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chore(lapis-docs): bump the minorandpatch group in /lapis-docs with 11 updates #1168

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@dependabot dependabot bot commented on behalf of github Apr 28, 2025 •
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Bumps the minorandpatch group in /lapis-docs with 11 updates:

Package From To
@astrojs/react 4.2.1 4.2.5
@astrojs/starlight 0.32.4 0.34.1
astro 5.5.4 5.7.7
sharp 0.33.5 0.34.1
swagger-ui 5.20.1 5.21.0
swagger-ui-react 5.20.1 5.21.0
yaml 2.7.0 2.7.1
zod 3.24.2 3.24.3
@playwright/test 1.51.1 1.52.0
@types/node 22.13.13 22.15.3
typescript 5.8.2 5.8.3

Updates @astrojs/react from 4.2.1 to 4.2.5

Release notes

Sourced from @​astrojs/react's releases.

@​astrojs/react@​4.2.5

Patch Changes

@​astrojs/react@​4.2.4

Patch Changes

@​astrojs/react@​4.2.3

Patch Changes

@​astrojs/react@​4.2.2

Patch Changes

Changelog

Sourced from @​astrojs/react's changelog.

4.2.5

Patch Changes

4.2.4

Patch Changes

4.2.3

Patch Changes

4.2.2

Patch Changes

Commits

Updates @astrojs/starlight from 0.32.4 to 0.34.1

Release notes

Sourced from @​astrojs/starlight's releases.

@​astrojs/starlight@​0.34.1

Patch Changes

  • #3140 f6eb1d5 Thanks @​HiDeoo! - Fixes a text selection issue for heading with a clickable anchor link when using double or triple click to select text.

  • #3148 dc8b6d5 Thanks @​HiDeoo! - Fixes a regression of the Starlight icon color when using the credits configuration option.

@​astrojs/starlight@​0.34.0

Minor Changes

  • #2322 f14eb0c Thanks @​HiDeoo! - Groups all of Starlight's CSS declarations into a single starlight cascade layer.

    This change allows for easier customization of Starlight's CSS as any custom unlayered CSS will override the default styles. If you are using cascade layers in your custom CSS, you can use the @layer CSS at-rule to define the order of precedence for different layers including the ones used by Starlight.

    We recommend checking your site’s appearance when upgrading to make sure there are no style regressions caused by this change.

  • #3122 3a087d8 Thanks @​delucis! - Removes default attrs and content values from head entries parsed using Starlight’s schema.

    Previously when adding head metadata via frontmatter or user config, Starlight would automatically add values for attrs and content if not provided. Now, these properties are left undefined.

    This makes it simpler to add tags in route middleware for example as you no longer need to provide empty values for attrs and content:

    head.push({
  tag: 'style',
  content: 'div { color: red }'
- attrs: {},
});
head.push({
  tag: 'link',
- content: ''
  attrs: { rel: 'me', href: 'https://example.com' },
});

    This is mostly an internal API but if you are overriding Starlight’s Head component or processing head entries in some way, you may wish to double check your handling of Astro.locals.starlightRoute.head is compatible with attrs and content potentially being undefined.

  • #3033 8c19678 Thanks @​delucis! - Adds support for generating clickable anchor links for headings.

    By default, Starlight now renders an anchor link beside headings in Markdown and MDX content. A new <AnchorHeading> component is available to achieve the same thing in custom pages built using <StarlightPage>.

    If you want to disable this new Markdown processing set the markdown.headingLinks option in your Starlight config to false:

    starlight({
  title: 'My docs',
  markdown: {
    headingLinks: false,
  },
}),

... (truncated)

Changelog

Sourced from @​astrojs/starlight's changelog.

0.34.1

Patch Changes

  • #3140 f6eb1d5 Thanks @​HiDeoo! - Fixes a text selection issue for heading with a clickable anchor link when using double or triple click to select text.

  • #3148 dc8b6d5 Thanks @​HiDeoo! - Fixes a regression of the Starlight icon color when using the credits configuration option.

0.34.0

Minor Changes

  • #2322 f14eb0c Thanks @​HiDeoo! - Groups all of Starlight's CSS declarations into a single starlight cascade layer.

    This change allows for easier customization of Starlight's CSS as any custom unlayered CSS will override the default styles. If you are using cascade layers in your custom CSS, you can use the @layer CSS at-rule to define the order of precedence for different layers including the ones used by Starlight.

    We recommend checking your site’s appearance when upgrading to make sure there are no style regressions caused by this change.

  • #3122 3a087d8 Thanks @​delucis! - Removes default attrs and content values from head entries parsed using Starlight’s schema.

    Previously when adding head metadata via frontmatter or user config, Starlight would automatically add values for attrs and content if not provided. Now, these properties are left undefined.

