2.0.0-beta.1

⚠️	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.

See the changelog: https://github.com/nextstrain/nextclade/blob/master/CHANGELOG.md#nextclade-200

Commit history

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• [cc157a4] docs: add recent changes to changelog

• [55635b4] fix(web): make 'invalid range' warning condition more optimistic

This avoids a warning when the range is empty as we now consider an empty range a valid case.

Notably, we've encountered this when a frame shift happens to be due to a 1-base deletion of a stop codon. In this case we still want to report a frame shift situation, even if the frame shift range is technically empty.

• [5c62641] fix(web): avoid race condition in fasta download vs analysis launch

Sometimes (timing-dependent) sequences were not fully downloaded when analysis started, because the recoil atom have not yet been set at this point.

This PR ensures that sequences are obtained from recoil in form of a Promise and launcher awaits until it resolves.

Additionally, I removed the useQuerySequences() custom hook usage in the app initialization, because App component can render multiple times and this have caused multiple copes of the same fasta added provided via URL params. Instead moved this code into the effect that runs only once.

• [11f14e8] fix(web): display 'empty range' even if begin == end

This is to make web and other views (e.g. csv) to behave consistently and it seems to the most logical result according to our discussion on Slack.

• [2e01416] Merge pull request #861 from nextstrain/fix/web-range-warning

fix(web): make 'invalid range' warning condition more optimistic

• [09bc091] Merge pull request #862 from nextstrain/fix/web-fasta-crash

• [d44ecaa] fix(web): prevent changelog to overflow its container

• [c5fc407] Merge pull request #864 from nextstrain/fix/changelog-overflow

• [2fb60f9] chore: release cli 2.0.0-beta.1

2.0.0-alpha.13

⚠️	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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• [d08b44d] feat(cli): allow downloading dataset zip

• [6e7aa17] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [9dfcd08] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [b2a6c74] chore: update cargo lock

• [55218bc] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [562fe93] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [9c00a4d] fix: conflicting zstd-sys subdependency between zstd and zip crates

• [138d004] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [0c0411e] feat(cli): allow --input-dataset to also accept a dataset zip archive

• [e8af7f6] fix: disable bzip2 subdependency in zip crate

Because it wont' build for wasm

• [8733405] feat(cli): mention dataset zip file in --dataset-input flag help

• [edf614a] feat(cli): better explain difference between --output-dir and --output-zip

• [a213512] fix(cli): ensure dataset zip files can be overridden by individual files

• [4f58fca] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [6cba472] feat(cli): make CLI log lines more compact

This makes the date, severity, file, line parts of the log messages shorter and dimmed, such that the actual messages are more pronounced and the log is less cluttered.

• [c143640] feat(cli): make input fasta arg positional, allow multiple files

• Removes --input-fasta flag in favor of providing input sequence file names as positional arguments

• Multiple files can be provided by passing multiple positional arguments

• Files can be plain fasta or compressed

• Different files can have different compression

• ?? Read from stdin if no positional arguments is provided

• ?? Read and parse multiple files in parallel

Examples:

nextclade run -D dataset/ -O out/ 1.fasta

nextclade run -D dataset/ -O out/ 1.fasta 2.fasta

nextclade run -D dataset/ -O out/ 1.fasta.gz 2.fasta.zst

nextclade run -D dataset/ -O out/ *.fasta

nextclade run -D dataset/ -O out/ *.fasta*

• [867c5a5] Merge pull request #858 from nextstrain/feat/cli-log-shorter

• [844dbad] Merge remote-tracking branch 'origin/master' into feat/cli-fasta-positional

• [f935a76] Merge remote-tracking branch 'origin/master' into feat/cli-dataset-zip

• [14eb6d7] fix: adjust function to changes on master branch

• [c41caeb] fix: add missing import

• [c489701] feat(cli): read input fasta from standard input if files aren't provided

• [1a6a6e9] feat(web): allow multiple input fasta and control over them

This adds a widget which displays a list of currently added fasta files, URLs and pasted snippets and allows to manage them.

Features:

• Add and remove files one by one
• One or multiple files can be dropped or selected using file manager
• Example sequences can also be added to the list by clicking to the usual link button

Quirks:

• "Run automatically" if enabled, launches analysis right after the last drop, file selection, url or sequence paste. Multiple files can still be dropped, but only once.

• [676cef4] feat(cli): warn if attempting to read fasta from a tty

• [e891f1c] feat(cli): write to stdout if filename is '-'

This adds special handling of filename '-'. If this filename is provided in one of the--output* flags, the corresponding content will be written to standard output.

