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react-app#13

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ivan-aksamentov wants to merge 127 commits intomasterneherlab/pan-genome-visualization:masterfrom react-appneherlab/pan-genome-visualization:react-appCopy head branch name to clipboard

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Commits

Commits on Aug 30, 2022

• chore: remove old app

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  3d90449

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• feat: scaffold react app

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• Merge remote-tracking branch 'origin/static-app' into react-app

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  4c0b15d

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• chore: remove unused files

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• chore: setup vercel

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Commits on Aug 31, 2022

• chore: fix env var name

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• feat: fetch data index, setup routing

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• fix: client-side routing in prod

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Commits on Sep 2, 2022

• chore(infra): ensure correct encoding is set for gz files

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• chore: format, lint

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• chore(infra): add script to find Lambda@Edge logs

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Commits on Sep 3, 2022

• feat: fetch multiple data files efficiently

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Commits on Sep 5, 2022

• feat: batch gene cluster data into tar archives

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Commits on Sep 6, 2022

• Merge branch 'static-app' into react-app

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• chore: convert remaining tars into zips

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• chore: generate index file in new format

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• feat: add species list table

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Commits on Sep 7, 2022

• fix: remove index column

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• fix: disable sorting of downloads column

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• feat: add fuzzy search of species

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• feat: add gene cluster table

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• chore: cleanup gene cluster json

  ivan-aksamentov

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• feat: adjust gene table to the new data format

  ivan-aksamentov

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• chore: add custom dev server for local data

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• feat: switch genes on table row click

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Commits on Sep 8, 2022

• feat: add metadata table

  ivan-aksamentov

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• refactor: reduce duplication in fetching hook code

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Commits on Sep 30, 2022

• feat: allow column reordering using drag-and-drop

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• feat: toggle and reorder columns

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• feat: hide column controls under dropdown

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• feat: add better popover implementation for table settings

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• feat: animate dnd list

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Commits on Oct 1, 2022

• refactor: extract row component

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Commits on Oct 3, 2022

• feat: add row drag and drop

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• feat: add table column resizing

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• refactor: lint

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• fix: set entire column header as a drag source

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• fix: avoid table header scrolling away

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• chore: allow webworker blob in script-src CSP

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Commits on Oct 4, 2022

• refactor: extract generic table component

  ivan-aksamentov

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• refactor: deduplicate table code for all tables

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• fix: center loading indicator

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• feat: add pulse animation for loader

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• fix: prevent loader blink

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• feat: reimplement table filtering

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• feat: extract and prettify search box component

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• refactor: lint

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• refactor: extract table spacer component

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• refactor: rename component to clarify purpose

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Commits on Oct 5, 2022

• refactor: extract table heading

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• feat: prettify table heading

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• feat: prettify table rows

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• fix: align heading text

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• feat: prettify species page

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• fix: make header and footer sticky and opaque

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• fix: remove sorting buttons for columns which cannot be sorted

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• feat: reduce table config boilerplate

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Commits on Nov 18, 2022

• fix: ensure row colors (stripes) of the table are correct after sorting

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• chore: add code of phyloTree

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• feat: add phylo tree

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• feat: wrap trees into cards

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• feat: add reduced alignment files

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• chore: add code for msa

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Commits on Nov 19, 2022

• feat: add msa viewer

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• chore: disable type-checking legacy code

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• fix: use correct fasta file depending on chosen seq type

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Commits on Nov 20, 2022

• chore: use temp data server

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• chore: disable type checks on vercel

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• feat: use gene tree json and fasta from tar archive

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• fix: react error "Maximum update depth exceeded"

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• refactor: convert require() to import

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• chore: remove unused files

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• refactor: remove unused code and packages

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Commits on Nov 22, 2022

• Merge remote-tracking branch 'origin/master' into react-app

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• chore: fix faulty merge

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• docs: update dev docs

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Commits on Nov 23, 2022

• refactor: lint

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• refactor: upgrade deps, lint, adjust to new interfaces

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• fix: init i18n in immediate mode

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• refactor: fix yarn resolutions

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• chore: make console less verbose

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  e4d71e5

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• refactor: remove unused files

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Commits on Nov 24, 2022

• fix: silence console messages from msa

  ivan-aksamentov

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• Merge remote-tracking branch 'origin/master' into react-app

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• feat(data): integrate metaConfiguration.js into species tree; cleanup data

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• feat: hardcode names of downloaded files

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Commits on Nov 30, 2022

• feat: reimplement tree/graph layout with React rendering

  ivan-aksamentov

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• feat: reimplement tree tooltips

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Commits on Dec 7, 2022

• refactor: fix typings in Tooltip

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• feat: colorize nodes

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• refactor: lint

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Commits on Dec 16, 2022

• chore: upgrade Node deps

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• fix: i18n warning

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• feat: show 'strain' instead of 'name' on graph nodes

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• feat: fit graph into available screen space

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Commits on Dec 17, 2022

• fix: downgrade react-table to avoid crash

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• feat: don't render node labels if there's more than 50

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• feat: reenable gene table and tree

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• feat: render graph into HTML5 canvas

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• feat: highlight nodes with the same name

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• feat: clear cache when restarting the app

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• chore: cleanup data deployment scripts

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Commits on Dec 19, 2022

• test: add tests for dfs graph traversal

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• pert: impl iterative depth-first search

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• perf: avoid graph traversal where possible

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• perf: remove unnecessary and repeated computations

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• perf: avoid unnecessary rerenders, memoize React components,

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• fix: prevent spinner on species tree when only gene tree is loading

  ivan-aksamentov

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• feat: animate tree layout transitions

  ivan-aksamentov

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• feat: animate node color

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Commits on Jan 17, 2023

• refactor: extend useToggle hook

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• refactor: lint

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• chore: disable eslint checks with false positives

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• feat: mirror gene tree horizontally

  ivan-aksamentov

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• fix: highlight nodes on another tree correctly

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• feat: scale tree branches

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• feat: add nuccore urls in metadata table

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Commits on Jan 18, 2023

• feat: adjust widget spacing

  ivan-aksamentov

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• feat: start re-implementing msa viewer

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• refactor: move components into separate modules

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• feat: make msa canvas scrollable

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• feat: add drag scroll to msa viewer

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• feat: pin ref sequence at the top of msa viewer

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• fix: prevent double drawing of ref sequence

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• feat: show position indices in msa viewer

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Commits on Jan 19, 2023

• feat: add msa toolbar buttons

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• refactor: cleanup drawing code

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