Nextstrain-cli

Documentation

* The AWS Batch documentation and 2.0.0 release notes (below) now include
information about the additional necessity of granting users the ability to
`iam:PassRole` for the role used by Batch jobs.

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.

Bug fixes

* AWS Batch builds are now more resilient in the face of transient network or
client errors when uploading the build directory and following build logs.
Thanks Tony Tung!

Bug fixes

* The previous release did not pass mypy's type checks due to a technicality;
mypy has now been placated.

Documentation

* check-setup: Success or failure is (hopefully) more clearly messaged now.
This was muddied over time by adding support for the native and AWS Batch
runners, and we've seen several support requests because of confusion here.

* Installation instructions in the README now document all supported computing
environments, or "runners". Pipx is also mentioned as a nice alternative to
Pip.

* Detaching from AWS Batch builds with `--detach` and Control-Z is now
mentioned in the AWS Batch documentation.

* A direct reference to the AWS Batch User Guide on memory management details
was added, because AWS docs can be hard to navigate.

* The units documented to be used by the `--aws-batch-memory` option are now
correct.

* Runner-selection options (`--docker`, `--native`, `--aws-batch`) are now in
their own option group to reduce clutter among the help output. They are
only visible with `--help-all` now, like development options. With the use
of `nextstrain check-setup --set-default` now emphasized, these options need
not be as prominent.

* The top-level description in `nextstrain --help` output now says more than
three words. :D

Features

* build: AWS Batch jobs now require Ctrl-C to be pressed twice _within 10s_ to
cancel a job. This is an additional guard on top of 1.16.4's change so that
if you accidentally press Ctrl-C once you can't accidentally press it again
30 minutes later and ruin your build.

Features

* build: AWS Batch jobs now require Ctrl-C to be pressed twice to cancel the
job. This guards a potentially unwanted action from being used accidentally
by requiring confirmation with a second Ctrl-C.

* build: AWS Batch jobs now report the current job status when re-attaching.
Previously the current job status was never reported, only the next status
transition. For a PENDING or RUNNING job, it might be some time to the next
transition.