From 7305e436644b05b7770efe5274e58fe64855920d Mon Sep 17 00:00:00 2001 From: Mariia Zueva Date: Fri, 24 Jul 2026 16:46:41 +0200 Subject: [PATCH 1/3] Adapt embedding to DMS data (peptide mode only), SDK update --- .changeset/embed-amplicon-sequence.md | 6 + .github/workflows/build.yaml | 3 +- .structure | 2 +- model/src/scopes.ts | 24 +- package.json | 14 +- pnpm-lock.yaml | 517 ++++++++++++-------------- pnpm-workspace.yaml | 19 +- software/package.json | 7 +- test/.oxfmtrc.json | 2 +- turbo.json | 20 +- 10 files changed, 311 insertions(+), 303 deletions(-) create mode 100644 .changeset/embed-amplicon-sequence.md diff --git a/.changeset/embed-amplicon-sequence.md b/.changeset/embed-amplicon-sequence.md new file mode 100644 index 0000000..ce8b89b --- /dev/null +++ b/.changeset/embed-amplicon-sequence.md @@ -0,0 +1,6 @@ +--- +'@platforma-open/milaboratories.sequence-embeddings.model': minor +'@platforma-open/milaboratories.sequence-embeddings': minor +--- + +Recognize synthetic-repertoire-profiler variant sequences: the peptide-family sequence selector now also matches `pl7.app/sequence` columns with the `amplicon-sequence` feature (in addition to `peptide`), so profiler outputs become embeddable via the peptide scope. diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index e82ec20..4d25b25 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -26,7 +26,8 @@ jobs: app-name-slug: 'block-sequence-embeddings' node-version: '20.x' gha-runner-label: hz-ubuntu-dind - build-script-name: 'build' + build-script-name: 'build:dev-local' + build-before-publish-script-name: 'build:release' pnpm-recursive-build: false test: true diff --git a/.structure b/.structure index 491d734..218abba 100644 --- a/.structure +++ b/.structure @@ -1 +1 @@ -{"version":1} \ No newline at end of file +{"version":2} \ No newline at end of file diff --git a/model/src/scopes.ts b/model/src/scopes.ts index 14a8671..c3a1b2b 100644 --- a/model/src/scopes.ts +++ b/model/src/scopes.ts @@ -34,8 +34,12 @@ export type SeqEntry = { id: SUniversalPColumnId; spec: PColumnSpec; label: stri /** * Selectors for candidate sequence columns under the `main` anchor's key axis. - * Peptide inputs match only the first; antibody/TCR inputs match the VDJ ones. - * Filtered on amino-acid alphabet — embeddings read AA sequence. + * Peptide-family inputs match the first two (`pl7.app/sequence` with a `peptide` + * or `amplicon-sequence` feature — the latter is the synthetic-repertoire-profiler's + * whole-variant sequence); antibody/TCR inputs match the VDJ ones. A selector's + * domain is a single fixed map and can't OR two feature values, so the two + * peptide-family features need two entries. All filtered on amino-acid alphabet — + * embeddings read AA sequence. */ export const SEQUENCE_SELECTORS: AnchoredPColumnSelector[] = [ { @@ -43,6 +47,14 @@ export const SEQUENCE_SELECTORS: AnchoredPColumnSelector[] = [ name: "pl7.app/sequence", domain: { "pl7.app/feature": "peptide", "pl7.app/alphabet": "aminoacid" }, }, + { + axes: [{ anchor: "main", idx: 1 }], + name: "pl7.app/sequence", + // synthetic-repertoire-profiler tags its whole-variant AA sequence with the + // generic `amplicon-sequence` feature (shared with other consumers), not + // `peptide`; treat it as a peptide-family scope so it becomes embeddable. + domain: { "pl7.app/feature": "amplicon-sequence", "pl7.app/alphabet": "aminoacid" }, + }, { axes: [{ anchor: "main", idx: 1 }], name: "pl7.app/vdj/sequence", @@ -123,7 +135,13 @@ export function buildScopeConfig( const d = e.spec.domain ?? {}; const assembling = isAssembling(e.spec); - if (name === "pl7.app/sequence" && d["pl7.app/feature"] === "peptide") { + // `peptide` (peptide-profiling) and `amplicon-sequence` + // (synthetic-repertoire-profiler whole-variant sequence) both map to the + // peptide scope feature — a single AA