[API Deprecate]Remove as_heterograph and as_immutable_graph #4851
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* [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
* [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 * refine code * refine test * refine code
…lc#4795) All tasks completed.
… ParMETIS execution (dmlc#4791) * check if stats file exists, if not create one before parmetis run * correct the typo error and correctly use constants.GRAPH_NAME
* alternative * fix * remove_todo * blabl * ablabl Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
…ery large messages and resulting in killed process (dmlc#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] 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>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
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frozenbugs
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Nov 9, 2022
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Why not open a PR to dmlc:deprecate? |
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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) 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 (#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 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 (#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 ec171c6. * [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> 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> * [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) Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal> Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-19.ap-northeast-1.compute.internal> Co-authored-by: czkkkkkk <zekucai@gmail.com> 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> 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: 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> Co-authored-by: Ubuntu <ubuntu@ip-172-31-16-19.ap-northeast-1.compute.internal> Co-authored-by: czkkkkkk <zekucai@gmail.com> Co-authored-by: kylasa <kylasa@gmail.com> Co-authored-by: Muhammed Fatih BALIN <m.f.balin@gmail.com> Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
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Description
Remove as_heterograph and as_immutable_graph API
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Please feel free to remove inapplicable items for your PR.
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