Nextstrain-cli

Bug fixes

* It is no longer a fatal error if the logs for a completed AWS Batch job
cannot be fetched for some reason. `nextstrain build` will warn about the
error but continue on with printing the job status (e.g. success or reason
for failure) and, if applicable, downloading job results.
([406](https://github.com/nextstrain/cli/pull/406))

Bug fixes

* Authentication established via `nextstrain login` and used by the `nextstrain
remote` family of commands no longer verifies the "issued at" (`iat`) time of
the received tokens in order to avoid the following error:

ImmatureSignatureError: The token is not yet valid (iat).

This error was seen by users who's system time was slightly lagged, and it
prevented them from logging in or renewing their authentication.
([394](https://github.com/nextstrain/cli/pull/394))

Bug fixes

* The suggested commands to run (i.e. potential solutions) in expected errors
from `nextstrain remote` now explicitly include the remote origin to avoid
being incorrect or misleading for origins other than nextstrain.org. For
example, if the error message suggested running `nextstrain login`, it now
suggests `nextstrain login https://nextstrain.org`.
([391](https://github.com/nextstrain/cli/pull/391))

Bug fixes

* `nextstrain remote download` now produces the expected local file names when
there are periods (dots) in the remote dataset name (e.g. `nextstrain remote
download /a/b.c/d` now produces `a_b.c_d.json` instead of `a_b.json`) and
when there are periods in the given local file name (e.g. `nextstrain remote
download /x/y/z x.y.z` now produces `x.y.z.json` instead of `x.y.json`).
([381](https://github.com/nextstrain/cli/pull/381))

Improvements

* Snakemake's per-input/output file metadata (stored in `.snakemake/metadata/`)
is now downloaded from AWS Batch builds by default. Like file modification
times (mtimes), which are already preserved from the remote build, this
additional metadata is used by Snakemake to track when inputs have changed
and when it should regenerate outputs. The metadata is also used in
[Snakemake report generation](https://snakemake.readthedocs.io/en/v8.14.0/snakefiles/reporting.html#rendering-reports)
and can be useful for gathering ad-hoc workflow statistics.

The runtime image used must be at least `nextstrain/base:build-20240617T235011Z`
for these Snakemake metadata files to be available for download from the AWS
Batch job.
([374](https://github.com/nextstrain/cli/pull/374))

This release adds explicit (i.e. tested) support for Python version 3.12.
([369](https://github.com/nextstrain/cli/pull/369))

Note that this Python version support only matters if you're installing
Nextstrain CLI from PyPI or Bioconda
([c.f.](https://docs.nextstrain.org/projects/cli/en/8.4.0/installation/)). It
does not apply if you're installing Nextstrain CLI using the standalone
installation method we recommend in the [Nextstrain installation
documentation](https://docs.nextstrain.org/page/install.html). In that case, a
supported Python version is always bundled with `nextstrain`.

Features

* `nextstrain build` now supports two new options when using the AWS Batch
runtime: [`--exclude-from-upload`][] and [`--exclude-from-download`][]. The
former is useful for avoiding the upload of large, ancillary files not needed
by the build. The latter exists to parallel the former and make it easier to
exclude files from both upload and download.
([370](https://github.com/nextstrain/cli/pull/370))

Improvements

* The Conda runtime now uses Micromamba 1.5.8 (upgraded from 1.1.0) to manage
the runtime environment. The newer version supports Zstandard-compressed
index files which speeds up `nextstrain setup` and `nextstrain update` for
the Conda runtime.
([367](https://github.com/nextstrain/cli/pull/367))

Bug fixes

* The [`--download`][] option of `nextstrain build` now supports passing _only_
negated patterns (e.g. `!…` and `!(…)`). All files which _don't_ match the
negated patterns will be downloaded. Previously, no files were downloaded
unless at least one positive pattern was given.
([370](https://github.com/nextstrain/cli/pull/370))


[`--exclude-from-upload`]: https://docs.nextstrain.org/projects/cli/en/8.4.0/commands/build/#cmdoption-nextstrain-build-exclude-from-upload
[`--exclude-from-download`]: https://docs.nextstrain.org/projects/cli/en/8.4.0/commands/build/#cmdoption-nextstrain-build-exclude-from-download
[`--download`]: https://docs.nextstrain.org/projects/cli/en/8.4.0/commands/build/#cmdoption-nextstrain-build-download