Nextstrain-cli

Bug fixes

* The [environment variables used by Augur](https://nextstrain-augur.readthedocs.io/en/stable/envvars.html)
are now passed through to --docker and --aws-batch builds.

Features

* The `view` command now sports a `--port` option to use an alternate port for
the viewer.

Features

* Add ability to specify vCPU and memory when running AWS Batch jobs via
`--aws-batch-cpus` and `--aws-batch-memory` or via specification in
`~/.nextstrain/config` or via environment variables
`NEXTSTRAIN_AWS_BATCH_CPUS` and `NEXTSTRAIN_AWS_BATCH_MEMORY`. This requires
corresponding proper setup of compute environment in AWS Batch console.

Features

* Restore the modification times of files when unzipping results from an AWS
Batch run. This allows Snakemake's dependency resolution to properly
determine file staleness, which in turn allows local builds to continue where
AWS Batch builds leave off (e.g. running the bulk of the computation on AWS
Batch and then iterating on subsequent trivial steps locally).

Features

* Builds run on AWS Batch no longer delete the build dir zip file from S3 or
the job log stream from CloudWatch, making it easier to debug and
troubleshoot Batch builds. The Batch setup documentation is updated to note
that the previously suggested retention policies are now the only thing
preventing runaway data storage costs (and thus a must).

Bug fixes

* Declare missing dep on setuptools, used via `pkg_resources` by the
`check-setup` and `update` commands. setuptools nearly always exists already
on Python installs, especially when nextstrain-cli is installed using pip,
but nearly always is not always.

Development

* Static type checking now passes again thanks to a work around for a mypy bug
related to namespace packages.

Features

* The `check-setup` command now tests if the local Docker image is new enough
for this version of the CLI.