    This makes it simpler to add tags in route middleware for example as you no longer need to provide empty values for attrs and content:

    head.push({
  tag: 'style',
  content: 'div { color: red }'
- attrs: {},
});
head.push({
  tag: 'link',
- content: ''
  attrs: { rel: 'me', href: 'https://example.com' },
});

    This is mostly an internal API but if you are overriding Starlight’s Head component or processing head entries in some way, you may wish to double check your handling of Astro.locals.starlightRoute.head is compatible with attrs and content potentially being undefined.

  • #3033 8c19678 Thanks @​delucis! - Adds support for generating clickable anchor links for headings.

    By default, Starlight now renders an anchor link beside headings in Markdown and MDX content. A new <AnchorHeading> component is available to achieve the same thing in custom pages built using <StarlightPage>.

    If you want to disable this new Markdown processing set the markdown.headingLinks option in your Starlight config to false:

    starlight({
  title: 'My docs',
  markdown: {
    headingLinks: false,

... (truncated)

Commits

Updates astro from 5.5.4 to 5.7.7

Release notes

Sourced from astro's releases.

[email protected]

Patch Changes

[email protected]

Patch Changes

  • #13703 659904b Thanks @​florian-lefebvre! - Fixes a bug where empty fallbacks could not be provided when using the experimental fonts API

  • #13680 18e1b97 Thanks @​florian-lefebvre! - Improves the UnsupportedExternalRedirect error message to include more details such as the concerned destination

  • #13703 659904b Thanks @​ascorbic! - Simplifies styles for experimental responsive images

    ⚠️ BREAKING CHANGE FOR EXPERIMENTAL RESPONSIVE IMAGES ONLY ⚠️

    The generated styles for image layouts are now simpler and easier to override. Previously the responsive image component used CSS to set the size and aspect ratio of the images, but this is no longer needed. Now the styles just include object-fit and object-position for all images, and sets max-width: 100% for constrained images and width: 100% for full-width images.

    This is an implementation change only, and most users will see no change. However, it may affect any custom styles you have added to your responsive images. Please check your rendered images to determine whether any change to your CSS is needed.

    The styles now use the :where() pseudo-class, which has a specificity of 0, meaning that it is easy to override with your own styles. You can now be sure that your own classes will always override the applied styles, as will global styles on img.

    An exception is Tailwind 4, which uses cascade layers, meaning the rules are always lower specificity. Astro supports browsers that do not support cascade layers, so we cannot use this. If you need to override the styles using Tailwind 4, you must use !important classes. Do check if this is needed though: there may be a layout that is more appropriate for your use case.

  • #13703 659904b Thanks @​ascorbic! - Adds warnings about using local font files in the publicDir when the experimental fonts API is enabled.

  • #13703 659904b Thanks @​ascorbic! - Renames experimental responsive image layout option from "responsive" to "constrained"

    ⚠️ BREAKING CHANGE FOR EXPERIMENTAL RESPONSIVE IMAGES ONLY ⚠️

    The layout option called "responsive" is renamed to "constrained" to better reflect its behavior.

    The previous name was causing confusion, because it is also the name of the feature. The responsive layout option is specifically for images that are displayed at the requested size, unless they do not fit the width of their container, at which point they would be scaled down to fit. They do not get scaled beyond the intrinsic size of the source image, or the width prop if provided.

    It became clear from user feedback that many people (understandably) thought that they needed to set layout to responsive if they wanted to use responsive images. They then struggled with overriding styles to make the image scale up for full-width hero images, for example, when they should have been using full-width layout. Renaming the layout to constrained should make it clearer that this layout is for when you want to constrain the maximum size of the image, but allow it to scale-down.

    Upgrading

    If you set a default image.experimentalLayout in your astro.config.mjs, or set it on a per-image basis using the layout prop, you will need to change all occurences to constrained:

... (truncated)

Changelog

Sourced from astro's changelog.

5.7.7

Patch Changes

5.7.6

Patch Changes

  • #13703 659904b Thanks @​ascorbic! - Fixes a bug where empty fallbacks could not be provided when using the experimental fonts API

  • #13680 18e1b97 Thanks @​florian-lefebvre! - Improves the UnsupportedExternalRedirect error message to include more details such as the concerned destination

  • #13703 659904b Thanks @​ascorbic! - Simplifies styles for experimental responsive images

    ⚠️ BREAKING CHANGE FOR EXPERIMENTAL RESPONSIVE IMAGES ONLY ⚠️

    The generated styles for image layouts are now simpler and easier to override. Previously the responsive image component used CSS to set the size and aspect ratio of the images, but this is no longer needed. Now the styles just include object-fit and object-position for all images, and sets max-width: 100% for constrained images and width: 100% for full-width images.

    This is an implementation change only, and most users will see no change. However, it may affect any custom styles you have added to your responsive images. Please check your rendered images to determine whether any change to your CSS is needed.

    The styles now use the :where() pseudo-class, which has a specificity of 0, meaning that it is easy to override with your own styles. You can now be sure that your own classes will always override the applied styles, as will global styles on img.

