Code

feat: use Auspice JSON as a dataset#1455

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Merged

ivan-aksamentov merged 20 commits intomasternextstrain/nextclade:masterfrom feat/ref-and-ann-from-tree-jsonnextstrain/nextclade:feat/ref-and-ann-from-tree-jsonCopy head branch name to clipboardMay 29, 2024

+876-284

Commits

Commits on May 13, 2024

• feat: add ref and annotation data to Auspice tree types

  ivan-aksamentov

  committed
  0ec7adc

Commits on May 16, 2024

• refactor: add pathogen nextclade extension to auspice tree type

  Show description for 1043b98
  ivan-aksamentov

  committed
  1043b98

• feat: use Auspice JSON as dataset

  Show description for 4334f32
  ivan-aksamentov

  committed
  4334f32

• fix: parsing auspice genome annotations

  ivan-aksamentov

  committed
  b843ada

Commits on May 17, 2024

• fix: off-by-one in landmark range

  ivan-aksamentov

  committed
  ff7e887

• fix: duplicated start and end fields in the annotation of output tree

  ivan-aksamentov

  committed
  9b952bf

• feat: accept Auspice JSON genome annotation in read-annotation command

  ivan-aksamentov

  committed
  48d163c

Commits on May 23, 2024

• refactor: aggregate inputs loading

  ivan-aksamentov

  committed
  1fc4936

• feat(web): add url parameterdataset-json-url

  Show description for a27ee66
  ivan-aksamentov

  committed
  a27ee66

• Merge remote-tracking branch 'origin/master' into feat/ref-and-ann-from-tree-json

  ivan-aksamentov

  committed
  fb029d5

• fix(web): prevent crash when an auspice dataset was used in prev session

  ivan-aksamentov

  committed
  b1b3f5f

• fix(web): prevent crash when auspice json has no .root_sequence

  ivan-aksamentov

  committed
  e5ee068

• refactor: lint

  ivan-aksamentov

  committed
  883a0d6

Commits on May 24, 2024

• fix(web): specifically accept json

  Show description for 9f3c1e0
  ivan-aksamentov

  committed
  9f3c1e0

• fix(web): hide "Load examples" button when examples are not in dataset

  ivan-aksamentov

  committed
  fc7b8bd

• Merge remote-tracking branch 'origin/master' into feat/ref-and-ann-from-tree-json

  ivan-aksamentov

  committed
  a3c120b

• fix: make dataset files optional

  Show description for ddd9925
  ivan-aksamentov

  committed
  ddd9925

• feat: allow to override dataset components when Auspice dataset

  Show description for fe260c6
  ivan-aksamentov

  committed
  fe260c6

• fix(web): don't error when ref missing from auspice json but is provided otherwise

  ivan-aksamentov

  committed
  82e69a1

• feat(web): take title, description and update date from Auspice JSON

  Show description for 44fb8a5
  ivan-aksamentov

  committed
  44fb8a5