chore(lapis-docs): bump mdast-util-to-hast from 13.0.2 to 13.2.1 in /lapis-docs

[dependabot]

Bumps mdast-util-to-hast from 13.0.2 to 13.2.1.

Release notes

Sourced from mdast-util-to-hast's releases.

13.2.1

Fix

• ab3a795 Fix support for spaces in class names

Types

• efb5312 Refactor to use @imports
• a5bc210 Add declaration maps

Full Changelog: syntax-tree/mdast-util-to-hast@13.2.0...13.2.1

13.2.0

Types

• 24f4576 Add type for data.meta on elements to hast

Full Changelog: syntax-tree/mdast-util-to-hast@13.1.0...13.2.0

13.1.0

Add

• 59ecd14 Add support for file in options

Full Changelog: syntax-tree/mdast-util-to-hast@13.0.2...13.1.0

Commits

• 174795b 13.2.1
• 3d05b3a Update Node in Actions
• ab3a795 Fix support for spaces in class names
• efb5312 Refactor to use @imports
• a5bc210 Add declaration maps
• b54955d Add .tsbuildinfo to .gitignore
• f511a93 13.2.0
• 24f4576 Add type for data.meta on elements to hast
• feeec02 Update dev-dependencies
• c7a658e 13.1.0
• Additional commits viewable in compare view

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Project	Deployment	Preview	Comments	Updated (UTC)
lapis	Ready	Preview	Comment	Dec 9, 2025 8:35am

[github-actions]

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:

0.7.0 (2025-12-09)

⚠ BREAKING CHANGES

• lapis: make generateLineageIndex in the database config a string field
• lapis: lapisAllowsRegexSearch on string metadata fields in the database config is not necessary anymore, regex search is always enabled for all string fields.
• lapis: No longer support .* wildcard in advanced queries. Use ? syntax instead.
• lapis: use dot symbol as string search regex separator
• lapis2: throw exception on invalid variant query Maybe operator is case sensitive (in contrast to SQL and my naive user expectation) #797
• lapis2: read data from SILO as NDJSON

Features

• include link to GitHub issues in LapisInfo #692 (ea42ac2)
• lapis-docs: document string search feature (ae098a9)
• lapis-docs: give examples for boolean queries (#1470) (d211119)
• lapis-docs: improve advanced queries docs (#1468) (6df0ed0)
• lapis-docs: mark sections of the docs that are generated from the config (b2009eb), closes #928
• lapis-docs: mention n-of syntax earlier (#1471) (d327c74)
• lapis-e2e: adjust test data to SILO 0.8 (4d785a7)
• 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: adapt to SILO changes that renamed the unaligned sequences to have the "unaligned_" prefix (#1225) (d669335)
• lapis: add fields property to mutation endpoints (#1149) (4d8df3a), closes #1092
• lapis: add siloVersion to response info (#1066) (c1edcf3)
• lapis: add advanced queries feature (#1144) (b8e8ca8)
• lapis: add aminoAcidMutationsOverTime (#1270) (c9adf26), closes #1214
• lapis: add endpoint /sample/alignedAminoAcidSequences to download all genes at once (#1242) (36dfd5f)
• lapis: add endpoint /sample/unalignedNucleotideSequences for multi-segmented organism to download several sequences at once (#1246) (f9275c2)
• lapis: add endpoint to download all aligned segments (or a subset) at once (for multi segmented organisms) (#1235) (6207d32)
• lapis: add example value to /phyloSubtree endpoints docs (#1337) (21e659e)
• 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: add mostRecentCommonAncestor endpoint (#1277) (e062ebc)
• lapis: add nucleotideMutationsOverTime endpoint (#1229) (cade8d9), closes #1205
• lapis: add parameter fastaHeaderTemplate to customize the fasta header in sequences endpoints (#1258) (ac7fc29), closes #857
• lapis: add phylo tree queries to variant filters (#1311) (26e3096)
• lapis: add PhyloDescendantOf filter option (#1284) (d5681e0)
• lapis: add phyloSubtree endpoint (#1293) (af5f2a3)
• lapis: allow customizable filename for file downloads (817d3f4), closes #869
• lapis: auto remove entries from cache when heap limit is reached (f804004)
• lapis: automate access key rotation (#1429) (edbcfa7)
• lapis: drop sorting by segment/gene from docs of sequence endpoints (#1268) (bc67a7c), closes #1248
• lapis: ensure order preservation for muts and dateRanges in mutationsOverTime (#1317) (8d2c731)
• lapis: expose the lineage definition files used by SILO (#1073) (2ac977c), closes #1034
• lapis: for protected data, require >= 10 sequences per request (#1428) (4f4c429)
• 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 generateLineageIndex in the database config a string field (#1377) (3f02855)
• lapis: make it possible to fetch sequences in JSON and NDJSON format (ba18956), closes #971
• lapis: make thread count for SILO client configurable (#1352) (d541fb8)
• lapis: mutationsOverTime endpoint: return total sequence count per dateRange (#1316) (b29c921)
• 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: rename phyloTreeNodeIdentifier as isPhyloTreeField (#1291) (ea4b5ba)
• lapis: return empty lineage definitions when SILO returns an empty file (#1126) (64651ad)
• lapis: stream JSON responses (#1053) (bfb5f99), closes #1047
• lapis: support random with seed (#1426) (0773dcd)
• lapis: support TSV with escaped special characters (#1295) (d2599f2)
• lapis: throw error when filtering by "equals" and "regex" for the same string field (540d63a), closes #899
• lapis: update CHANGELOG.md with details of backported LAPIS v0.5.19 (#1405) (00bdcfb)
• 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)
• return structured mutation and insertion responses #718 (af38e93)