• [03c2b1a] Merge pull request #850 from nextstrain/feat/cli-dataset-zip

• [0133ba7] Merge pull request #857 from nextstrain/feat/cli-fasta-positional

• [55d9750] Merge pull request #859 from nextstrain/feat/web-additive-inputs

• [426f116] chore: release cli 2.0.0-alpha.13

2.0.0-alpha.12

⚠️	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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• [5254aac] fix: don't treat a lack of extension as error

After transparent compression was introduced, file extension extraction function extension() was implemented such that it fails when there is no file extension.

When gradually removing extensions from compressed files like .fasta.gz there are 2 calls tomade extension(), which correctly detect 2 extensions. However, it was failing on plain .fasta files, because after a single extension was removed there wasn't any more.

Here I chose to treat lack of extension as not an error. extension() now returns an Option<String>, and when there's no extension it returns None. The calling code is updated accordingly.

If there's a situation when we need to fail on lack of file extension, then the Option can be converted to an error in the calling code or we might introduce another version of this function.

• [8ffeefe] Merge pull request #856 from nextstrain/fix/cli-extension-error

• [d424e0e] chore: release cli 2.0.0-alpha.12

2.0.0-alpha.9

⚠️	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.

See changelog: https://github.com/nextstrain/nextclade/blob/master/CHANGELOG.md

Commit history

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• [2975f42] chore(ci): remove nextclade_cli context

• [6b304a2] chore: release cli 2.0.0-alpha.9

• [c201545] chore(ci): add missing env var

2.0.0-alpha.8

⚠️	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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• [b2d929e] fix(ci): make sure DATA_FULL_DOMAIN var has effect

• [a47e718] Merge pull request #852 from nextstrain/fix/ci-data-var

• [a1179ba] chore: release cli 2.0.0-alpha.8

2.0.0-alpha.7

⚠️	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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• [a068d78] feat(cli): make dataset table prettier

• [5ab4c74] Merge pull request #849 from nextstrain/feat/cli-table-prettier

• [490a395] chore(ci): use master, staging or release data server depending on branch

• [82b4671] Merge pull request #851 from nextstrain/chore/ci-cli-release-data-server

• [26c91dc] chore: release cli 2.0.0-alpha.7

2.0.0-alpha.11

⚠️	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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• [2492358] docs: start changelog for v2

• [4a658fa] chore: CHANGELOG for striped alignment

• [b509ae8] Merge remote-tracking branch 'origin/master' into docs/changelog-v2

• [11ce301] Merge remote-tracking branch 'origin/master' into docs/changelog-v2

• [c0e951b] docs: add to changelog

• [38b9478] Merge remote-tracking branch 'origin/master' into docs/changelog-v2

• [59800e3] Merge remote-tracking branch 'origin/master' into docs/changelog-v2

• [46bc271] docs: add more items to the changelog

• [c246815] Merge branch 'docs/changelog-v2'

• [a5e1718] chore: pre-release web v2.0.0

• [e4f839a] chore: fix release commit message [skip ci]

• [f5e270e] chore: update lockfile [skip ci]

• [da85e65] chore: remove pre-release commit message [skip ci]

Just release always, because we cannot really distinguish web pre-releases from branch. They all start from master and then gradually promoted to staging and release.

• [540255e] chore(ci): trigger ci

• [2e546a4] fix(cli): correctly find base name in cases like .fasta.gz

This allows to strip not only .fasta, but also .fasta.gz and similar, when deducing file base name which is used for creating output file names.

• [9fb1042] Merge pull request #854 from nextstrain/fix/cli-basename

• [c739833] fix(cli): prevent writing duplicate csv row

Some of the CLI CSV and TSV files had two header rows due to an extra function call

• [e31dcd3] Merge pull request #855 from nextstrain/fix/cli-duplicated-csv-headers

• [3a404ca] chore: release cli 2.0.0-alpha.11

2.0.0-alpha.10

⚠️	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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• [76aff10] feat(gff): accept locus_tag and gene in addition, warn if neither locus_tag nor gene_name present

• [817bede] feat(cli): make nextalign require one of the output flags

• [bb9e9b3] feat(cli): add --output-all, --output-translations and redesign Nextalign cli args

• [b22ce3f] feat(cli): add --output-all, --output-translations and redesign Nextalign cli args

• [aa72b65] fix: correctly extract base name from path

• [071c8c8] feat(cli): clarify cli arg descriptions

• [431b7d9] feat(cli): add list of required output flags to the cli args decriptions

• [b9f95f7] feat(web): upload multiple files

• [0e8ace2] feat(web): adjust upload box text - multiple files

• [656a465] feat(cli): support compressed fasta files

• [a739125] fix: ignore case when guessing compression from file extension

• [ee28ee8] fix: disable bzip2, xz2 and zstd for wasm

These crates cannot be built for wasm32-unknown-unknown target, hence disabling

• [33d1819] Merge remote-tracking branch 'origin/master' into feat/web-upload-multiple-files