    An exception is Tailwind 4, which uses cascade layers, meaning the rules are always lower specificity. Astro supports browsers that do not support cascade layers, so we cannot use this. If you need to override the styles using Tailwind 4, you must use !important classes. Do check if this is needed though: there may be a layout that is more appropriate for your use case.

  • #13703 659904b Thanks @​ascorbic! - Adds warnings about using local font files in the publicDir when the experimental fonts API is enabled.

  • #13703 659904b Thanks @​ascorbic! - Renames experimental responsive image layout option from "responsive" to "constrained"

    ⚠️ BREAKING CHANGE FOR EXPERIMENTAL RESPONSIVE IMAGES ONLY ⚠️

    The layout option called "responsive" is renamed to "constrained" to better reflect its behavior.

    The previous name was causing confusion, because it is also the name of the feature. The responsive layout option is specifically for images that are displayed at the requested size, unless they do not fit the width of their container, at which point they would be scaled down to fit. They do not get scaled beyond the intrinsic size of the source image, or the width prop if provided.

    It became clear from user feedback that many people (understandably) thought that they needed to set layout to responsive if they wanted to use responsive images. They then struggled with overriding styles to make the image scale up for full-width hero images, for example, when they should have been using full-width layout. Renaming the layout to constrained should make it clearer that this layout is for when you want to constrain the maximum size of the image, but allow it to scale-down.

    Upgrading

... (truncated)

Commits

Updates sharp from 0.33.5 to 0.34.1

Commits

Updates swagger-ui from 5.20.1 to 5.21.0

Release notes

Sourced from swagger-ui's releases.

Swagger UI v5.21.0 Released!

5.21.0 (2025-04-13)

Bug Fixes

  • align OpenAPI 3.x.y file uploads with specification (#10409) (c29e712), closes #9278
  • json-schema-2020-12: infer type string when contentEncoding or contentMediaType is present (#10411) (22adad3), closes #9278

Features

  • oas31: display file upload input when contentMediaType or contentEncoding keywords are present (#10412) (2696730), closes #9278

Swagger UI v5.20.8 Released!

5.20.8 (2025-04-10)

Bug Fixes

  • docker: address multiple HIGH security vulnerabilities (#10410) (6e0cc0e)

image

Swagger UI v5.20.7 Released!

5.20.7 (2025-04-07)

Bug Fixes

  • style: prevent operationId from wrapping when space is available (#10259) (da5935e)

Swagger UI v5.20.6 Released!

5.20.6 (2025-04-04)

Bug Fixes

  • json-schema-2020-12-samples: use zero as default example value for int32 and int64 (#10230) (7c346e7)
  • json-schema-2020-12: use consistent comparison operators for displaying min/max constraints (#10159) (d9c778e)

Swagger UI v5.20.5 Released!

5.20.5 (2025-04-03)

Bug Fixes

  • utils: fix error messages for range validation of number parameters (#10344) (a78278e)

Swagger UI v5.20.4 Released!

... (truncated)

Commits
  • fceaec6 chore(release): cut the v5.21.0 release
  • 2696730 feat(oas31): display file upload input when contentMediaType or contentEncodi...
  • c29e712 fix: align OpenAPI 3.x.y file uploads with specification (#10409)
  • 22adad3 fix(json-schema-2020-12): infer type string when contentEncoding or contentMe...
  • 255142a chore(release): cut the v5.20.8 release
  • 6e0cc0e fix(docker): address multiple HIGH security vulnerabilities (#10410)
  • 189f7d3 chore(deps-dev): bump koa from 2.15.4 to 2.16.1 (#10407)
  • 1c0f094 chore(release): cut the v5.20.7 release
  • da5935e fix(style): prevent operationId from wrapping when space is available (#10259)
  • 784d62c chore(release): cut the v5.20.6 release
  • Additional commits viewable in compare view

Updates swagger-ui-react from 5.20.1 to 5.21.0

Release notes

Sourced from swagger-ui-react's releases.

Swagger UI v5.21.0 Released!

5.21.0 (2025-04-13)

Bug Fixes

  • align OpenAPI 3.x.y file uploads with specification (#10409) (c29e712), closes #9278
  • json-schema-2020-12: infer type string when contentEncoding or contentMediaType is present (#10411) (22adad3), closes #9278

Features

  • oas31: display file upload input when contentMediaType or contentEncoding keywords are present (#10412) (2696730), closes #9278

Swagger UI v5.20.8 Released!

5.20.8 (2025-04-10)

Bug Fixes

  • docker: address multiple HIGH security vulnerabilities (#10410) (6e0cc0e)

image

Swagger UI v5.20.7 Released!

5.20.7 (2025-04-07)

Bug Fixes

  • style: prevent operationId from wrapping when space is available (#10259) (da5935e)

Swagger UI v5.20.6 Released!

5.20.6 (2025-04-04)

Bug Fixes

  • json-schema-2020-12-samples: use zero as default example value for int32 and int64 (#10230) (7c346e7)
  • json-schema-2020-12: use consistent comparison operators for displaying min/max constraints (#10159) (d9c778e)

Swagger UI v5.20.5 Released!

