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[API Deprecation]Change DGLHeteroGraph to DGLGraph in DOC#4840

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peizhou001 merged 17 commits intodmlc:masterfrom
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Nov 10, 2022
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[API Deprecation]Change DGLHeteroGraph to DGLGraph in DOC#4840
peizhou001 merged 17 commits intodmlc:masterfrom
peizhou001:peizhou/DGLHeterroDocDeprecare

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@peizhou001 peizhou001 commented Nov 8, 2022

Description

Checklist

Please feel free to remove inapplicable items for your PR.

  • The PR title starts with [$CATEGORY] (such as [NN], [Model], [Doc], [Feature]])
  • I've leverage the tools to beautify the python and c++ code.
  • The PR is complete and small, read the Google eng practice (CL equals to PR) to understand more about small PR. In DGL, we consider PRs with less than 200 lines of core code change are small (example, test and documentation could be exempted).
  • All changes have test coverage
  • Code is well-documented
  • To the best of my knowledge, examples are either not affected by this change, or have been fixed to be compatible with this change
  • Related issue is referred in this PR
  • If the PR is for a new model/paper, I've updated the example index here.

Changes

mufeili and others added 11 commits September 19, 2022 16:38
@mufeili @chang-l
@nv-dlasalle @yaox12 @isratnisa @peizhou001 @ndickson-nvidia @jermainewang @Rhett-Ying @frozenbugs @ZHITENGLI @rudongyu @BarclayII @VibhuJawa
Update from master (dmlc#4584)
70ab844 
* [Example][Refactor] Refactor graphsage multigpu and full-graph example (dmlc#4430)

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

* Fix format

* Update

* Update

* Update

* [Cleanup] Remove async_transferer (dmlc#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) (dmlc#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 (dmlc#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 (dmlc#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 dmlc#4323 dmlc#4316) (dmlc#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 (dmlc#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 (dmlc#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 (dmlc#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 (dmlc#4450)

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

* [Example][Refactor] Refactor RGCN example (dmlc#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 (dmlc#4468)

* [Example] directional_GSN for ogbg-molpcba (dmlc#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'. (dmlc#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. (dmlc#4461)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Example] SEAL for OGBL (dmlc#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 (dmlc#4488)

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

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

* fix test failure in TF

* [Feature] Make TensorAdapter Stream Aware (dmlc#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 (dmlc#4465)

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

* reformat

* reformat

* Auto fix update-version

* Auto fix setup.py

* reformat

* reformat

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>
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 (dmlc#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 (dmlc#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 (dmlc#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 (dmlc#4558)

* [examples]educe memory consumption

* reffine help message

* refine

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

This reverts commit ec171c6.

* [Misc] Add flake8 lint workflow. (dmlc#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. (dmlc#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 (dmlc#4565)

* [CI] refine stage logic

* refine

* refine

* remove (dmlc#4570)

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

* Add Pylint workflow for flake8. (dmlc#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. (dmlc#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. (dmlc#4574)

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

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

* Update pylint.

* Use another workflow.

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

* Update pylint. (dmlc#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. (dmlc#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 (dmlc#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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
Co-authored-by: ndickson-nvidia <99772994+ndickson-nvidia@users.noreply.github.com>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
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>
@mufeili
[Deprecation] Dataset Attributes (dmlc#4546)
38c3235 
* Update

* CI

* CI

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
@mufeili
[Example] Bug Fix (dmlc#4665)
2c7d3dc 
* Update

* CI

* CI

* Update

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
@mufeili
Merge branch 'master' into deprecate
c753e3e
Update
18f1e5c
@mufeili
Merge branch 'master' into deprecate
f751794
@peizhou001
Merge branch 'master' into deprecate
c6283ee
@mufeili
Update (dmlc#4724)
0b85238 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
@mufeili
Merge branch 'master' into deprecate
f041893
Merge branch 'master' into deprecate
4cbad92
change DGLHeteroGraph to DGLGraph in DOC
88f37d1
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dgl-bot commented Nov 8, 2022

To trigger regression tests:

  • @dgl-bot run [instance-type] [which tests] [compare-with-branch];
    For example: @dgl-bot run g4dn.4xlarge all dmlc/master or @dgl-bot run c5.9xlarge kernel,api dmlc/master

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dgl-bot commented Nov 8, 2022

Commit ID: 7798286c4d355fa51db056712937c5c79cb29df7

Build ID: 1

Status: ✅ CI test succeeded

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@peizhou001 peizhou001 requested a review from mufeili November 8, 2022 04:01
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Commit ID: cdd5936

Build ID: 2

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Commit ID: 17d08a0

Build ID: 3

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dgl-bot commented Nov 8, 2022

Commit ID: 718f03b

Build ID: 4

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@peizhou001 peizhou001 marked this pull request as ready for review November 9, 2022 01:35
@peizhou001 peizhou001 requested a review from frozenbugs November 9, 2022 02:41
mufeili
mufeili reviewed Nov 9, 2022
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Comment thread src/graph/serialize/heterograph_serialize.cc
/**
* Copyright (c) 2019 by Contributors
* @file graph/serialize/heterograph_serialize.cc
* @brief DGLHeteroGraph serialization implementation
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@mufeili mufeili Nov 9, 2022

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Let's not modify C/C++ files for the time being.

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@peizhou001 peizhou001 Nov 9, 2022

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Make sense. Let me revert it.

mufeili
mufeili previously requested changes Nov 9, 2022
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One minor comment

frozenbugs
frozenbugs reviewed Nov 9, 2022
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Comment thread src/graph/serialize/heterograph_serialize.cc
* @brief DGLGraph serialization implementation
*
* The storage structure is
* {
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@frozenbugs frozenbugs Nov 9, 2022

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In Line 11, there is kDGLHeteroGraph, should that be replaced or already outdated?

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I suggest not touching .cc files for the time being.

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@peizhou001 peizhou001 Nov 9, 2022

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Revert C code.

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Commit ID: 4b8ece0

Build ID: 5

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dgl-bot commented Nov 9, 2022

Commit ID: 4838aff

Build ID: 6

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@peizhou001 peizhou001 merged commit 9699b93 into dmlc:master Nov 10, 2022
@peizhou001 peizhou001 deleted the peizhou/DGLHeterroDocDeprecare branch June 28, 2023 10:34
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