Bug Fixes

• 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: fix invalid insertion indices (#1421) (53f2dab)
• 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: advanced queries: make .regex case-insensitive (#1198) (fd85fa5)
• lapis: advanced queries: tell which metadata fields exist when finding an unknown one (#1209) (1011154)
• lapis: allow advanced queries to be used with simple variant and metadata queries (#1212) (8a1409e)
• lapis: also don't log the stack trace when SILO says that it's not available yet (#1376) (b4ee14d)
• lapis: also regard request parameters for non-GET requests (#1427) (4c8cf32)
• lapis: also return CSV header when there are no data (#1138) (aba1320), closes #1090
• lapis: also return sequences that are null when requesting JSON or NDJSON (#1256) (a888965), closes #1255
• lapis: always return a data version (#1467) (57e1cfa)
• lapis: close connection to SILO if client cancels request to LAPIS (#1393) (17012a8)
• lapis: don't show the single segmented sequence download when there are no nucleotide sequences (#1054) (f27f94b)
• lapis: don't spam the log with stack traces when SILO can't be reached (#1373) (0e35d0f)
• lapis: fix 500 server error in *mutationsOverTime endpoints (#1357) (d056d6c)
• 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: fix response schema of /phyloSubtree in OpenAPI spec (#1336) (c3c3e75)
• lapis: fix Swagger UI layout of GET requests (#1217) (70b0089), closes #1193
• lapis: get rid of logger config deprecation warnings in the log (e7c3908), closes #972
• lapis: increase maximum string length in JSON parser (#1332) (1765428)
• lapis: make sure that the downloaded database config has all field that the original file had (#1327) (c10673c)
• lapis: mutations over time need only aggregatedDataAccessKey (#1303) (baadcee)
• 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: prevent errors for mutationsOverTime endpoint and potentially other endpoints (#1322) (bed930b)
• 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
• lapis: truncate error details if they are too long (#1334) (b51157d)
• speed up compressing responses #717 (1624580)
• write empty string to CSV/TSV for null values #708 (c8872ba)

[fengelniederhammer]

@dependabot rebase

[dependabot]

Looks like mdast-util-to-hast is up-to-date now, so this is no longer needed.