Release 4.2.0 · nextstrain/cli

These release notes are automatically extracted from the full changelog.

Bug fixes

Using remote delete on nextstrain.org now correctly outputs the "Deleting…"
message before performing each delete, as intended (and as S3 remotes do).
Previously, the message was misleadingly output after each delete was
already performed.
(#209)
Detection of the installation method during self-upgrade checks in
nextstrain update and nextstrain check-setup now looks for explicit
installer metadata files and no longer assumes Pip as the final fallback. If
the installation method is not explicitly detected, then no upgrade
instructions are shown. Better to suggest nothing than to suggest the wrong
thing.
(#207)
An uncaught StopIteration error that could have occurred in very specific
and limited circumstances during self-upgrade checks in nextstrain update
and nextstrain check-setup can no longer occur.
(#207)

The nextstrain remote download, upload, and delete commands now support
a --dry-run mode.

This mode, as is broader convention, goes through the motions of doing the
thing, as much as possible, but doesn't actually do the thing. That is, no
changes should occur when --dry-run is active.

This is particularly useful for seeing what will happen if you're unsure of
how a path or argument is handled. Dry runs of the list (ls) command
don't make sense and aren't included.
(#210)
Installations via a Conda package are now detected during self-upgrade checks
and the suggested upgrade command uses mamba install or conda install.
(#207)
Suggested upgrade commands now specify the expected new version so they fail
if that version is not found rather than succeed but do nothing (or do
something different).
(#207)

A new debugging mode can be enabled by setting the NEXTSTRAIN_DEBUG
environment variable to 1 (or another truthy value). Currently the only
effect is to print more information about handled (i.e. anticipated) errors.
For example, stack traces and parent exceptions in an exception chain are
normally omitted for handled errors, but setting this env var includes them.
Future debugging and troubleshooting features, like verbose operation
logging, will likely also condition on this new debugging mode.
We now avoid a runtime dep on setuptools by switching from
pkg_resources.parse_version to packaging.version.parse. The latter was
already transitively in our dep tree.
(#207)