5.20.5 (2025-04-03)

Bug Fixes

  • utils: fix error messages for range validation of number parameters (#10344) (a78278e)

Swagger UI v5.20.4 Released!

... (truncated)

Commits
  • fceaec6 chore(release): cut the v5.21.0 release
  • 2696730 feat(oas31): display file upload input when contentMediaType or contentEncodi...
  • c29e712 fix: align OpenAPI 3.x.y file uploads with specification (#10409)
  • 22adad3 fix(json-schema-2020-12): infer type string when contentEncoding or contentMe...
  • 255142a chore(release): cut the v5.20.8 release
  • 6e0cc0e fix(docker): address multiple HIGH security vulnerabilities (#10410)
  • 189f7d3 chore(deps-dev): bump koa from 2.15.4 to 2.16.1 (#10407)
  • 1c0f094 chore(release): cut the v5.20.7 release
  • da5935e fix(style): prevent operationId from wrapping when space is available (#10259)
  • 784d62c chore(release): cut the v5.20.6 release
  • Additional commits viewable in compare view

Updates yaml from 2.7.0 to 2.7.1

Release notes

Sourced from yaml's releases.

v2.7.1

  • Do not allow seq with single-line collection value on same line with map key (#603)
  • Improve warning & avoid TypeError on bad YAML 1.1 nodes (#610)
Commits
  • a141bc0 2.7.1
  • a880b42 fix: Do not allow seq with single-line collection value on same line with map...
  • 923d67b test: Add test for tab after indent spaces for flow-in-block (#604)
  • 7cf843c test: Add descriptive names to tests with issue references
  • 9cf06d2 fix: Improve warning & avoid TypeError on bad YAML 1.1 nodes (fixes #610)
  • 50cf76b chore: Update docs-slate to skip its CI tests
  • 3b2362a docs: Add install option deno add jsr:@eemeli/yaml
  • 83cb780 chore: Update docs to use Slate 2.13.1
  • 9b02456 chore: Fix JSR version
  • See full diff in compare view

Updates zod from 3.24.2 to 3.24.3

Release notes

Sourced from zod's releases.

v3.24.3

Main feature: massive tsc performance improvement in .extend() courtesy of @​Andarist: #4150

Commits:

  • de1f090c98b40884aafc4f324010ab484da2be1e Switch to featured sponsors (#4001)
  • eea05ae3dab628e7a834397414e5145e935e418b Fix headers (#4003)
  • 446644f1095667f9bd6c1704ddbd35854d5ef132 Tweak feature layout (#4008)
  • 1d6e1cb842ece3b2d4d583da126bc22f26367623 docs(README): add GQLoom to tools and integrations section (#3995)
  • e2b9a5f9ac67d13ada61cd8e4b1385eb850c7592 Update feature (#4009)
  • 0b5d29e5d9524ab9d5f08c12651a3385462298d1 Feature Mintlify (#4014)
  • 47dbb2dbf3e611db08e84d6c13f66f19427c8172 Update mintlify feature (#4015)
  • 69d8436f36db10d256c01da333754ea1e33d1708 Add Clerk fellowship mention (#4020)
  • 850871defc2c98928f1c7e8e05e93d4a84ed3c5f Fix table format
  • f204123863a3524a5659ec696ffd38952e20e4ac WIP (#4028)
  • 5041dfa3521ec98066e60f97681adf9604b66e52 WIP (#4045)
  • cb2b8577665d7ce2214d20b10b49c4be7deef7a0 docs: add TanStack Form to Ecosystem/Form integrations (#4055)
  • 099fe85fbb5b6f8434f22ee3dbfc8a6d26b54019 docs: add oRPC to Ecosystem (#4042)
  • b999b4bf340480d64bc7fef1ca5ab56b29430eca docs: Remove outdated doc 'avoid coercions that throw uncaught errors' (#4005)
  • 19c6d2e2c497b2d2498cc3f9db142965617e7c2c docs: update README_KO (#4025)
  • 1061293a18c8a698b082c8a4e2a65ebd3333d543 WIP (#4060)
  • 07ff0da057f4df2aab299a454735d8398b4c0b54 Update link
  • 4c7d8e503a324e7a9873d4c17af2a19738c63364 Update Fern art/link (#4062)
  • 91dcd30ff85f92bc2140c26d7b1294e394ff0ea4 removed unnecessary console logs (#4059)
  • 859ad2495e3d24559d3c8e33a00cf56e2dbaa16a Update alt tag for Retool and Stainless URL (#4071)
  • 220aeda3b63460ab02b2187e460665a4bcb2572e Fix images
  • b865062bf3fe086a26a8b8a52116653f570eb9bc update readme.md with zod-csv library (#4021)
  • 0615af80451fe42da3c04c76b5c4b2b4a5260267 Fix formatting
  • 12e58668345116601453392e2c8237acde7a5b39 Add zod 4 beta anno (#4081)
  • faac697f27ba56023d5384564fc594f98c589915 Fix CI
  • 8cca93b7cc3f8c5fa17303bbb82d5c531ec24f33 Fix CI
  • d114394027b76c56e389d00292f5f92f137e5553 Added FullProduct.dev to 'Powered by Zod' in Ecosystem section (#4131)
  • a801ddd380196778e45a59920f167bfab8f32106 Fix broken logo link (#3974)
  • 8fc309a8000493a86d60a8a31cb9d73850f427dc Add packages/docs
  • bfd0913f08d77b0e6d1633bc0f21b56712e37720 Remove packages/docs
  • 3e602d43124220ae0001ae761f76ff117cc2f741 Optimize extendShape (#4150)
  • 06db7f855f49f75acc7d53ec0d7c4cd3b4dcaa17 3.24.3
  • a18d25b297d1a47dca8f1701afb18079c05e1e4c add back packages/docs
Commits

