Nextstrain-cli

Improvements

* `nextstrain build --aws-batch --attach …` no longer offers to cancel (via
Control-C) or detach (via Control-Z) from the job if it's already complete.
Instead, Control-C will exit the program without delay and without trying to
cancel the job.
([253][])

* `nextstrain build` now supports a `--no-logs` option to suppress the fetching
and printing of job logs when attaching to a completed AWS Batch build. As
log fetching can often take longer than a selective download of the results
(i.e. via `--download`), this is a time (and terminal scrollback) saver when
all you want are a few of the results files.
([253][])

[253]: https://github.com/nextstrain/cli/pull/253

Bug fixes

* An error message that's printed by `nextstrain remote upload` when unknown
files are given for upload to destinations on nextstrain.org now properly
includes the actual list of unknown files instead of the placeholder
`{files}`.
([260](https://github.com/nextstrain/cli/pull/260))

* When running on Python ≥3.10, the `--help` output of `nextstrain build`,
`nextstrain view`, and `nextstrain shell` once again shows just the most
common options. All options are still shown with `--help-all`. A regression
since Python 3.10 meant that `--help` acted the same as `--help-all` before
this fix. This affected any installation on Python ≥3.10, including
standalone installations, since the standalone binaries bundle Python 3.10.
([259](https://github.com/nextstrain/cli/pull/259))

Documentation

* Minor improvements to the way we list and describe our computing platforms.

Improvements

* We've added a new Singularity runtime based on our existing Docker runtime.

Singularity is a container system freely-available for Linux platforms. It
is commonly available on institutional HPC systems as an alternative to
Docker, which is often not supported on such systems. When you use
Singularity with the Nextstrain CLI, you don't need to install any other
Nextstrain software dependencies as validated versions are already bundled
into a container image by the Nextstrain team.

Run `nextstrain setup singularity` to get started.
([248](https://github.com/nextstrain/cli/pull/248))

Improvements

* The output of `nextstrain check-setup` for the Conda runtime will now hint
about running `nextstrain setup conda` first if the runtime seems supported
but not yet set up.
([250][])

Documentation

* Documentation and `--help` output now standardizes on the term _runtime_ to
describe the various ways Nextstrain CLI provides access to the Nextstrain
software tools. Previously we used a mix of _build environment_, _runner_,
and _runtime_ in user-facing messages. This brings Nextstrain CLI in line
with the rest of our documentation.
([250][])

* The installation documentation now includes the standalone installer as well
as installing from Bioconda. It now covers all the ways our releases are
distributed.
([250][])

* The output of `nextstrain --help` now notes how to find command-specific
usage info and our online documentation.
([250][])

* An out-of-date description in `nextstrain build --help` has been revised and
updated.
([250][])

Development

* A new [glossary page in our documentation](https://docs.nextstrain.org/projects/cli/page/glossary/)
will help keep our shared understanding of terms straight.
([250][])

* Links to our online documention in the `--help` output of commands will now
omit any [local part](https://peps.python.org/pep-0440/#local-version-identifiers),
e.g. `+git`, of the running CLI version. This makes links correct even when
running development builds.
([250][])

[250]: https://github.com/nextstrain/cli/pull/250

_See also changes in 6.0.1 which was an unreleased version._

Bug fixes

* A new deprecation warning from the `cryptography` module (version 39) when
running on Python 3.6 is now suppressed as it's just noise to an end user.
This probably moves us closer to dropping 3.6 support ourselves, but it's not
so onerous yet.
([246](https://github.com/nextstrain/cli/issues/246))

_Unreleased due to [test failures](https://github.com/nextstrain/cli/issues/245). Changes first released as part of 6.0.2._

Improvements

* The standalone installation archives used by the standalone installer will
now work on even older Linux distributions:

|distro |now |was |
|-------------|-------|-------|
|Ubuntu |14\.04 |18\.04 |
|Debian |8 |10 |
|RHEL/CentOS |7 |8 |
|Fedora |19 |28 |
|OpenSUSE |12\.3 |15\.3 |

If you've previously encountered errors like the following:

/lib64/libc.so.6: version `GLIBC_2.27' not found (required by […]/.nextstrain/cli-standalone/nextstrain)

when using the standalone installer (or standalone archives directly), i.e.:

curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/linux | bash

then this change should resolve that error! The new minimum required glibc
version is 2.17 (was 2.27 previously).
([243](https://github.com/nextstrain/cli/pull/243))

Bug fixes

* The automatic opening of a browser tab (or window) by `nextstrain view`—a
feature introduced in the last release (6.0.0)—now also works for standalone
installations.
([244](https://github.com/nextstrain/cli/pull/244))