protein sequence embedded as-is. + if ( + name === "pl7.app/sequence" && + (d["pl7.app/feature"] === "peptide" || d["pl7.app/feature"] === "amplicon-sequence") + ) { scopes.push({ id: e.id, feature: "peptide", diff --git a/package.json b/package.json index 3004571..d605189 100644 --- a/package.json +++ b/package.json @@ -6,18 +6,20 @@ "scripts": { "fmt": "turbo run fmt", "check": "turbo run check", - "build": "turbo run build", - "build:dev": "env PL_PKG_DEV=local turbo run build", - "build:dev-remote": "env PL_PKG_DEV=local PL_DOCKER_BUILD=1 PL_DOCKER_AUTOPUSH=1 turbo run build", - "test": "env PL_PKG_DEV=local turbo run test --concurrency 1", - "test:dry-run": "env PL_PKG_DEV=local turbo run test --dry-run=json", + "build:dev-remote": "env PL_BUILD_CHANNEL=dev PL_BUILD_VARIANT=all PL_BUILD_LOCATION=remote turbo run build", + "test": "env PL_BUILD_CHANNEL=dev PL_BUILD_VARIANT=binary PL_BUILD_LOCATION=local turbo run test --concurrency 1", + "test:dry-run": "env PL_BUILD_CHANNEL=dev PL_BUILD_VARIANT=binary PL_BUILD_LOCATION=local turbo run test --dry-run=json", "mark-stable": "turbo run mark-stable", "watch": "turbo watch build", "changeset": "changeset", "version-packages": "changeset version", "update-sdk": "block-tools structure refresh --update-deps-only", "do-pack": "turbo run do-pack", - "upgrade-sdk": "block-tools structure refresh --update-deps-only && pnpm i && block-tools structure refresh && pnpm i && pnpm fmt" + "upgrade-sdk": "block-tools structure refresh --update-deps-only && pnpm i && block-tools structure refresh && pnpm i && pnpm fmt", + "build:dev-local": "env PL_BUILD_CHANNEL=dev PL_BUILD_VARIANT=all PL_BUILD_LOCATION=local turbo run build", + "build:dev-no-software": "env PL_BUILD_CHANNEL=dev PL_BUILD_VARIANT=none turbo run build", + "build:dev-binary-existing": "env PL_BUILD_CHANNEL=dev PL_BUILD_USE_PUBLISHED=true turbo run build", + "build:release": "env PL_BUILD_CHANNEL=release PL_BUILD_VARIANT=all PL_BUILD_LOCATION=remote turbo run build" }, "devDependencies": { "@changesets/cli": "catalog:", diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index c6c7d42..c096faa 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -10,11 +10,11 @@ catalogs: specifier: 2.29.8 version: 2.29.8 '@milaboratories/ts-builder': - specifier: 1.6.0 - version: 1.6.0 + specifier: 1.6.1 + version: 1.6.1 '@milaboratories/ts-configs': - specifier: 1.3.0 - version: 1.3.0 + specifier: 1.3.1 + version: 1.3.1 '@platforma-open/milaboratories.protein-embeddings-assets': specifier: 1.2.0 version: 1.2.0 @@ -22,26 +22,23 @@ catalogs: specifier: 1.10.7 version: 1.10.7 '@platforma-sdk/block-tools': - specifier: 2.12.7 - version: 2.12.7 + specifier: 2.12.9 + version: 2.12.9 '@platforma-sdk/model': - specifier: 1.80.2 - version: 1.80.2 - '@platforma-sdk/package-builder': - specifier: 3.14.1 - version: 3.14.1 + specifier: 1.80.10 + version: 1.80.10 '@platforma-sdk/tengo-builder': - specifier: 4.0.18 - version: 4.0.18 + specifier: 4.0.20 + version: 4.0.20 '@platforma-sdk/test': - specifier: 1.80.5 - version: 1.80.5 + specifier: 1.80.11 + version: 1.80.11 '@platforma-sdk/ui-vue': - specifier: 1.80.4 - version: 1.80.4 + specifier: 1.80.10 + version: 1.80.10 '@platforma-sdk/workflow-tengo': - specifier: 6.8.0 - version: 6.8.0 + specifier: 6.8.2 + version: 6.8.2 ag-grid-enterprise: specifier: ~34.1.2 version: 34.1.2 @@ -80,10 +77,10 @@ importers: version: 2.29.8(@types/node@25.9.1) '@milaboratories/ts-builder': specifier: 'catalog:' - version: 1.6.0(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@6.0.3))(yaml@2.9.0) + version: 1.6.1(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@6.0.3))(yaml@2.9.0) '@platforma-sdk/block-tools': specifier: 'catalog:' - version: 2.12.7(@types/node@25.9.1) + version: 2.12.9(@types/node@25.9.1) shx: specifier: 'catalog:' version: 0.4.0 @@ -95,10 +92,10 @@ importers: