chore: update prod from main#1263
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…rameterized function (#1261) ## Summary - Replaces the two separate `wastewaterOrganismConfigs`/`wastewaterOrganismStagingConfigs` objects and the `withResistanceCollectionOverrides` helper with a single `buildWastewaterOrganismConfigs(isStaging: boolean)` function - Env-specific values (`collectionsUserId`, variant `collectionId`) are now expressed as inline ternaries, making prod/staging differences visible at the point of definition - Corrects the prod variant `collectionId` to 4943 (was 4961, the staging value) - All call sites are unchanged — the two exported constants remain 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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…sm enum value (#1262) Closes #1258 ## Summary - Renames the Astro route directory `collections/[organism]` → `collections/[pathFragment]` so the URL segment is the kebab-case path fragment (e.g. `west-nile`, `rsv-a`) consistent with the rest of the site - Updates the four URL builders in `pages.ts` to use `organismConfig[organism].pathFragment` instead of the raw enum key - Updates all four collection Astro pages to resolve `pathFragment` → `Organism` via `allOrganisms.find()` ## Test plan - [x] Visit `/collections/west-nile`, `/collections/rsv-a`, `/collections/rsv-b`, `/collections/ebola-sudan`, `/collections/ebola-zaire`, `/collections/influenza-a`, `/collections/influenza-b` and verify they load correctly - [x] Verify the old URLs (e.g. `/collections/westNile`) now 404 - [x] Verify collection detail, edit, and create pages work for the affected organisms - [x] Verify organisms where enum key = pathFragment (e.g. `covid`, `mpox`) are unaffected 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
## Summary - Bumps `@genspectrum/dashboard-components` from 1.17.0 to 1.18.0 ## Test plan - [ ] CI passes 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Closes #1242 ## Summary Adds RSV resistance mutation annotations. They are different from the covid annotations, in that we really use only one annotation for multiple mutations, whereas with covid we use one annotation per mutation. We do this because we want to name each mutation individually. This difference is now encoded with `annotationMode`, see below. - Adds `annotationMode: 'per-variant' | 'per-collection'` (required, no default) to `ResistanceMutationCollectionConfig` - Updates `buildResistanceData` to branch on the mode: `per-variant` keeps existing COVID behaviour (one annotation per mutation, name = variant name); `per-collection` emits one annotation for the whole collection with all mutations flattened - Enables `resistanceAnalysisModeEnabled` on RSV-A and RSV-B. Prod collection IDs are 4983/4984 (RSV-A) and 4985/4986 (RSV-B); staging overrides these to 5001/5002 (RSV-A) and 5003/5004 (RSV-B) via `wastewaterOrganismStagingConfigs`. - Sets `annotationMode: 'per-variant'` on all three existing COVID collections ## Screenshot <img width="1512" height="751" alt="image" src="https://github.com/user-attachments/assets/3becdefc-bbf8-4b77-a295-c8c15a188f53" /> ## Test plan - [x] `resistanceData.spec.ts` — existing per-variant tests still pass; new per-collection describe block covers flattened annotation and query-variant skipping - [x] TypeScript compiles cleanly (`tsc --noEmit`) - [x] Verify resistance tab appears on RSV-A and RSV-B wastewater dashboard pages on staging 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Bumps [gradle/actions](https://github.com/gradle/actions) from 6 to 6.1.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/gradle/actions/releases">gradle/actions's releases</a>.</em></p> <blockquote> <h2>v6.1.0</h2> <h2>New: Basic Cache Provider</h2> <p>A new MIT-licensed <strong>Basic Caching</strong> provider is now available as an alternative to the proprietary <strong>Enhanced Caching</strong> provided by <code>gradle-actions-caching</code>. Choose Basic Caching by setting <code>cache-provider: basic</code> on <code>setup-gradle</code> or <code>dependency-submission</code> actions.</p> <ul> <li>Built on <code>@actions/cache</code> -- fully open source</li> <li>Caches <code>~/.gradle/caches</code> and <code>~/.gradle/wrapper</code> directories</li> <li>Cache key derived from build files (<code>*.gradle*</code>, <code>gradle-wrapper.properties</code>, etc.)</li> <li>Clean cache on build file changes (no restore keys, preventing stale entry accumulation)</li> </ul> <p><strong>Limitations vs Enhanced Caching:</strong> No cache cleanup, no deduplication of cached content, cached content is fixed unless build files change.