Updates @playwright/test from 1.51.1 to 1.52.0

Release notes

Sourced from @​playwright/test's releases.

v1.52.0

Highlights

  • New method expect(locator).toContainClass() to ergonomically assert individual class names on the element.

    await expect(page.getByRole('listitem', { name: 'Ship v1.52' })).toContainClass('done');

  • Aria Snapshots got two new properties: /children for strict matching and /url for links.

    await expect(locator).toMatchAriaSnapshot(`
  - list
    - /children: equal
    - listitem: Feature A
    - listitem:
      - link "Feature B":
        - /url: "https://playwright.dev"
`);

Test Runner

  • New property testProject.workers allows to specify the number of concurrent worker processes to use for a test project. The global limit of property testConfig.workers still applies.
  • New testConfig.failOnFlakyTests option to fail the test run if any flaky tests are detected, similarly to --fail-on-flaky-tests. This is useful for CI/CD environments where you want to ensure that all tests are stable before deploying.
  • New property testResult.annotations contains annotations for each test retry.

Miscellaneous

  • New option maxRedirects in apiRequest.newContext() to control the maximum number of redirects.
  • New option ref in locator.ariaSnapshot() to generate reference for each element in the snapshot which can later be used to locate the element.
  • HTML reporter now supports NOT filtering via !@my-tag or !my-file.spec.ts or !p:my-project.

Breaking Changes

  • Changes to glob URL patterns in methods like

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This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog.

Note that this might contain changes that are on main, but not yet released.

Changelog:

0.5.0 (2025-05-15)

