nextstrain/nextclade: 2.3.0

Nextclade CLI 2.3.0, Nextclade Web 2.3.0

This release brings back entries for failed sequences into output files.

It was reported by @tseemann that in Nextclade v2 CSV and TSV rows are not written for failed sequences. While in v1 they were. This was unintended.

In this release:

• CSV, TSV, NDJSON rows for failed entries are now also written (only seqName and errors columns are populated). Note, it's important to check for errors column and disregard other columns if there are errors. For example, in case of an error, the substitutions column will be empty, but it does not mean that the failed sequence has no substitutions.
• JSON output now has a separate errors field at the root of the object, with all failed entries
• NDJSON rows are also written for failed entries. They only contain index, seqName and errors fields.
• new columns are written into CSV and TSV outputs: warnings and failedGenes, which include any warnings emitted for a sequence as well as a list of genes that failed translation. Now all columns of the "errors.csv" file are also in the CSV and TSV results files

<details> <summary><h3>Commit history</h3> (click to expand)</summary> - [[`0e7971e`](https://github.com/nextstrain/nextclade/commit/0e7971e4580b58d33d06a7eea2e424bb687579bb)] test(cli): scaffold functional cli tests with cram - [[`606fad8`](https://github.com/nextstrain/nextclade/commit/606fad890f141c868f0059169efd02ce886bc5d0)] Merge pull request #920 from nextstrain/test/cli-func - [[`72695f6`](https://github.com/nextstrain/nextclade/commit/72695f6ab3d90c6d579e3714af7f26abeb4d250e)] Update CHANGELOG.md - [[`bdfd9cf`](https://github.com/nextstrain/nextclade/commit/bdfd9cff73f8181bb5891a9a9c49eb0218e7e868)] chore(ci): fix gnu linux build Apparently Debian 7 has no pip3 package. So let's install it using get-pip script - [[`6bf4e03`](https://github.com/nextstrain/nextclade/commit/6bf4e035e1d90f8548bcb420ea47ef6ffaaa67a5)] docs(dev): add a note about CORS in dev guide - [[`52d0f50`](https://github.com/nextstrain/nextclade/commit/52d0f5020d549a08b271bf6ca485a4fd85755743)] fix(cli): write failed sequence results (errors) to csv and tsv outputs It was reported by @tseemann that In Nextclade v2 csv and tsv outputs are not written for failed sequences. While in v1 they were. This was unintended. Here I bring back writing CSV and TSV rows for failed sequences (only "errors" column is populated) - [[`f9280c4`](https://github.com/nextstrain/nextclade/commit/f9280c4ad849e58731e07cfec6145d4b5259683b)] feat(cli): add 'warnings' and 'failedGenes' columns to results csv/tsv This adds new columns to main nextclade results CSV and TSV outputs: `warnings` and `failedGenes`, which include any warnings emitted for a sequence as well as a list of genes that failed translation. Now all columns of the "errors.csv" file are also in the CSV and TSV results files. - [[`2fdf81a`](https://github.com/nextstrain/nextclade/commit/2fdf81a3c7c7c9e599142d6776ac1d9e285b6c30)] docs: fix typos Noted in an email to our support address (ticket 510). - [[`ca1c74d`](https://github.com/nextstrain/nextclade/commit/ca1c74dffa2b4e71e2e65faa49983fa0f5457f68)] Merge pull request #924 from nextstrain/docs/fix-typos docs: fix typos - [[`773b1e6`](https://github.com/nextstrain/nextclade/commit/773b1e6ea096a1d6cb4422099a99d04033818005)] chore: remove unnecessary variable - [[`7951530`](https://github.com/nextstrain/nextclade/commit/79515303f3b0368875cd488a3af156b7a2f9ffbe)] Merge remote-tracking branch 'origin/master' into fix/cli-csv-output-errors - [[`b0d41e6`](https://github.com/nextstrain/nextclade/commit/b0d41e66dd3ee7eb3c346901b3799a3fd99c167d)] fix(cli): write failed sequences to json and ndjson outputs - [[`c1f9a72`](https://github.com/nextstrain/nextclade/commit/c1f9a72a0d022551dbe53ab663268dc2a0a1816a)] Revert "chore: upgrade Cargo.toml's" This reverts commit 2290adc08adb14752c465465746b0ff1f69e8254. - [[`55f3342`](https://github.com/nextstrain/nextclade/commit/55f33420d18a8e5f61fab647ccc3e7206a31aae4)] Revert "chore: update dependencies, rust to 1.61" This reverts commit 46a8a53a840b84418415abba2a0949a85698e4cd. - [[`381c3ab`](https://github.com/nextstrain/nextclade/commit/381c3ab1f2c1cb0696e2c62aaf840246f0078e18)] Merge pull request #925 from nextstrain/chore/revert-dep-upgrade - [[`5a5a060`](https://github.com/nextstrain/nextclade/commit/5a5a0609f47bf12972943bdddc578910fee486aa)] Merge remote-tracking branch 'origin/master' into fix/cli-csv-output-errors - [[`b33d343`](https://github.com/nextstrain/nextclade/commit/b33d343b1217b0cae930fa968989e956065d076a)] fix(web): add failed sequences to downloaded outputs in the web app - [[`01f5076`](https://github.com/nextstrain/nextclade/commit/01f5076e27ed31fbfe9c0911a84dcf0bba567290)] fix(web): typo in download dialog - [[`7062ced`](https://github.com/nextstrain/nextclade/commit/7062ced0cb8f4d2f5b97a8321c4511735ccae90e)] fix(web): enable download button even if all sequences faield Currently the button stays disabled when a ran ended in no successful results. However, this prevents downloading errors.csv and other files containing errors, which might still be useful. - [[`e55f31b`](https://github.com/nextstrain/nextclade/commit/e55f31ba65fbc6f08cc883d6aa872c07120c5dc2)] Merge pull request #926 from nextstrain/fix/web-typo - [[`da679ac`](https://github.com/nextstrain/nextclade/commit/da679ac32713579b078f121caeb3f62a6040bff6)] feat(web): improve unsupported browser warning This makes the warning to appear in a modal, so that it's harder to miss. Also adds links to official websites of Chrome and Firefox. - [[`ab00f35`](https://github.com/nextstrain/nextclade/commit/ab00f35cb0cffb7d6a321707a93877c2f8102169)] fix: add failed sequences to insertions.csv of nextalign and nextclade - [[`f4d4480`](https://github.com/nextstrain/nextclade/commit/f4d448079cabd1e60619a0f65d060225f476d1f0)] docs: document outputs on failures - [[`fe9bb44`](https://github.com/nextstrain/nextclade/commit/fe9bb443ebc7682e7fd7310d2aa3bd5813a682e8)] fix: make error entries in JSON and NDJSON outputs similar to normal - [[`cd9ed49`](https://github.com/nextstrain/nextclade/commit/cd9ed490deadf9f78d262b449ecb9c5177432140)] Merge pull request #922 from nextstrain/fix/cli-csv-output-errors - [[`88238a8`](https://github.com/nextstrain/nextclade/commit/88238a8d4dd5907b08326e4fb6060c375d78ce1c)] docs: document limitations of JSON outputs Adds a few warnings explaining how JSON outputs can cause increased memory consumption. > ⚠️ For CLI users: Note that due to technical limitations of the JSON format, it cannot be streamed entry-by entry, i.e. before writing the output to the file, all entries need to be accumulated in memory. If the JSON results output or tree output is requested (through --output-json, --output-tree or --output-all arguments), for large input data, it can cause very high memory consumption, disk swapping, decreased performance and crashes. Consider removing these outputs for large input data, running on a machine with more RAM, or processing data in smaller chunks. - [[`5c73286`](https://github.com/nextstrain/nextclade/commit/5c73286a4e3200fa60c5f21d69c7ec2905a831d2)] docs: document output compression - [[`cb569e5`](https://github.com/nextstrain/nextclade/commit/cb569e5be0418eb74cf30c67d1cd4627f0e32e88)] docs: document how failed sequences are reflected in output files - [[`8986a95`](https://github.com/nextstrain/nextclade/commit/8986a95a088b27458ad5fbb0f663ebaba6cdbe35)] Merge pull request #929 from nextstrain/docs/outputs - [[`4f56bd9`](https://github.com/nextstrain/nextclade/commit/4f56bd9b0e0c80a20be1fcd7886fa51227d61a84)] Let user use relative url for nextclade datasets server when the DATA_FULL_DOMAIN is started with '/', the HTTP Origin will be added automatically in front of it to make an absolute url - [[`4ab84c8`](https://github.com/nextstrain/nextclade/commit/4ab84c84448fe4fb86ca9fb4122578df395b20cb)] Replace var with let - [[`ee12aab`](https://github.com/nextstrain/nextclade/commit/ee12aab3c3eedcd45ab25b03d4c64f971368b609)] Merge pull request #930 from xzhub/master - [[`0200b6e`](https://github.com/nextstrain/nextclade/commit/0200b6e47e7416afd99ec8fbae5557655fb88b7f)] Merge branch 'fix/web-enable-dl-btn' - [[`34fc40a`](https://github.com/nextstrain/nextclade/commit/34fc40a13d201eaa7f869b2968083ed4406eee51)] Merge branch 'feat/web-improved-unsupported-browser-warning' - [[`bbaff7b`](https://github.com/nextstrain/nextclade/commit/bbaff7b66da438bd96179a5530c780253794a94b)] feat(cli): add a note about CSV and TSV delimiters - [[`356c100`](https://github.com/nextstrain/nextclade/commit/356c1005fdf265cd7a5458bfb000c9d4030777ea)] Merge pull request #933 from nextstrain/feat/cli-help-csv-delimiters feat(cli): add a note about CSV and TSV delimiters - [[`7c38af8`](https://github.com/nextstrain/nextclade/commit/7c38af8f38e0eb6c2e5feff33f062024ef090efc)] docs: update changelog [skip ci] - [[`4b70821`](https://github.com/nextstrain/nextclade/commit/4b70821049d883e17514126e1adfc3333db00240)] chore: release cli 2.3.0 </details>