• [77964d8] Merge remote-tracking branch 'origin/master' into feat/compression

• [869a56f] Merge pull request #819 from nextstrain/feat-accept-locus-tag-in-gff

• [1c0c43c] Merge pull request #843 from nextstrain/feat/cli-v2

• [4be720e] Merge remote-tracking branch 'origin/master' into feat/compression

• [8e3c64e] Merge remote-tracking branch 'origin/master' into feat/web-upload-multiple-files

• [145009a] chore(ci): set data server in cli dependeing on version and branch

• [3dec0cc] chore: release cli 2.0.0-alpha.10

• [b5b0cf1] Merge pull request #846 from nextstrain/feat/web-upload-multiple-files

• [58241d2] Merge pull request #847 from nextstrain/feat/compression

• [fd76ee9] chore(ci): fix missing var

2.0.0-alpha.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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• [0448e2a] fix(algo): ensure aa context is properly complemented

• [37bf3fe] Merge branch 'master' into fix/aa-context-minus-strand

• [4f85983] refactor: move grouping of adjacent aa changes into Rust

• [8b562b6] refactor: move extract_gene function into coord mapper

• [ec1bd3d] feat(web): add a note for peptide contexts of reverse strands

• [80271df] Merge remote-tracking branch 'origin/master' into fix/aa-context-minus-strand

• [b8c4103] Merge remote-tracking branch 'origin/master' into fix/aa-context-minus-strand

• [81b5b2b] refactor: extract common coord map and gene conversions into methods

• [c18bec3] Merge remote-tracking branch 'origin/master' into fix/aa-context-minus-strand

• [29b1fd5] fix(web): remove extra import

• [81df207] test: port coord map tests

• [dcf913e] feat: extract method for converting codon range to nuc range

• [6514b3d] feat: extract more conversion methods

• [28f0cc1] Merge remote-tracking branch 'origin/master' into fix/aa-context-minus-strand

• [9b541b9] tests: add gene extraction tests for fwd and rev strand

• [e0c3726] tests: add more tests for coordMap, rename scalar->position

• [3d8b6e0] fix: fix nuc_to_codon_range to not overrun gene length

• [ca74b01] feat: add feature-to-feature function in the coordmap

• [7048102] fix: make nuc context merging of aaGroups obey strand

• [fd2b901] fix: context merging of amino acid changes

• [0775c80] fix: sort aa changes by gene, then by position

• [c25e7e5] feat: shift genemap markers up/down for +/- strand

• [8258924] feat: add strand to tooltip

• [6f6d8a8] fix: context peptide numbering

• [c9b45bb] reafactor: remove debug print statements

• [5ad4bdd] feat(web): combine gene offsets for frame and for strand in gene map

• [ee94f31] fix: this prevents out-of-bounds error when the margin is wider than the length of the sequence

• [23556a4] feat(web): reduce delay of gene map tooltip

• [f9e8a0d] Merge branch 'master' into fix/aa-context-minus-strand

• [d8c66c9] refactor: move variables into the function to avoid extra arguments

This branch is based on #815

This moves 2 variables along with the computation logic into the function, closer to the usage. These variables were not used anywhere outside the function.

Helped me to better understand the changes in #815, and can perhaps allow to simplify logic in it.

• [06dfaeb] fix: remove missing but unused var

• [47ae893] refactor: lint

• [53786e2] fix: aggregate components logic, adjust nuc ranges depending on strand

• [724f994] refactor: merge multiple useMemo calls into one

• [0ca5282] feat: add preview version warning

This adds an alert at the top of the page, when:

• the app is build from a git branch that is not release branch
• and it's not a dev build (NODE_ENV != 'development')

Alert can be dismissed with a button, but reappears on page refresh (or next visit).

This tries to be minimalistic and to not introduce too many differences between prod and non-prod builds.

• [481d4dd] Merge pull request #840 from nextstrain/feat/preview-alert

• [3972a4a] Merge pull request #839 from nextstrain/refactor/move-vars-into-function

refactor: move variables into the function to avoid extra arguments

• [2ca5a09] Merge pull request #815 from nextstrain/fix/aa-context-minus-strand

• [54b72aa] Merge pull request #838 from nextstrain/fix/crash-on-short-sequences

• [abc2ba1] fix: how to serve local datasets

resolves #841

• [76e99bd] chore: remove crossed over seed warning

• [b9ff70d] chore: remove seed_match warning only useful for algo devs

• [09ba91f] chore: release cli 2.0.0-alpha.6

2.0.0-alpha.5

⚠️	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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• [07eafb8] chore(ci): fix missing .env file before wasm build

• [8736c6f] feat(cli): print info when making HTTP requests

• [42f4dc0] Merge pull request #837 from nextstrain/feat/cli-info-http-req

• [0225fb5] chore(release): remove lockfile check from release script

• [90b45d0] chore: release cli 2.0.0-alpha.5