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Update manifest and pin newer numpy in containers (#444)
As of #405 the presubmit CI is based on package versions listed in the `manifest.yaml` that is committed to the repository. This has not been updated for ~1 month, so the presubmit CI is testing ~1 month old versions of the ecosystem. This PR updates it using the commit from https://github.com/NVIDIA/JAX-Toolbox/tree/znightly-2024-01-03-7395605285, generated by the nightly CI run. Because this bumps the JAX version by ~1 month, we have to include fixes for deprecations. In particular replacing `jax.random.KeyArray` with plain `jax.Array` (nvjax-svc-0/t5x@4d5ec2f). The deprecated name is used in older versions of the `chex` package, which are being selected by pip's dependency resolver despite newer versions being available. We avoid this by giving pip a helping hand and nudging it to use a newer `numpy` version, which allows it to select a newer `chex`. But it's easy to imagine similar issues in future with other packages. Closes #448.
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