nextstrain/nextclade: 2.7.0

Nextclade Web 2.7.0 (2022-10-05) Hide custom clade columns

We added ability to mark certain custom clade columns as hidden. In this case they are not shown in Nextclade Web. This prepares the web application for the upcoming reorganization of clade columns. It should not affect current users.

Remove unused fields from output files, add custom phenotype key list

We removed extra repetitive fields related to custom phenotype columns (e.g. "Immune escape" and "ACE-2 binding") entries from JSON and NDJSON output files. We also added keys for custom phenotype columns to the header section of output JSON, for symmetry with custom clade columns. These changes should not affect most users.

<details> <summary><h3>Commit history</h3> (click to expand)</summary> - [[`21c5e5e`](https://github.com/nextstrain/nextclade/commit/21c5e5ef3d760c4dd7933dca05830bc665540f77)] chore: apply automatic clippy lint fixes - [[`d71864c`](https://github.com/nextstrain/nextclade/commit/d71864ce54bf7e14501618022b3626870f187814)] chore: lint - [[`de4079a`](https://github.com/nextstrain/nextclade/commit/de4079ad798321a9204cdbc6879819408aaa68ff)] chore: format - [[`296e9f8`](https://github.com/nextstrain/nextclade/commit/296e9f8a3ae10e5ba553a243d6aed8a9e848eb9d)] Merge pull request #1003 from nextstrain/chore/lint - [[`362f280`](https://github.com/nextstrain/nextclade/commit/362f280e687d1d09680891aa45183502fe62b217)] chore(ci): only release cli from release-cli branch - [[`8337dc0`](https://github.com/nextstrain/nextclade/commit/8337dc099467fc4c26cdd8a732972bd1f8830c4d)] fix: link to release dataset changlog Currently release users see master dataset changelog. Here I change the link such that they see dataset changelog on release branch, i.e. only released dataset changes. - [[`95bda16`](https://github.com/nextstrain/nextclade/commit/95bda160675cbdacdde4c88d07db6fbe8b13f19a)] Merge pull request #1004 from nextstrain/fix/web-dataset-changelog-link - [[`ccb35e9`](https://github.com/nextstrain/nextclade/commit/ccb35e97d43eecbbf666c0f32e43e08bdb0deb70)] feat(web): format tooltip text Format text of custom phenotype columns. This text comes from a JSON string, so formatting capabilities are very limited. Here I split the incoming string on `\n` and create paragraphs (`<p>`) from each fragment. - [[`6f48b17`](https://github.com/nextstrain/nextclade/commit/6f48b175495097fecf5f08a79b8479f41a3115d2)] Merge pull request #1005 from nextstrain/feat/web-format-tooltip-text - [[`f7d3ae8`](https://github.com/nextstrain/nextclade/commit/f7d3ae85d20719c3a0675aa461f51da9bbc43aeb)] chore: release web v2.6.1 - [[`7f6cd6b`](https://github.com/nextstrain/nextclade/commit/7f6cd6bdc1cf5dd70491ef36496f549a195a2009)] feat: allow hiding custom clade columns - [[`8e7eb64`](https://github.com/nextstrain/nextclade/commit/8e7eb6468099a40ebba11f190cc7c4083f70b6de)] fix: show custom clade columns by default Let's flip the boolean, so that it's natural default is `false` - [[`54117cf`](https://github.com/nextstrain/nextclade/commit/54117cf874a501233de65f136747d7c62718f276)] fix: remove unused data from outputs Removes `results[].phenotypeValues.nameFriendly` and `results[].phenotypeValues.description` from output JSON and NDJSON. These fields were not intended to be used, are repeated and increase file size needlessly. - [[`ee0c659`](https://github.com/nextstrain/nextclade/commit/ee0c659d3df32c226dd1cefc6d738bebf831f499)] fix: add descriptions for phenotype attributes to outputs Adds descriptions of phenotype attributes to `.phenotypeAttrKeys` of JSON output. This is for symmetry with the similarly implemented `.cladeNodeAttrKeys` attributes. - [[`f145b45`](https://github.com/nextstrain/nextclade/commit/f145b45eae843a5489378058b220c7f0dd673c90)] Merge pull request #1009 from nextstrain/fix/remove-unused-output-data - [[`c8fe93e`](https://github.com/nextstrain/nextclade/commit/c8fe93ef9ddc7e887a6dddaa41590c74df8c4f9c)] Merge pull request #1010 from nextstrain/fix/add-phenotype-descriptions-to-outputs - [[`d30d608`](https://github.com/nextstrain/nextclade/commit/d30d60885f8a68d382b04570f388cdeb094503aa)] fix: reset node attr state correctly across runs - [[`ade06e2`](https://github.com/nextstrain/nextclade/commit/ade06e267f3ab54976caff792f414368c9fd7f2a)] Merge pull request #1006 from nextstrain/feat/allow-hiding-custom-clade-columns feat: allow hiding custom clade columns - [[`1c3377b`](https://github.com/nextstrain/nextclade/commit/1c3377b22b43acb5b7231300897d29636b78dd02)] chore: speedup wasm dev build Here for wasm dev build I replace the `wasm-pack` which is nice, but behind its defaults it hides lots of useful stuff, and I call `cargo build`, `wasm-bindgen` and `wasm-opt` explicitly. Notably `wasm-pack` does not allow custom cargo profiles (https://github.com/rustwasm/wasm-pack/issues/1111). I also add the new "opt-dev" cargo profile, which is something in the middle between `release` and `dev` - a balance between rebuild speed and runtime performance. This should save lots of time during day-to-day work. The production version still uses `wasm-pack` and a more tried solution. The dev version now requires cargo wasm toolchain, `wasm-bindgen` and `wasm-opt` (from `binaryen` project) installed manually. Previously `wasm-pack` would handle that. The dev docker image was updated accordingly. - [[`ae49768`](https://github.com/nextstrain/nextclade/commit/ae497682278c2319fa5013e35479359d4a8a5dc8)] fix: adjust import For the changes in 1c3377b22b43acb5b7231300897d29636b78dd02 (there no longer is `package.json`, so import of the directory does not work) - [[`4f5db09`](https://github.com/nextstrain/nextclade/commit/4f5db091285a390bccc966283aafa78b61e7d21e)] fix(web): crash when exporting files in web Followup of https://github.com/nextstrain/nextclade/pull/1006 The PR https://github.com/nextstrain/nextclade/pull/1006 introduced a bug: it filters away hidden columns from recoil state, thus making them unavailable for export functions. The mismatch in expected columns caused crash on Rust side. Here I modify the filtering logic, moving it to the actual rendering site, instead of filtering globally. This way, hidden columns are not rendered, but are still be available for export. - [[`f0975a2`](https://github.com/nextstrain/nextclade/commit/f0975a2914b6f073dd1a3314c9006e5bab7463ef)] chore: remove unused script [skip ci] - [[`19b1932`](https://github.com/nextstrain/nextclade/commit/19b1932d2cd252e85745e0e3fac3bc83121e0669)] chore: document dev scripts [skip ci] - [[`70122ce`](https://github.com/nextstrain/nextclade/commit/70122ce5c018718cd36f008ca26dbbb6c76e5147)] Merge pull request #1011 from nextstrain/fix/web-crash-on-export - [[`66c6dd2`](https://github.com/nextstrain/nextclade/commit/66c6dd25b01a762afe915c2f349c9a876b0d53ea)] chore: release web and cli 2.7.0 </details>