluding self edges in knn_graph and segmented_knn_graph
* Added test cases for more than k coincident points

* * Updated doc comments for output_batch parameters for clarity

* * Linter formatting fixes

* * Extracted out common function for test_knn_cpu and test_knn_cuda, to add the new test cases to test_knn_cpu

* * Rewording in doc comments

* * Removed output_batch parameter from knn_graph and segmented_knn_graph, in favour of always setting the batch information, except in knn_graph if x is a 2D tensor
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [CI] only known devs are authorized to trigger CI (#4518)

* [CI] only known devs are authorized to trigger CI

* fix if author is null

* add comments

* [Readability] Auto fix setup.py and update-version.py (#4446)

* Auto fix update-version

* Auto fix setup.py

* Auto fix update-version

* Auto fix setup.py

* [Doc] Change random.py to random_partition.py in guide on distributed partition pipeline (#4438)

* Update distributed-preprocessing.rst

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* fix unpinning when tensoradaptor is not available (#4450)

* [Doc] fix print issue in tutorial (#4459)

* [Example][Refactor] Refactor RGCN example (#4327)

* Refactor full graph entity classification

* Refactor rgcn with sampling

* README update

* Update

* Results update

* Respect default setting of self_loop=false in entity.py

* Update

* Update README

* Update for multi-gpu

* Update

* [doc] fix invalid link in user guide (#4468)

* [Example] directional_GSN for ogbg-molpcba (#4405)

* version-1

* version-2

* version-3

* update examples/README

* Update .gitignore

* update performance in README, delete scripts

* 1st approving review

* 2nd approving review
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Clarify the message name, which is 'm'. (#4462)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* [Refactor] Auto fix view.py. (#4461)
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Example] SEAL for OGBL (#4291)

* [Example] SEAL for OGBL

* update index

* update

* fix readme typo

* add seal sampler

* modify set ops

* prefetch

* efficiency test

* update

* optimize

* fix ScatterAdd dtype issue

* update sampler style

* update
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* [CI] use https instead of http (#4488)

* [BugFix] fix crash due to incorrect dtype in dgl.to_block() (#4487)

* [BugFix] fix crash due to incorrect dtype in dgl.to_block()

* fix test failure in TF

* [Feature] Make TensorAdapter Stream Aware (#4472)

* Allocate tensors in DGL's current stream

* make tensoradaptor stream-aware

* replace TAemtpy with cpu allocator

* fix typo

* try fix cpu allocation

* clean header

* redirect AllocDataSpace as well

* resolve comments

* [Build][Doc] Specify the sphinx version (#4465)
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* reformat

* reformat

* Auto fix update-version

* Auto fix setup.py

* reformat

* reformat
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Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* Move mock version of dgl_sparse library to DGL main repo (#4524)

* init

* Add api doc for sparse library

* support op btwn matrices with differnt sparsity

* Fixed docstring

* addresses comments

* lint check

* change keyword format to fmt
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* [DistPart] expose timeout config for process group (#4532)

* [DistPart] expose timeout config for process group

* refine code

* Update tools/distpartitioning/data_proc_pipeline.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Feature] Import PyTorch's CUDA stream management (#4503)

* add set_stream

* add .record_stream for NDArray and HeteroGraph

* refactor dgl stream Python APIs

* test record_stream

* add unit test for record stream

* use pytorch's stream

* fix lint

* fix cpu build

* address comments

* address comments

* add record stream tests for dgl.graph

* record frames and update dataloder

* add docstring

* update frame

* add backend check for record_stream

* remove CUDAThreadEntry::stream

* record stream for newly created formats

* fix bug

* fix cpp test

* fix None c_void_p to c_handle

* [examples]educe memory consumption (#4558)

* [examples]educe memory consumption

* reffine help message

* refine

* [Feature][REVIEW] Enable DGL cugaph nightly CI  (#4525)

* Added cugraph nightly scripts

* Removed nvcr.io//nvidia/pytorch:22.04-py3 reference
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* Revert "[Feature][REVIEW] Enable DGL cugaph nightly CI  (#4525)" (#4563)

This reverts commit ec171c64

.

* [Misc] Add flake8 lint workflow. (#4566)

* Add pyproject.toml for autopep8.

* Add pyproject.toml for autopep8.

* Add flake8 annotation in workflow.

* remove

* add

* clean up
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Try use official pylint workflow. (#4568)

* polish update_version

* update pylint workflow.

* add

* revert.
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [CI] refine stage logic (#4565)

* [CI] refine stage logic

* refine

* refine

* remove (#4570)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Add Pylint workflow for flake8. (#4571)

* remove

* Add pylint.
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Update the python version in Pylint workflow for flake8. (#4572)

* remove

* Add pylint.

* Change the python version for pylint.
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Update pylint. (#4574)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Use another workflow. (#4575)

* Update pylint.

* Use another workflow.
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Update pylint. (#4576)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Update pylint.yml

* Update pylint.yml

* Delete pylint.yml

* [Misc]Add pyproject.toml for autopep8 & black. (#4543)

* Add pyproject.toml for autopep8.

