Nextstrain-cli

Features

* build: AWS Batch jobs now include more detail about why the container exited
when available. This surfaces useful messages like "OutOfMemoryError:
Container killed due to memory usage" in addition to the exit status.

Documentation

* check-setup: Describe how `--set-default` chooses an environment. Thanks Mary
Larrousse!

Bug fixes

* Fix missing import in our gzip utilities which could cause a runtime error
(NameError) when running `nextstrain remote download` on S3 objects with a
`Content-Encoding` header set to a value other than `gzip` or `deflate`.
This circumstance is unlikely, but not impossible.

Development

* Use Flake8 for static runtime safety and correctness checks

Bug fixes

* deploy/remote upload: Some files, but not all, were being truncated during
upload due to a bug in gzip compression handling. Now the whole file makes
it to its destination. More details in
[62](https://github.com/nextstrain/cli/pull/63).

* build: The default arguments for `snakemake` are no longer used if a
different program to run is specified with `--exec`.

Documentation

* Update README to include the latest usage information, which mentions the new
`remote` command.

Features

* The `deploy` command is now an alias for the `remote upload` command.

* The new `remote list`, `remote download`, and `remote delete` commands allow
listing, downloading, and deleting remote datasets and narratives which were
uploaded using `deploy` / `remote upload`. Currently only direct s3://
destinations are supported, but its anticipated that Nextstrain Groups will
be supported as first-class destinations in the future.

Bug fixes

* deploy/remote upload: Invalid credentials are now properly caught and messaged about.

* deploy/remote upload: Files are now deployed/uploaded using streaming
compression instead of buffering the whole file in memory first.

Features

* Environment variables for [AWS
credentials](https://boto3.amazonaws.com/v1/documentation/api/latest/guide/configuration.html#environment-variables)
(`AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, and `AWS_SESSION_TOKEN`) are
now passed through to builds. This lets builds which use data on S3 to work
transparently, for example.

* Environment variables for [ID3C](https://github.com/seattleflu/id3c)
(`ID3C_URL`, `ID3C_USERNAME`, and `ID3C_PASSWORD`) are now passed through to
builds. This lets Seattle Flu Study builds which use data in an ID3C
instance to work transparently.

_No changes since 1.14.0b1, described below._