</p> <h2>Revamped Licensing & Distribution Documentation</h2> <ul> <li>New <strong>DISTRIBUTION.md</strong> documents the licensing of each component (particularly Basic Caching vs Enhanced Caching)</li> <li>Simplified licensing notices in README, docs, and runtime log output</li> <li>Clear usage tiers: Enhanced Caching is free for public repos and in Free Preview for private repos</li> </ul> <h2>What's Changed</h2> <ul> <li>Use a unique cache entry for wrapper-validation test by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/921">gradle/actions#921</a></li> <li>Update Dependencies by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/922">gradle/actions#922</a></li> <li>Update dependencies and resolve npm vulnerabilities by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/933">gradle/actions#933</a></li> <li>Add open-source 'basic' cache provider and revamp licensing documentation by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/930">gradle/actions#930</a></li> <li>Restructure caching documentation for basic and enhanced providers by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/934">gradle/actions#934</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/gradle/actions/compare/v6.0.1...v6.1.0">https://github.com/gradle/actions/compare/v6.0.1...v6.1.0</a></p> <h2>v6.0.1</h2> <blockquote> <p>[!IMPORTANT] The release of <code>gradle/actions@v6</code> contains important changes to the license terms. More details in <a href="https://blog.gradle.org/github-actions-for-gradle-v6">this blog post</a>. <strong>TL;DR</strong>: By upgrading to v6, you accept the <a href="https://gradle.com/legal/terms-of-use/">Terms of Use</a> for the <code>gradle-actions-caching</code> component.</p> </blockquote> <h2>Summary</h2> <p>The <a href="https://blog.gradle.org/github-actions-for-gradle-v6">license changes in v6</a> introduced a <code>gradle-actions-caching</code> license notice that is printed in logs and in each job summary.</p> <p>With this release, the license notice will be muted if build-scan terms have been accepted, or if a Develocity access key is provided.</p> <h2>What's Changed</h2> <ul> <li>Bump actions used in docs by <a href="https://github.com/Goooler"><code>@Goooler</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/792">gradle/actions#792</a></li> <li>Add typing information for use by typesafegithub by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/910">gradle/actions#910</a></li> <li>Mute license warning when terms are accepted by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/911">gradle/actions#911</a></li> <li>Mention explicit license acceptance in notice by <a href="https://github.com/bigdaz"><code>@bigdaz</code></a> in <a href="https://redirect.github.com/gradle/actions/pull/912">gradle/actions#912</a></li> <li>Bump com.fasterxml.jackson.dataformat:jackson-dataformat-smile from 2.21.1 to 2.21.2 in /sources/test/init-scripts in the gradle group across 1 directory by <a href="https://github.com/dependabot"><code>@dependabot</code></a>[bot] in <a href="https://redirect.github.com/gradle/actions/pull/907">gradle/actions#907</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/gradle/actions/compare/v6.0.0...v6.0.1">https://github.com/gradle/actions/compare/v6.0.0...v6.0.1</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/gradle/actions/commit/50e97c2cd7a37755bbfafc9c5b7cafaece252f6e"><code>50e97c2</code></a> Link to docs for caching providers</li> <li><a href="https://github.com/gradle/actions/commit/f2e6298504c4b1f20294637059e1d0d89422409a"><code>f2e6298</code></a> Restructure caching documentation for basic and enhanced providers (<a href="https://redirect.github.com/gradle/actions/issues/934">#934</a>)</li> <li><a href="https://github.com/gradle/actions/commit/b294b1e2dbcf270bfe835590dedbbc7e2024618c"><code>b294b1e</code></a> Really fix integ-test-full</li> <li><a href="https://github.com/gradle/actions/commit/83d3189aae3332f1b2235b42d8804258f2348213"><code>83d3189</code></a> Revise license details for gradle-actions-caching</li> <li><a href="https://github.com/gradle/actions/commit/1d5db06d2662829845876553d61cf3df3cf997d1"><code>1d5db06</code></a> Update license link for gradle-actions-caching component</li> <li><a href="https://github.com/gradle/actions/commit/1c809615505fae9768e2610dc6dbecdc3a796443"><code>1c80961</code></a> Fix license link for Enhanced Caching component</li> <li><a href="https://github.com/gradle/actions/commit/9e99920b14b9dc5a9bf8c72e94ba47ebf5bbaee6"><code>9e99920</code></a> Fix integ-test-full workflow</li> <li><a href="https://github.com/gradle/actions/commit/bb8aaaf9d56f25afd4a90925425facf294f31fcf"><code>bb8aaaf</code></a> Fix workflow permissions</li> <li><a href="https://github.com/gradle/actions/commit/f5dfb43fc8c99c758ebf2324d102118e5faf6cb6"><code>f5dfb43</code></a> [bot] Update dist directory</li> <li><a href="https://github.com/gradle/actions/commit/ff9ae24c39252301b448088d2c7d9f0a2d8066dd"><code>ff9ae24</code></a> Add open-source 'basic' cache provider and revamp licensing documentation (<a href="https://redirect.github.com/gradle/actions/issues/930">#930</a>)</li> <li>Additional commits viewable in <a href="https://github.com/gradle/actions/compare/v6...v6.1.0">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
## Summary - Adds `name:` fields to both `actions/upload-artifact` steps in the E2E workflow so they show up as "Upload container logs" and "Upload Playwright report" in the Actions UI instead of being unlabeled. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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This pull request updates the
prodbranch with the latest changes from themainbranch.Make sure to merge this creating a merge commit.