2.0.0-beta.6

⚠️	This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases.

Commit history

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• [aa31635] chore(ci): trigger ci

• [e27dc48] chore: add script for testing on different gnu linux distros [skip ci]

• [3dfb00d] fix(web): rectify incorrect filed name

This was sometimes causing a crash of the web app when filtering by aminoacids. The filed queryAa was not spelled correctly and the lodash intersectionWith() function's typings did not catch the type mismatch.

• [444ceaa] fix(cli): don't crash on unknown nucleotide characters

Nextclade v2 crashes when encounters unknown nucleotide letters which converting fasta string to the internal sequence representation.

This PR aligns behavior with v1: sequences with unknown nucleotide letters are now ignored, excluded from results, added to errors.csv and the run continues.

• [f4627bb] Merge pull request #875 from nextstrain/fix/web-crash-on-filtering

• [bad2f65] Merge pull request #876 from nextstrain/fix/cli-crash-on-unknown-nuc

• [9462d8d] fix: add missing custom node attrs to tree json

This adds custom node attrs (e.g. pango lineages) to the tree json, that were previously missing.

This should ensure that they are shown on the tree viz as it was in Nextclade v1.

• [6bc986d] fix: add missing qc status to tree json

This adds qc status to the tree json, previously missing.

This should ensure that they QC status is shown on the tree viz as it was in Nextclade v1.

• [ae0bc80] Merge pull request #878 from nextstrain/fix/tree-missing-custom-attrs

• [0e48641] Merge remote-tracking branch 'origin/master' into fix/tree-missing-qc-status

• [1573e62] Merge pull request #879 from nextstrain/fix/tree-missing-qc-status

fix: add missing qc status to tree json

• [4b9fa41] refactor: rename file to clarify intent

It will contain both compression and decompression functions

• [78d0cd3] feat(cli): add output file compression

Adds compression support for output files: if output filename contains one of the supported extensions, the outputs will be transparently compressed. Example --output-fasta=aligned.fasta.xz. Supported formats as the same as for input decompression: gz, bz2, xz, zstd. Default compression levels are used.

To make it compile, I had to additionally:

• change some of the lifetime parameters in CSV and NDJSON writer, because they were unnecessarily limiting

• remove a very tricky into_inner() methods in CSV and NDJSON writer, which required Synctrait on inner writer, while zstd writer did not support that. For that, in a few places, instead of getting inner writer and getting a string out of it, I managed to just use vec as an inner writer in these places. So into_inner() method was no longer needed, same as Sync trait bound.

• [b8abb99] Merge pull request #880 from nextstrain/feat/cli-output-compression

• [f029502] feat(cli): improve help messages for input fasta arg

• [5d45010] feat(cli): mention compression of outputs in cli help messages

• [ef842bb] Merge pull request #881 from nextstrain/feat/cli-improve-help

• [7ed87ff] docs: mention output file compression in changelog

• [7af69da] fix(cli): remove stdin from description of --output-translations arg

Translations cannot be written to stdout because there are many files

• [a18e311] Merge pull request #882 from nextstrain/fix/cli-help-translations

• [2cba8ff] chore: release cli 2.0.0-beta.6