Nextstrain-cli

Bug fixes

* Docker images between `build-20190115T232255Z` and `build-20190116T000613Z`
(inclusive) broke the `nextstrain view` command. It is fixed in this version
of the CLI, 1.8.0, in tandem with new images, starting with
`build-20190119T045444Z`. If your `view` command is broken, running
`nextstrain update` and following the instructions to upgrade to version
1.8.0 of the CLI should resolve the issue.

* AWS Batch builds now avoid uploading files matching `environment*` in the
build directory, as such files are commonly used for storing sensitive
environment values.

Features

* The automatic check for newer versions of the CLI, which happens on the
`update` and `check-setup` commands, now produces a better,
more-likely-to-work suggested invocation of pip to perform the upgrade.

Features

* The `build` command now runs `snakemake` with the `--printshellcmds` option
for improved log output.

Bug fixes

* User-provided paths are now resolved strictly—they must exist—on both Python
3.5 and ≥3.6, not just 3.5. This discrepancy was unlikely to result in any
noticeable problems because of other existence checks which were performed.
Nevertheless, the change is good housekeeping and helps ensure robustness.

* The `update` command no longer errors on Python 3.6.0 and 3.6.1 when the
`~/.nextstrain/` does not exist (for example, when upgrading from CLI
versions before 1.7.0). [37](https://github.com/nextstrain/cli/issues/37)

Development

* Continuous integration testing now includes a much fuller range of Python
versions in order to more quickly catch bugs like the one affecting `update`
above.

* Continuous integration testing switched to running the
[zika-tutorial](https://github.com/nextstrain/zika-tutorial), a simplified
build more suitable for our needs.

Bug fixes

* The `shell` command no longer throws an unexpected exception about a missing
`warn()` function when a non-existent build directory is given. The
user-friendly error is printed instead, as expected.

Features

* Builds can now be run remotely on [AWS Batch](https://aws.amazon.com/batch/)
by passing the `--aws-batch` flag to the `build` command. See `nextstrain
build --help` for more information. Setup required to support this is
documented in [`doc/aws-batch.md`](doc/aws-batch.md).

* The `update` command now pulls down new images by their `build-*` tag instead
of tracking the mutable `latest` tag. Our build tags are, most importantly,
not updated after creation and thus are suitable references for reproducible
runs. The output of `nextstrain version --verbose` now includes the specific
build tag.

* The `check-setup` command now tests the amount of memory available to
containers and warns if it less than 2GB. This is particularly important on
Windows and macOS where Linux containers are run inside a VM on the host.
The VM may have limited memory allocated to it, leading to out-of-memory
errors in builds.

Documentation

* Installation instructions in the README are now more detailed.

* A big picture overview of where the CLI fits into the Nextstrain ecosystem is
included in the README for situating newcomers.

* The README now refers to Docker Desktop, the new name for Docker Community
Edition.

Features

* The `shell` command announces you're entering the build environment, prints
information about mapped volumes, and describes how to leave the environment.