2.0.0-alpha.4

⚠️	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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• [c8f3174] docs(dev): add ad note about custom dataset server into dev guide

• [4e86cd3] Merge pull request #822 from nextstrain/docs/dev-guide-datasets

• [719f217] chore(ci): attempt to push git tag after web build

• [e923bf6] chore(ci): create git tags on for release web builds

• [7ebae91] chore(ci): use full dev script command names in ci [skip ci]

• [ba28c64] chore: remove simplealign example

• [4263547] Merge pull request #823 from nextstrain/chore/remove-simplealign

• [28ae075] fix(web): ensure truncated text is not repeated in insertions tooltip

This is a port of 79e1f3b, which got lost during rust transition

• [939b57b] Merge pull request #824 from nextstrain/fix/insetions-tooltip

• [d0db03a] feat(web): limit tooltips to 20 insertions max

• [474e633] fix: ensure aa muts are attached to the tree

This fixes an omission: only nuc mutations were attached to the tree JSON object, and aa mutations were missing.

• [82bb53b] feat(web): display nuc insertions in sequence views

• [b7b51bb] feat(web): display aa insertions in sequence views

• [9f31264] feat(web): display total number of markers and limit in the message

• [48b5132] feat(web): increase seq marker limit to 3000

• [0217b06] Merge pull request #828 from nextstrain/feat/web-show-marker-limit

• [7dcc25e] Merge remote-tracking branch 'origin/master' into feat/web-ins-markers

• [27a58c9] feat(web): account insertions in seq marker limit

• [0008108] refactor(web): move insertion colors into theme

• [58f529f] feat(web): make insertion markers black

• [c721968] feat(web): limit number of aa mut badges in nuc gap tooltips

This limits number of aminoacid mutation badges in the tooltip of the nucleotide gap marker in sequence view.

This avoid screen overflow when there's too many mutations.

This happens with aa deletions mostly, so ideally we need to group aa deletions into ranges. But it have negative impact to other places which need access to individual deletions and is more work overall. Maybe later.

• [88e2483] fix: accumulate aa node mutations correctly in preprocess

This bug went unnoticed because we only every diffed the nextclade.tsv
Since we don't surface nextclade.json which contains private muts, this problem didn't show in automated equivalence testing.

• [d407a23] Merge pull request #826 from nextstrain/fix/tree-aa-muts

fix: ensure aa muts are attached to the tree

• [4b0247c] Merge pull request #829 from nextstrain/fix/web-limit-tooltip-badges

• [3180e8b] web: make insertions makers purple/yellow (IGV uses purple)

• [a6de7ba] Merge pull request #827 from nextstrain/feat/web-ins-markers

feat(web): display nuc and aa insertions in sequence views

• [4ce81cf] chore(build): speedup debug binaries

In order to improve deb experience, this configures build to optimize dependency packages even in dev mode. Nextclade packages themselves stay unoptimized, so that full debug information is available.

Also increases number of codegen units to speedup incremental build process.

• [c4ce28e] Merge pull request #831 from nextstrain/chore/faster-debug-build

• [4b7ac6f] Merge pull request #825 from nextstrain/feat/limit-insertions

feat(web): limit tooltips to 20 insertions max

• [81d1cef] chore(ci): make sure .env file is read properly

• [d330857] chore: release cli 2.0.0-alpha.4