Nextstrain-cli

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1.14.0b1

Features

* The `build` command now supports detaching from and re-attaching to builds
run on AWS Batch (`--aws-batch`).

This adds a feature we've wanted from the beginning of the CLI. By starting
the build with `--detach`, a remote job is submitted and the command
necessary to `--attach` to the job later is printed. This command includes
the job id and can be used as many times as desired, including while the
remote job is running or after it has completed. It will even work on other
computers or for other people, although you may need to modify the local
build path to a directory of your choosing. The directory may be empty, in
which case all build context will be restored there from the remote job.

AWS Batch builds may also be interactively detached by pressing Control-Z.
Normally this would suspend a Unix process (which could then be resumed with
`fg` or `bg` or SIGCONT), but in the same spirit, `nextstrain build` will
detach from the remote job instead and exit the local process. This also
parallels nicely with our existing Control-C job cancellation support.

There are currently no facilities to track job state locally or list
outstanding jobs, but these features may be added later if it seems they'd be
useful. As it stands with this new feature, one pattern for launching
multiple detached jobs and picking them up later is:

Loop over several `nextstrain build` commands, appending the last
line to a shell script.
nextstrain build --aws-batch --detach build-a/ | tail -n1 | tee -a pickup-jobs.sh
nextstrain build --aws-batch --detach build-b/ | tail -n1 | tee -a pickup-jobs.sh


Then, sometime later:
bash pickup-jobs.sh

* The `--aws-batch` runner for the `build` command no longer requires
permission to perform the globally-scoped AWS IAM action
`s3:ListAllMyBuckets`. Instead, it uses the `HEAD <bucket>` S3 API which
requires either `s3:ListBucket`, which can be scoped to specific buckets in
IAM grants, or `s3:HeadBucket`, which is globally-scoped but does not reveal
bucket names. More details on these IAM actions are in the
[S3 documentation](https://docs.aws.amazon.com/AmazonS3/latest/dev/using-with-s3-actions.html#using-with-s3-actions-related-to-buckets).

1.13.0

Features

* The `deploy` command no longer requires permission to perform the
globally-scoped AWS IAM action `s3:ListAllMyBuckets`. Instead, it uses the
`HEAD <bucket>` S3 API which requires either `s3:ListBucket`, which can be
scoped to specific buckets in IAM grants, or `s3:HeadBucket`, which is
globally-scoped but does not reveal bucket names. More details on these IAM
actions are in the [S3 documentation](https://docs.aws.amazon.com/AmazonS3/latest/dev/using-with-s3-actions.html#using-with-s3-actions-related-to-buckets).

1.12.0

Features

* The `deploy` command now supports files other than JSON data files, such as
Markdown narratives, by setting the correct content type on upload.

1.11.2

Bug fixes

* This release fixes a regression in the `view` command which caused
"connection reset" or "empty response" errors. The regression only affected
versions 1.11.0 and 1.11.1 of the Nextstrain CLI when used with Auspice 1.38.0
via the `nextstrain/base:build-20190828T223744Z` image. Thanks to Thomas
Adams for the excellent bug report!

1.11.1

Bug fixes

* The `check-setup` command no longer errors when Docker isn't installed.

1.11.0

Features

* The `view` command now supports `--native` flag to run in the native ambient
environment.

* The `check-setup` command now supports a `--set-default` flag to save the
first supported environment to the Nextstrain CLI's config file. This means
that you don't have to specify `--native` (or `--aws-batch`) every time if
you don't have/want Docker support.

Bug fixes

* The `--verbose` flag to the `version` command will no longer cause the Docker
image to be downloaded when it isn't available locally.

Documentation

* Describe the somewhat annoying process of how to increase the disk space
available to AWS Batch jobs in the AWS Web Console.

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