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Docs/v3#1236

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ivan-aksamentov merged 45 commits intomasternextstrain/nextclade:masterfrom docs/v3nextstrain/nextclade:docs/v3Copy head branch name to clipboardOct 31, 2023

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Commits on Aug 10, 2023

• docs: update description of alignment algorithm

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• docs: update translation docs to use CDS instead of gene

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• docs: small edits to PCR and mutation calling docs

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• docs: update tree building docs

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• docs: edits to clade and tree docs

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Commits on Sep 20, 2023

• doc: v3 input files

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Commits on Oct 5, 2023

• docs: split away old changelog file; scaffold new changelog

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Commits on Oct 9, 2023

• docs: update links in changelog

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• docs: update dev guide for v3

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Commits on Oct 10, 2023

• docs: add a note about release schedule

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Commits on Oct 11, 2023

• Merge remote-tracking branch 'origin/master' into docs/v3

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• chore: fix docker docs build

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Commits on Oct 12, 2023

• docs: extend changelog

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Commits on Oct 16, 2023

• docs(input-files): second pass

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• doc(output-files): general improvements and v3 adjustments

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• docs(output-files): remove deprecated output files

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Commits on Oct 17, 2023

• doc: remove nextalign-cli docs for v3

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• doc(output-files): small edits

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• docs(nextclade-cli): update for v3 and add "compile from source"

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• docs(datasets): Update for v3

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Commits on Oct 26, 2023

• docs: split away migration docs; document new URL params

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• docs: split "Input files" section into separate files

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• docs: split cli installation and usage docs into separate files

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• feat(cli): automatically generate cli reference docs in markdown format

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Commits on Oct 27, 2023

• docs: fix font size in headings containing code

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• chore: add script to re-generate cli docs

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• chore(ci): add ci check for generated cli docs

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• Merge pull request #1295 from nextstrain/docs/v3-cli-reference

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• docs: split output files docs into multiple sections

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• docs: edit output files section

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Commits on Oct 30, 2023

• docs: edit of datasets.md

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• docs: edit migration guide

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• docs: edit of ref seq and annotation input files

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• docs: typo

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• docs: align changelog and migration guide

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• chore(ci): show diff when checking cli docs

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• Merge remote-tracking branch 'origin/master' into docs/v3

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• chore(ci): colorize output of git diff

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• docs: update cli ref docs

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• feat(cli): mark removed arg as removed

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• docs: remove removed and renamed args from cli reference

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• docs: remove runtime-defined default values from cli reference

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Commits on Oct 31, 2023

• feat(docs): move cli help preprocessing to rust

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• docs(CHANGELOG): don't treat ambiguous nucs as reversions

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• docs: reword changelog entry for ambiguous reversions

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