⚠ BREAKING CHANGES

Features

  • add /sample to query paths #501 (7ad9746)
  • add access key parameter to /sample/info and remove downloadAsFile (340f2ac)
  • add config generator page (45c9827)
  • add info controller (78f9c69)
  • add info to lapis response (afff4ae)
  • add sample to info route (b703a9c)
  • add unaligned nucleotide sequence route (adda1dc)
  • allow loweer case for mutations (caa8713)
  • allow lower case for genes in variant queries (5434e49)
  • allow lower case for insertions (79c9f2d)
  • allow lower case for segments and genes (74b41bb)
  • allow lower case letters for mutations and insertions in variant queries (fe3f8da)
  • allow string arrays as filter for string and pango lineage fields #507 (4d06713)
  • allow that fields only contains the primary key in protected mode #623 (0ac0709)
  • also get database config from info controller as YAML (cd6536d)
  • amino acid and nucleotide insertion filters are case-insensitive (667f487)
  • change content type to text/plain when asking for csv/tsv without headers #930 (8313996)
  • docs: add LAPIS host to query Url #522 (305e91c)
  • docs: add more important parts of the arc42 docs #535 (13644e4)
  • docs: database config spec #561 (a1c21d9)
  • docs: description of references/fields #604 (5b02ca8)
  • docs: document how to provide data to the SILO preprocessing #565 (2e0080d)
  • docs: document that there is a cache now #137 (88906a4)
  • docs: generate correct URLs for nucleotide sequences endpoints in multi-segmented case #521 (6058b99)
  • docs: implement order by, limit and offset in query generator #524 (6995d28)
  • docs: improve introduction with ChatGPT #561 (e026ccd)
  • docs: improve reference/filters #604 (31bb706)
  • docs: list valid nucleotide and amino acid symbols #573 (35ccf58)
  • docs: move architecture docs to Starlight docs #530 (a663067)
  • docs: reference how to start LAPIS and SILO #569 #570 (0cc0d40)
  • docs: references/additional-request-properties #604 (837e474)
  • docs: separate maintainer docs from user docs #561 (98a9e30)
  • docs: transfer ambiguous symbols explanation #551 (066f5b6)
  • docs: transfer lapis and silo tutorial #547 (db4932d)
  • docs: update mutation filters to reflect the reference genomes (03079d7)
  • fix authentication, don't document authentication for now #553 (f593073)
  • forward Retry-After header when SILO is not available yet #667 (62bcc7c)
  • implement a request cache for mutation and insertion queries #137 (17ff89c)
  • implement a request id to trace requests #586 (194e7fd)
  • implement compressing the response as zstd and gzip #600 (d6e8d9d)
  • implement downloadAsFile #599 (c522296)
  • implement leftover variant query parts #498 (556552f)
  • implement maybe mutation filters #551 (fab1c72)
  • implement the header parameter "headers=false" to disable the header in the returned CSV/TSV #624 (a216e0c)
  • include link to GitHub issues in LapisInfo #692 (ea42ac2)
  • lapis-docs: document string search feature (ae098a9)
  • lapis-docs: mark sections of the docs that are generated from the config (b2009eb), closes #928
  • lapis2-docs: document url encoded forms (8c3ba60), closes #765
  • lapis2: allow filtering for null (f680305)
  • lapis2: clear cache when SILO is restarting (6100bff)
  • lapis2: delete insertions metadata types #804 (dd0ecd1)
  • lapis2: implement boolean columns (7718b4f), closes #740
  • lapis2: make "maybe" mutation queries case-insensitive #797 (0af9c7f)
  • lapis2: read data from SILO as NDJSON (767b19d), closes #741
  • lapis2: stream data from SILO (8fcf360), closes #744
  • lapis2: support url encoded form POST requests (f2f62b1), closes #754
  • lapis2: use entrypoint.sh to allow passing JVM_OPTS through env variable (#823) (9b35b8a), closes #821
  • lapis: abort on startup when silo url has invalid syntax (373d662), closes #939
  • lapis: adapt to new generalized lineage system (508bc8e), closes #961
  • lapis: add fields property to mutation endpoints (#1149) (4d8df3a), closes #1092
  • lapis: add siloVersion to response info (#1066) (c1edcf3)
  • lapis: add healthcheck to Docker containers (0944990), closes #813
  • lapis: add instance name to landing page json (6c5f81b)
  • lapis: add LAPIS version to info response (#1019) (7d8d713)
  • lapis: allow customizable filename for file downloads (817d3f4), closes #869
  • lapis: auto remove entries from cache when heap limit is reached (f804004)
  • lapis: expose the lineage definition files used by SILO (#1073) (2ac977c), closes #1034
  • lapis: hint to which regex syntax is used in Swagger docs (ca4fcdc), closes #903
  • lapis: ignore false-positive compiler warning and add comment (#1174) (6c61a48)
  • lapis: implement landing page when calling / #856 (b886b7d)
  • lapis: make it possible to fetch sequences in JSON and NDJSON format (ba18956), closes #971
  • lapis: omit sequences with null values in unaligned fasta downloads (f1931a6), closes #912
  • lapis: only allow regex search for fields that have lapisAllowsRegexSearch: true configured (d146717), closes #898
  • lapis: order CSV/TSV columns of aggregated/details data as specified in the request fields or as in the database config (6cf8704), closes #910
  • lapis: pass through coverage from SILO in mutation endpoints (#1094) (ed90514), closes #1091
  • lapis: regex filtering for string columns #898 (b3e7775)
  • lapis: return empty lineage definitions when SILO returns an empty file (#1126) (64651ad)
  • lapis: stream JSON responses (#1053) (bfb5f99), closes #1047
  • lapis: throw error when filtering by "equals" and "regex" for the same string field (540d63a), closes #899
  • lapis: use dot symbol as regex separator #908 (3728c7e)
  • lapis: validate that lapisAllowsRegexSearch-fields are of type string (97b3ce9)
  • lapis: validate that metadata fields do not contain the reserved character . (97b3ce9), closes #976
  • log to files again (additionally to stdout) #692 (1acedad)
  • log whether request was cached #717 (3de90f1)
  • make fields case-insensitive #502 (45e931e)
  • make headers accessible to browser despite CORS (4877c04)
  • pass request id to SILO (901e08a)
  • provide full reference genome, and database config to new endpoints (e406023)
  • return bad request error when unknown compression format in request #647 (decaea5)
  • return structured mutation and insertion responses #718 (af38e93)
  • set Content-Type header to application/gzip|zstd when the compression property in the request was set #665 (5592857)
  • show instance name on "not found" page (4e444f1)
  • support order by random #658 (598b05f)
  • try whether also caching aggregated queries makes cov spectrum faster (bbfaf22)
  • use multiple access keys (3ecc11a)

