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CHANGES: Document the Singularity (and Conda) fixes since the last re…
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tsibley committed May 26, 2023
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Expand Up @@ -13,6 +13,61 @@ development source code and as such may not be routinely kept up to date.

# __NEXT__

This release is mostly a bug fix release for our Conda and Singularity
runtimes. However, it contains a **potentially-breaking change** for existing
usages of the Singularity runtime: **the minimum required Singularity version
has changed from 2.6.0 to 3.0.0**. This change was required for a critical bug
fix. If you do not use the Singularity runtime, there are no
potentially-breaking changes in this release.

## Improvements

* `nextstrain shell` now notes which runtime is being entered in its initial
messaging to establish more context for the user (and for developers when
troubleshooting).
([#283][])

* The Singularity runtime now checks for the minimum required Singularity
version (3.0.0 with this release) during `nextstrain check-setup`.
([#283][])

## Bug fixes

* Setup and upgrade of the Conda runtime now only uses stable "main" channel
releases when determining the latest release version, as intended.
Previously, testing and development releases could be selected if they were
newer than the last stable release. Additionally, if there are multiple
builds for a release version, the highest numbered build (i.e. newest) is now
used instead of the lowest.
([#280](https://github.com/nextstrain/cli/pull/280))

* The Singularity runtime now works with our container runtime images from
`build-20230411T103027Z` onwards. The Snakemake upgrade in that image
version resulted in "read-only file system" errors which referenced the
user's home directory. Those errors are now fixed.
([#283][])

* The prompt for `nextstrain shell`—a stylized variant of the Nextstrain
wordmark—now works when using the Singularity runtime regardless of
Singularity version. Previously Singularity's default prompt of
`Singularity> ` overrode ours when using Singularity versions ≥3.5.3.
([#283][])

* More robust command-line processing is used for the Singularity runtime on
Singularity versions ≥3.10.0. Singularity's early (and unexpected)
evaluation of arguments that look like (but aren't) shell variable
substitutions is disabled.
([#283][])

## Development

* The command lines and environment overrides of many (but not all) process
invocations are now logged when `NEXTSTRAIN_DEBUG` is enabled.
([#283][])


[#283]: https://github.com/nextstrain/cli/pull/283


# 6.2.1 (24 March 2023)

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