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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
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Bump jax from 0.3.25 to 0.4.6 in /docker/openproblems-python-pytorch #846

Closed dependabot[bot] closed 1 year ago

dependabot[bot] commented 1 year ago

Bumps jax from 0.3.25 to 0.4.6.

Release notes

Sourced from jax's releases.

JAX release v0.4.6

No release notes provided.

jaxlib release v0.4.6

No release notes provided.

JAX release v0.4.5

jax version 0.4.5

Jax release v0.4.4

No release notes provided.

Jaxlib release v0.4.4

No release notes provided.

JAX release v0.4.3

No release notes provided.

jaxlib release v0.4.3

No release notes provided.

JAX release v0.4.2

No release notes provided.

jaxlib release v0.4.2

No release notes provided.

Jax release v0.4.1

  • Changes
    • Support for Python 3.7 has been dropped, in accordance with JAX's {ref}version-support-policy.
    • We introduce jax.Array which is a unified array type that subsumes DeviceArray, ShardedDeviceArray, and GlobalDeviceArray types in JAX. The jax.Array type helps make parallelism a core feature of JAX, simplifies and unifies JAX internals, and allows us to unify jit and pjit. jax.Array has been enabled by default in JAX 0.4 and makes some breaking change to the pjit API. The jax.Array migration guide can help you migrate your codebase to jax.Array. You can also look at the Distributed arrays and automatic parallelization tutorial to understand the new concepts.
    • PartitionSpec and Mesh are now out of experimental. The new API endpoints are jax.sharding.PartitionSpec and jax.sharding.Mesh. jax.experimental.maps.Mesh and jax.experimental.PartitionSpec are deprecated and will be removed in 3 months.
    • with_sharding_constraints new public endpoint is jax.lax.with_sharding_constraint.
    • If using ABSL flags together with jax.config, the ABSL flag values are no longer read or written after the JAX configuration options are initially populated from the ABSL flags. This change improves performance of reading

... (truncated)

Changelog

Sourced from jax's changelog.

jax 0.4.6 (Mar 9, 2023)

  • Changes

    • jax.tree_util now contain a set of APIs that allow user to define keys for their custom pytree node. This includes:

      • tree_flatten_with_path that flattens a tree and return not only each leaf but also their key paths.
      • tree_map_with_paths that can map a function that takes the key path as argument.
      • `register_pytree_with_keys`` to register how the key path and leaves should looks like in a custom pytree node.
      • keystr that pretty-prints a key path.

    • {func}jax2tf.call_tf has a new parameter output_shape_dtype (default None) that can be used to declare the output shape and type of the result. This enables {func}jax2tf.call_tf to work in the presence of shape polymorphism. ({jax-issue}[#14734](https://github.com/google/jax/issues/14734)).

  • Deprecations

    • The old key-path APIs in jax.tree_util are deprecated and will be removed 3 months from Mar 10 2023:
      • register_keypaths: use {func}jax.tree_util.register_pytree_with_keys instead.
      • AttributeKeyPathEntry : use GetAttrKey instead.
      • GetitemKeyPathEntry : use SequenceKey or DictKey instead.

jaxlib 0.4.6 (Mar 9, 2023)

jax 0.4.5 (Mar 2, 2023)

  • Deprecations
    • jax.sharding.OpShardingSharding has been renamed to jax.sharding.GSPMDSharding. jax.sharding.OpShardingSharding will be removed in 3 months from Feb 17, 2023.
    • The following jax.Array methods are deprecated and will be removed 3 months from Feb 23 2023:
      • jax.Array.broadcast: use {func}jax.lax.broadcast instead.
      • jax.Array.broadcast_in_dim: use {func}jax.lax.broadcast_in_dim instead.
      • jax.Array.split: use {func}jax.numpy.split instead.

jax 0.4.4 (Feb 16, 2023)

  • Changes
    • The implementation of jit and pjit has been merged. Merging jit and pjit changes the internals of JAX without affecting the public API of JAX. Before, jit was a final style primitive. Final style means that the creation of jaxpr was delayed as much as possible and transformations were stacked on top of each other. With the jit-pjit implementation merge, jit becomes an initial style primitive which means that we trace to jaxpr as early as possible. For more information see this section in autodidax. Moving to initial style should simplify JAX's internals and make development of features like dynamic shapes, etc easier. You can disable it only via the environment variable i.e.

... (truncated)

Commits
  • f1f4840 Merge pull request #14881 from skye:version
  • 1aa08fd Update WORKSPACE and setup.py for jax/jaxlib 0.4.6 release
  • 7fd1e2f Split _src/traceback_util.py into its own Bazel target.
  • 01b00c4 Increase sharding of shard_map test on CPU.
  • 9912a8e Split _src/pretty_printer.py into its own Bazel target.
  • d216d98 Remove the disassemble into single devices arrays in ExecuteReplicated.__call...
  • 08789fd Exclude "util.py" and "config.py" from the main JAX bazel target.
  • 560fe73 [jax2tf] Disable some failing tests
  • 0e05a79 Split some submodules out of //jax under Bazel.
  • 5c91453 [jax2tf] Add check that native lowering should not include custom calls not g...
  • Additional commits viewable in compare view


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github-actions[bot] commented 1 year ago

Current build status

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 97.38% and project coverage change: -0.12 :warning:

Comparison is base (9d16650) 95.60% compared to head (468e74a) 95.48%.

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scottgigante-immunai commented 1 year ago

Tests at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/3HogatCTJuWVn1