Nextstrain-cli

Bug fixes

* On Windows, fix an issue where the `build` and `shell` commands spawn the
`docker run` process but also immediately return the user to the
command-line. For `shell`, the situation was weirder still because the user
ended up with _two_ command prompts (cmd.exe and bash) but only one appeared
to win when reading from the shared stdin.

Features

* The `build` command now supports a `--native` flag to run the build outside
of any container image, that is, within the ambient environment. That
environment might be provided by conda or a cluster module system or custom
installs or some other thing. Docker remains the default, although it
may be explicitly specified with `--docker`. Other runners are planned for
the future. The idea is that the cli as a user-facing tool for Nextstrain is
separate from a containerized Nextstrain environment (although the two work
well together).

* The `build`, `view`, and `shell` commands now show an abbreviated set of
common options when passed `--help`. The full set of options is available
using `--help-all`. The idea is to make the initial output more approachable.

Development

* The README now describes how to annotate the type of variable and use other
typing features in a way that's compatible with Python 3.5

* Package metadata for PyPi is slightly improved.

Documentation

* Minor updates to README and command help strings

Features

* A new `shell` command launches an interactive shell (bash) inside the build
environment, which is useful for running ad-hoc commands and debugging.

Features

* The `update` command now prunes old Docker images after downloading new ones.
This functionality relies on our new, labeled images. Older images will have
to be manually pruned as a one-time step. See `docker image prune` for more
information. Note that locally built images which are tagged
nextstrain/base:latest will be pruned when `update` is run. Protect such
images by giving them an additional tag.

* The versions of the Docker image and individual Nextstrain components in the
image are shown when the `version` command is run with the `--verbose` flag.

Features

* A new `deploy` command supports uploading data files to S3, allowing the
complete pathogen build lifecycle to happen using this package.

* The `check-setup` and `update` commands now check if the CLI itself is out of
date and could be updated.

Documentation

* Brief descriptions of the changes in each release are now kept in the
`CHANGES.md` file. You're reading it!

Development

* Describe basic development practices for this package in the README.

* Commit to [semantic versioning](https://semver.org), which I'd been
neglecting previously when bumping versions.

* Static type checking is now supported for a small fraction of the source code
and runs clean under mypy. This is included in Travis CI testing. The goal
is to add more type annotations going forward.