Features
* build: The AWS Batch runner now supports overriding the image hardcoded in
the Batch job definition. Use the `--image` command-line option, the
`NEXTSTRAIN_DOCKER_IMAGE` environment variable, or the `docker.image` config
setting. This means that both `--docker` and `--aws-batch` builds will now
use the same container image, increasing reproducibility and customizability.
This is a **potentially-breaking change**, as it requires your AWS IAM users
are allowed to perform the `batch:RegisterJobDefinition` action and
`iam:PassRole` for the your configured job role (typically
_NextstrainJobsRole_). The [example _NextstrainJobsAccessToBatch_ IAM
policy](doc/aws-batch.mdnextstrainjobsaccesstobatch) in the [AWS Batch
docs](doc/aws-batch.md) is updated to reflect these new privileges.
* build: The new `--cpus` and `--memory` options allow limits to be specified
for containerized (Docker, AWS Batch) builds. These both automatically
inform Snakemake's resource scheduler and the AWS Batch instance size
selection. If your builds use Snakemake-based workflows, using these new
options is better than specifying `--cores …` or `--resources mem_mb=…`
directly.
* version: Verbose output now includes the "native" versions of Augur and
Auspice, if available.
Bug fixes
* view: Auspice v2 dataset JSONs are now detected and included in the list of
available datasets message printed to the console.
* view: Auspice v1 datasets are now only listed if both the tree and meta JSON
files exist. Previously, incomplete datasets with only the tree JSON were
listed.
Documentation
* The README now documents known issues with Windows.
Development
* Pipenv is now used to provide an easier and more consistent development
environment.
* pytest is now used to run mypy, flake8, and doctests.