* Add pyproject.toml for autopep8.
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Feature] Bump DLPack to v0.7 and decouple DLPack from the core library (#4454)

* rename `DLContext` to `DGLContext`

* rename `kDLGPU` to `kDLCUDA`

* replace DLTensor with DGLArray

* fix linting

* Unify DGLType and DLDataType to DGLDataType

* Fix FFI

* rename DLDeviceType to DGLDeviceType

* decouple dlpack from the core library

* fix bug

* fix lint

* fix merge

* fix build

* address comments

* rename dl_converter to dlpack_convert

* remove redundant comments
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>
Co-authored-by: Israt Nisa <neesha295@gmail.com>
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: peizhou001 <110809584+peizhou001@users.noreply.github.com>
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
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Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Vibhu Jawa <vibhujawa@gmail.com>

* [Deprecation] Dataset Attributes (#4546)

* Update

* CI

* CI

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* [Example] Bug Fix (#4665)

* Update

* CI

* CI

* Update

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* Update

* Update (#4724)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* [API Deprecation]Rename DGLHeterpGraph to DGLGraph in Py files (#4835)

* rename DGLHeterpGraph to DGLGraph

* [Sparse] Add sparse matrix C++ implementation (#4773)

* [Sparse] Add sparse matrix C++ implementation

* Add documentation

* Update

* Minor fix

* Move Python code to dgl/mock_sparse2

* Move headers to include

* lint

* Update

* Add dgl_sparse directory

* Move src code to dgl_sparse

* Add __init__.py in tests to avoid naming conflict

* Add dgl sparse so in Jenkinsfile

* Complete docstring & SparseMatrix basic op

* lint

* Disable win tests

* fix lint issue

* [Misc] clang-format auto fix. (#4831)

* [Misc] clang-format auto fix.

* blabla

* nolint

* blabla
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Dist] enable access DistGraph.edges via canonical etype (#4814)

* [Dist] enable access DistGraph.edges via canonical etype

* refine code

* refine test

* refine code

* Reading files in chunks to reduce the memory footprint of pyarrow (#4795)

All tasks completed.

* [Dist] Create <graph_name>_stats.txt file if it does not exist before ParMETIS execution (#4791)

* check if stats file exists, if not create one before parmetis run

* correct the typo error and correctly use constants.GRAPH_NAME

* alltoall returns tensor list with None values, which is failing torch.cat(). (#4788)

* replace batch_hetero

* [Misc] Add // NOLINT for the very long code. (#4834)

* alternative

* fix

* remove_todo

* blabl

* ablabl
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* fix (#4841)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* a better way to init threadlocal prng (#4808)
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* [DIST] Message size to retrieve SHUFFLE_GLOBAL_NIDs is resulting in very large messages and resulting in killed process (#4790)

* Send out the message to the distributed lookup service in batches.

* Update function signature for allgather_sizes function call.

* Removed the unnecessary if statement .

* Removed logging.info message, which is not needed.

* [Misc] Minor code style fix.  (#4843)

* [Misc] Change the max line length for cpp to 80 in lint.

* blabla

* blabla

* blabla

* ablabla
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Sparse] Lint C++ files (#4845)

* [Dist] Fix typo of metis preprocess in dist partitin pipeline

* Fix ogb/ogbn-mag/heter-RGCN example (#4839)
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* fix issue

* [Misc] Update cpplint. (#4844)
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Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: kylasa <kylasa@gmail.com>
Co-authored-by: Muhammed Fatih BALIN <m.f.balin@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* [API Deprecate]Remove as_heterograph and  as_immutable_graph (#4851)

* Remove batch_hetero and unbatch_hetero

* [API Deprecate]Rename DGLHeterpGraph to DGLGraph in python files (#4833)

* remove training new line

* remove node_attrs and edge_attrs in batch.py (#4890)

* [API Deprecation] Remove copy_src,copy_edge,src_mul_edge in dgl.function (#4891)

* remove emb_tensor in NodeEmbedding (#4892)

* [API Deprecation]Remove 5 APIs in DGLGraph (#4902)

* [API Deprecation]Remove APIs in old dgl section in DGLGraph (#4901)

* [API Deprecation]Remove adjacency_matrix_scipy and inplace args in candidates  (#4895)

* [API Deprecation] Remove add_edge in DGLGraph (#4894)

* [API Derepcation]Remove __contains__ in DGLGraph (#4937)

* [API Deprecation]Remove edge_id() and force_multi argument in edge_ids() (#4896)

* fix issue

* remove deprecated_kwargs

* remove unused import
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
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* Revert "[Sparse] Add SpMM and SDDMM. (#4999)"

This reverts commit 15365d78.

* lint

* [Sparse] Add SpMM and SDDMM

* Update

* Add CSR and CSC SpMM tests

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* Update

* Update

* Update

* Update

* update

* lint

* CI

* CI

* CI
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* Add GraphTransformerLayer (dense)

* beautify the python code with black

* refine according to mufei's comments

* fix AttributeError in unit test

* rename module as GraphormerLayer

* fix name issue
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* turn off use_alternate_stream when tensoradaptor is not enabled

* add docstring