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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
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Update torch requirement from ==1.12.* to ==1.13.* in /docker/openproblems-python-pytorch #751

Closed dependabot[bot] closed 1 year ago

dependabot[bot] commented 1 year ago

Updates the requirements on torch to permit the latest version.

Release notes

Sourced from torch's releases.

PyTorch 1.13: beta versions of functorch and improved support for Apple’s new M1 chips are now available

Pytorch 1.13 Release Notes

  • Highlights
  • Backwards Incompatible Changes
  • New Features
  • Improvements
  • Performance
  • Documentation
  • Developers

Highlights

We are excited to announce the release of PyTorch 1.13! This includes stable versions of BetterTransformer. We deprecated CUDA 10.2 and 11.3 and completed migration of CUDA 11.6 and 11.7. Beta includes improved support for Apple M1 chips and functorch, a library that offers composable vmap (vectorization) and autodiff transforms, being included in-tree with the PyTorch release. This release is composed of over 3,749 commits and 467 contributors since 1.12.1. We want to sincerely thank our dedicated community for your contributions.

Summary:

  • The BetterTransformer feature set supports fastpath execution for common Transformer models during Inference out-of-the-box, without the need to modify the model. Additional improvements include accelerated add+matmul linear algebra kernels for sizes commonly used in Transformer models and Nested Tensors is now enabled by default.

  • Timely deprecating older CUDA versions allows us to proceed with introducing the latest CUDA version as they are introduced by Nvidia®, and hence allows support for C++17 in PyTorch and new NVIDIA Open GPU Kernel Modules.

  • Previously, functorch was released out-of-tree in a separate package. After installing PyTorch, a user will be able to import functorch and use functorch without needing to install another package.

  • PyTorch is offering native builds for Apple® silicon machines that use Apple's new M1 chip as a beta feature, providing improved support across PyTorch's APIs.

Stable Beta Prototype
Better TransformerCUDA 10.2 and 11.3 CI/CD Deprecation Enable Intel® VTune™ Profiler's Instrumentation and Tracing Technology APIsExtend NNC to support channels last and bf16Functorch now in PyTorch Core LibraryBeta Support for M1 devices Arm® Compute Library backend support for AWS Graviton CUDA Sanitizer

You can check the blogpost that shows the new features here.

Backwards Incompatible changes

Python API

uint8 and all integer dtype masks are no longer allowed in Transformer (#87106)

Prior to 1.13, key_padding_mask could be set to uint8 or other integer dtypes in TransformerEncoder and MultiheadAttention, which might generate unexpected results. In this release, these dtypes are not allowed for the mask anymore. Please convert them to torch.bool before using.

1.12.1

>>> layer = nn.TransformerEncoderLayer(2, 4, 2)
>>> encoder = nn.TransformerEncoder(layer, 2)
>>> pad_mask = torch.tensor([[1, 1, 0, 0]], dtype=torch.uint8)
>>> inputs = torch.cat([torch.randn(1, 2, 2), torch.zeros(1, 2, 2)], dim=1)
# works before 1.13
>>> outputs = encoder(inputs, src_key_padding_mask=pad_mask)

... (truncated)

Changelog

Sourced from torch's changelog.

Releasing PyTorch

General Overview

Releasing a new version of PyTorch generally entails 3 major steps:

  1. Cutting a release branch preparations
  2. Cutting a release branch and making release branch specific changes
  3. Drafting RCs (Release Candidates), and merging cherry picks
  4. Promoting RCs to stable and performing release day tasks

Cutting a release branch preparations

Following Requirements needs to be met prior to final RC Cut:

  • Resolve all outstanding issues in the milestones(for example 1.11.0)before first RC cut is completed. After RC cut is completed following script should be executed from builder repo in order to validate the presence of the fixes in the release branch :

... (truncated)

Commits


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codecov[bot] commented 1 year ago

Codecov Report

Base: 94.73% // Head: 94.73% // No change to project coverage :thumbsup:

Coverage data is based on head (a3ad1c1) compared to base (d31f78c). Patch has no changes to coverable lines.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #751 +/- ## ======================================= Coverage 94.73% 94.73% ======================================= Files 155 155 Lines 4119 4119 Branches 213 213 ======================================= Hits 3902 3902 Misses 144 144 Partials 73 73 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `94.73% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#carryforward-flags-in-the-pull-request-comment) to find out more. Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio)

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dependabot[bot] commented 1 year ago

A newer version of torch exists, but since this PR has been edited by someone other than Dependabot I haven't updated it. You'll get a PR for the updated version as normal once this PR is merged.

dependabot[bot] commented 1 year ago

OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting @dependabot ignore this major version or @dependabot ignore this minor version. You can also ignore all major, minor, or patch releases for a dependency by adding an ignore condition with the desired update_types to your config file.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.