2.1.0

Nextclade CLI 2.1.0

• Fix #907: If --ouput-basename contains dots, the last component is no longer omitted (report: @KatSteinke, fix: @ivan-aksamentov)

• Fix #908: Files passed as --input-virus-properties were interpreted like passed to --input-pcr-primers and vice versa (report: @BCArg, fix: @corneliusroemer)

Commit history

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• [9e98a42] docs: fix download links [skip ci]

• [46a8a53] chore: update dependencies, rust to 1.61

• [2290adc] chore: upgrade Cargo.toml's

• [bb9f276] Merge pull request #905 from nextstrain/update-deps

• [6935a9a] Fix link to bioconda package

• [cff9f9f] Merge pull request #906 from nextstrain/victorlin/fix-doc-link

• [29a92cb] fix: mixed up input-prc and input-virus-properties

• [dbb0ca9] chore: add bug fix to changelog

• [e9df843] Merge pull request #911 from nextstrain/fix-mangled-input-files

fix: mixed up input-prc and input-virus-properties

• [d0d550a] fix(cli): prevent truncation of components if basename contains dots

Resolves: #907

This rolls an in-house version of add_extension() function which always adds an extension to a PathBuf. This is different from PathBuf::with_extension() which may replace or add extension depending on what the path is.

This solves a problem with basenames containing dots, as described in the issue: PathBuf::with_extension() thought that they are extensions and replaced the last one. But we always want to add, not replace.

• [d5ef6bb] docs: add new cli changes to changelog

• [249adda] docs: add recent web changes to changelog

• [75d0ecd] Merge pull request #913 from nextstrain/fix/cli-basename-dots

• [95f20df] Merge remote-tracking branch 'origin/master' into docs/web-changelog

• [daa5c02] docs: fix md syntax

• [74e7334] Merge branch 'docs/web-changelog'

• [91e77c6] chore: release cli 2.1.0