Bug Fixes

  • add info route to endpoints that server aggregated data to allow access (5b10e2b)
  • allow access in authorized mode when fields is specified non-fine-grained (eaa832c)
  • allow stop codon symbol for AminoAcidMutations (74cfa74)
  • consider context path in Swagger UI link (4b12b53)
  • consider only servlet URL when checking auth (0006ac2)
  • consider only servlet URL when checking auth behind a proxy (6b1767a)
  • details does no longer return insertions (3686658)
  • docs: display everything on the mutation filters page (d912f59)
  • docs: schema for uploaded config (ecd2f9c)
  • docs: some minor improvements (c77bf6f)
  • don't set Transfer-Encoding twice #600 (7e49aa5)
  • e2e tests with new silo ordering of insertions and mutations (4a75342)
  • end to end tests failing due to timeout and new pango lineage alias in return (d265809)
  • exact n of query with more elements than n (1402019)
  • file ending when downloading compressed file #685 (6a51de0)
  • import of property (848f4b6)
  • lapis-docs: allow all hosts (#1129) (d0ea4e2), closes #1124
  • lapis-docs: config generator: dateToSortBy, partitionBy and features is optional (4e905e8)
  • lapis-docs: correct invalid gene in example (#1165) (42b79a2)
  • lapis-docs: fix condition when to show the "variant queries are not available" banner (#1186) (6fe60fe)
  • lapis-docs: fix link on landing page (d4137b3)
  • lapis-docs: mention how arrays must be supplied in form urlencoded requests (#1128) (4f24a76), closes #1089
  • lapis-docs: Sequence file naming scheme uses indexes now not names (1e7cd60)
  • lapis-e2e: remove tests that rely on order without specifying lapis to sort output (#1163) (9d30e29)
  • lapis2-docs: relative links must not end with a / (992210d)
  • lapis2-docs: use relative links so that they work when deployed behind a proxy #725 (0cfa8ec)
  • lapis2: also log which line of the SILO response failed to parse (d1badea)
  • lapis2: bring back request id header in OpenAPI docs (eb75391), closes #627
  • lapis2: log request id again (26f83c9)
  • lapis2: only accept a single variant query in a request #798 (54df8e5)
  • lapis2: prefer zstd over gzip #738 (1fb67ac)
  • lapis2: throw exception on invalid variant query #797 (980806a)
  • lapis: add missing dataFormat to amino acid mutation GET endpoint in Swagger UI (#1160) (5c4dbe2), closes #1159
  • lapis: also return CSV header when there are no data (#1138) (aba1320), closes #1090
  • lapis: don't show the single segmented sequence download when there are no nucleotide sequences (#1054) (f27f94b)
  • lapis: fix computation of downloaded file ending with multiple accept headers (3b679a8), closes #890
  • lapis: fix description of mutation objects in OpenApi spec (#1051) (c6f625e)
  • lapis: fix download file ending for csv-without-headers data format (65afba0), closes #871
  • lapis: get rid of logger config deprecation warnings in the log (e7c3908), closes #972
  • lapis: never show whitelabel error page (eb03345), closes #890
  • lapis: nucleotideInsertionContains correctly handles segment (4776a3e)
  • lapis: only keep old log files for 30 days (#1111) (66952c5)
  • lapis: pass correctly escaped stop codon to SILO (be1bb87), closes #1105
  • lapis: reject unknown data formats (#1093) (b1cc7fd), closes #1078
  • lapis: return proper error message when lineage definition from SILO is invalid YAML (#1117) (cdf9b63), closes #1104
  • make stop codon a valid symbolFrom for amino acid mutations (43e5e9e)
  • orderBy is an array (0260036)
  • recognition of which endpoint was called to determine the filename of a download (6c1674c)
  • reduce log level when unable to read from cached request (6810696)
  • remove header output from mutations and insertion endpoints (ffd6b55)
  • remove request id header -> make Swagger UI work again #610 (0afa2a5)
  • return valid gzip when LAPIS returns an error response #656 (db1c6cb)
  • Sending unknown value in fields returns incomprehensible error (107396d)
  • set default min proportion (d033b34)
  • speed up compressing responses #717 (1624580)
  • test #685 (f52d68d)
  • update e2e tests: deletions are also mutations (from SILO) (886a8f1)
  • use authorization filter before other filters #660 (0dab1e7)
  • variant query with nextcladePangolineageQuery (9158575)
  • write empty string to CSV/TSV for null values #708 (c8872ba)

@dependabot dependabot bot force-pushed the dependabot/npm_and_yarn/lapis-docs/minorandpatch-7ef214e361 branch from e7c7077 to 7cc39e7 Compare May 5, 2025 19:28
@dependabot dependabot bot force-pushed the dependabot/npm_and_yarn/lapis-docs/minorandpatch-7ef214e361 branch from 7cc39e7 to 37a0438 Compare May 12, 2025 19:14
@dependabot
chore(lapis-docs): bump the minorandpatch group
2c2e48f 
Bumps the minorandpatch group in /lapis-docs with 11 updates:

| Package | From | To |
| --- | --- | --- |
| [@astrojs/react](https://github.com/withastro/astro/tree/HEAD/packages/integrations/react) | `4.2.1` | `4.2.5` |
| [@astrojs/starlight](https://github.com/withastro/starlight/tree/HEAD/packages/starlight) | `0.32.4` | `0.34.1` |
| [astro](https://github.com/withastro/astro/tree/HEAD/packages/astro) | `5.5.4` | `5.7.7` |
| [sharp](https://github.com/lovell/sharp) | `0.33.5` | `0.34.1` |
| [swagger-ui](https://github.com/swagger-api/swagger-ui) | `5.20.1` | `5.21.0` |
| [swagger-ui-react](https://github.com/swagger-api/swagger-ui) | `5.20.1` | `5.21.0` |
| [yaml](https://github.com/eemeli/yaml) | `2.7.0` | `2.7.1` |
| [zod](https://github.com/colinhacks/zod) | `3.24.2` | `3.24.3` |
| [@playwright/test](https://github.com/microsoft/playwright) | `1.51.1` | `1.52.0` |
| [@types/node](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/node) | `22.13.13` | `22.15.3` |
| [typescript](https://github.com/microsoft/TypeScript) | `5.8.2` | `5.8.3` |


