Nextstrain-cli

Documentation

* A new page describes how to upgrade Nextstrain CLI.

* The doc page for `nextstrain remote` now links to the pages for its
subcommands.

* A placeholder in the `nextstrain remote list` command usage now matches the
placeholder used elsewhere in its `--help` output.

Bug fixes

* `remote upload` no longer gzip compresses files which are already compressed
when uploading them to an S3 remote. This isn't expected in typical usage
when uploading Nextstrain dataset (JSON) or narrative (Markdown) files but
arises when uploading related files to an S3 remote (e.g. a `metadata.tsv.gz`
file to `s3://nextstrain-data/files/zika/`).
([161](https://github.com/nextstrain/cli/pull/161))

Development

* The CI workflow setup steps were simplified a bit.

Bug fixes

* `check-setup` no longer errors when, on some systems, awk outputs a large
number (bytes of memory reported by /proc/meminfo) in exponential notation.
([159](https://github.com/nextstrain/cli/pull/159))

Features

* The `view` and `remote` family of commands now support "measurements" dataset
sidecar files.
([156](https://github.com/nextstrain/cli/pull/156))

Bug fixes

* The Docker runtime now avoids merging stdout and stderr together when at
least one of stdout or stderr isn't a console (TTY), e.g. when redirecting
one or both streams to a file or piping output to another command.
([155](https://github.com/nextstrain/cli/pull/155))

* A global lockfile is now used for reading/writing config files instead of
locking the config files themselves. This resolves a regression on Windows
introduced in 3.0.4 which manifested as an `[Errno 13] Permission denied`
error when running `nextstrain update` and `nextstrain check-setup
--set-default`.
([157](https://github.com/nextstrain/cli/pull/157))

Documentation

* The changelog now notes two minor (har har) semantic versioning mistakes in
previous releases.

Features

* `remote` family of commands now support interacting with nextstrain.org's web
API using the credentials established by the `login` command.

See the [nextstrain.org
remote](https://docs.nextstrain.org/projects/cli/page/remotes/nextstrain.org/)
documentation for more information.

* `login` now sports a `--renew` flag to request new tokens with refreshed user
information (e.g. group memberships).

Bug fixes

* `build` now exits 1 (an error) when the AWS Batch job fails due to
infrastructural issues like the EC2 instance its running on being terminated.
Previously it exited 0 (success) despite the job not being successful.

* `check-setup` now supports Docker hosts with cgroups v2 and better handles
failures in the memory limits check.

* Messages related to automatic login (authn) management are now send to stderr
instead of stdout.

* `remote delete` messages now correctly imply each deletion is just about to
happen instead of just happened already.

* The messages produced when an internal error is detected now suggest filing
an issue on GitHub to report the bug.

Documentation

* The specific release version will now be displayed under the project name in
the sidebar of the documentation pages.

Development

* Many breakages of our CI caused by external changes in upstream testing deps
are now resolved.

Documentation

* The organization of the documentation sidebar menu is now improved to show
more of the pages instead of burying them in subpage table of contents.

* The formatting of `--help` output is now slightly improved with regard to
links, but more importantly, richer formatting of content shared between
`--help` and the online documentation is now possible.