Updates `@astrojs/react` from 4.2.1 to 4.2.5
- [Release notes](https://github.com/withastro/astro/releases)
- [Changelog](https://github.com/withastro/astro/blob/main/packages/integrations/react/CHANGELOG.md)
- [Commits](https://github.com/withastro/astro/commits/@astrojs/[email protected]/packages/integrations/react)

Updates `@astrojs/starlight` from 0.32.4 to 0.34.1
- [Release notes](https://github.com/withastro/starlight/releases)
- [Changelog](https://github.com/withastro/starlight/blob/main/packages/starlight/CHANGELOG.md)
- [Commits](https://github.com/withastro/starlight/commits/@astrojs/[email protected]/packages/starlight)

Updates `astro` from 5.5.4 to 5.7.7
- [Release notes](https://github.com/withastro/astro/releases)
- [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md)
- [Commits](https://github.com/withastro/astro/commits/[email protected]/packages/astro)

Updates `sharp` from 0.33.5 to 0.34.1
- [Release notes](https://github.com/lovell/sharp/releases)
- [Commits](lovell/sharp@v0.33.5...v0.34.1)

Updates `swagger-ui` from 5.20.1 to 5.21.0
- [Release notes](https://github.com/swagger-api/swagger-ui/releases)
- [Changelog](https://github.com/swagger-api/swagger-ui/blob/master/.releaserc)
- [Commits](swagger-api/swagger-ui@v5.20.1...v5.21.0)

Updates `swagger-ui-react` from 5.20.1 to 5.21.0
- [Release notes](https://github.com/swagger-api/swagger-ui/releases)
- [Changelog](https://github.com/swagger-api/swagger-ui/blob/master/.releaserc)
- [Commits](swagger-api/swagger-ui@v5.20.1...v5.21.0)

Updates `yaml` from 2.7.0 to 2.7.1
- [Release notes](https://github.com/eemeli/yaml/releases)
- [Commits](eemeli/yaml@v2.7.0...v2.7.1)

Updates `zod` from 3.24.2 to 3.24.3
- [Release notes](https://github.com/colinhacks/zod/releases)
- [Changelog](https://github.com/colinhacks/zod/blob/main/CHANGELOG.md)
- [Commits](colinhacks/zod@v3.24.2...v3.24.3)

Updates `@playwright/test` from 1.51.1 to 1.52.0
- [Release notes](https://github.com/microsoft/playwright/releases)
- [Commits](microsoft/playwright@v1.51.1...v1.52.0)

Updates `@types/node` from 22.13.13 to 22.15.3
- [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases)
- [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/node)

Updates `typescript` from 5.8.2 to 5.8.3
- [Release notes](https://github.com/microsoft/TypeScript/releases)
- [Changelog](https://github.com/microsoft/TypeScript/blob/main/azure-pipelines.release-publish.yml)
- [Commits](microsoft/TypeScript@v5.8.2...v5.8.3)

---
updated-dependencies:
- dependency-name: "@astrojs/react"
  dependency-version: 4.2.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minorandpatch
- dependency-name: "@astrojs/starlight"
  dependency-version: 0.34.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: astro
  dependency-version: 5.7.7
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: sharp
  dependency-version: 0.34.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: swagger-ui
  dependency-version: 5.21.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: swagger-ui-react
  dependency-version: 5.21.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: yaml
  dependency-version: 2.7.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minorandpatch
- dependency-name: zod
  dependency-version: 3.24.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minorandpatch
- dependency-name: "@playwright/test"
  dependency-version: 1.52.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: "@types/node"
  dependency-version: 22.15.3
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: minorandpatch
- dependency-name: typescript
  dependency-version: 5.8.3
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: minorandpatch
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot force-pushed the dependabot/npm_and_yarn/lapis-docs/minorandpatch-7ef214e361 branch from 37a0438 to 2c2e48f Compare May 15, 2025 07:55
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dependabot bot commented on behalf of github May 19, 2025

Looks like these dependencies are updatable in another way, so this is no longer needed.

@dependabot dependabot bot closed this May 19, 2025
@dependabot dependabot bot deleted the dependabot/npm_and_yarn/lapis-docs/minorandpatch-7ef214e361 branch May 19, 2025 19:10
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