devDependencies: '@milaboratories/ts-builder': specifier: 'catalog:' - version: 1.6.0(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@5.9.3))(yaml@2.9.0) + version: 1.6.1(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@5.9.3))(yaml@2.9.0) '@milaboratories/ts-configs': specifier: 'catalog:' - version: 1.3.0 + version: 1.3.1 '@platforma-open/milaboratories.sequence-embeddings.model': specifier: workspace:* version: link:../model @@ -110,10 +107,10 @@ importers: version: link:../workflow '@platforma-sdk/block-tools': specifier: 'catalog:' - 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'@milaboratories/pframes-rs-wasip2': 1.1.55 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/pl-model-middle-layer': 1.30.13 + '@milaboratories/pframes-rs-wasip2': 1.1.56 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/pl-model-middle-layer': 1.30.15 - '@milaboratories/pl-client@3.14.2': + '@milaboratories/pl-client@3.14.4': dependencies: '@grpc/grpc-js': 1.13.5 '@milaboratories/pl-http': 1.2.4 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/ts-helpers': 1.8.6 '@protobuf-ts/grpc-transport': 2.11.1(@grpc/grpc-js@1.13.5) '@protobuf-ts/runtime': 2.11.1 '@protobuf-ts/runtime-rpc': 2.11.1 @@ -6204,19 +6194,19 @@ snapshots: utility-types: 3.11.0 yaml: 2.9.0 - '@milaboratories/pl-config@1.8.4': + '@milaboratories/pl-config@1.8.5': dependencies: - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/ts-helpers': 1.8.6 upath: 2.0.1 yaml: 2.9.0 - '@milaboratories/pl-deployments@3.0.12': + '@milaboratories/pl-deployments@3.0.14': dependencies: - '@milaboratories/pl-config': 1.8.4 - '@milaboratories/pl-healthcheck': 1.0.3 + '@milaboratories/pl-config': 1.8.5 + '@milaboratories/pl-healthcheck': 1.0.4 '@milaboratories/pl-http': 1.2.4 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/ts-helpers': 1.8.6 decompress: 4.2.1 ssh2: 1.17.0 tar: 7.5.16 @@ -6225,15 +6215,15 @@ snapshots: yaml: 2.9.0 zod: 3.25.76 - '@milaboratories/pl-drivers@1.16.10': + '@milaboratories/pl-drivers@1.16.12': dependencies: '@grpc/grpc-js': 1.13.5 - '@milaboratories/computable': 2.9.7 - '@milaboratories/helpers': 1.14.4 - '@milaboratories/pl-client': 3.14.2 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/pl-tree': 1.13.1 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/computable': 2.9.8 + '@milaboratories/helpers': 1.14.5 + '@milaboratories/pl-client': 3.14.4 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/pl-tree': 1.13.3 + '@milaboratories/ts-helpers': 1.8.6 '@protobuf-ts/grpc-transport': 2.11.1(@grpc/grpc-js@1.13.5) '@protobuf-ts/plugin': 2.11.1 '@protobuf-ts/runtime': 2.11.1 @@ -6256,16 +6246,16 @@ snapshots: json-stringify-safe: 5.0.1 zod: 3.25.76 - '@milaboratories/pl-errors@1.4.31': + '@milaboratories/pl-errors@1.4.33': dependencies: - '@milaboratories/pl-client': 3.14.2 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/pl-client': 3.14.4 + '@milaboratories/ts-helpers': 1.8.6 zod: 3.25.76 - '@milaboratories/pl-healthcheck@1.0.3': + '@milaboratories/pl-healthcheck@1.0.4': dependencies: '@grpc/grpc-js': 1.13.5 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/ts-helpers': 1.8.6 '@protobuf-ts/grpc-transport': 2.11.1(@grpc/grpc-js@1.13.5) '@protobuf-ts/runtime': 2.11.1 '@protobuf-ts/runtime-rpc': 2.11.1 @@ -6274,29 +6264,29 @@ snapshots: dependencies: undici: 7.16.0 - '@milaboratories/pl-middle-layer@1.66.4(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1)': - dependencies: - '@milaboratories/columns-collection-driver': 0.2.1 - '@milaboratories/computable': 2.9.7 - '@milaboratories/helpers': 1.14.4 - '@milaboratories/pf-driver': 1.8.2(@bytecodealliance/preview2-shim@0.17.9) - '@milaboratories/pf-spec-driver': 1.4.21(@bytecodealliance/preview2-shim@0.17.9) - '@milaboratories/pframes-rs-node': 1.1.55 - '@milaboratories/pframes-rs-wasm': 1.1.55(@bytecodealliance/preview2-shim@0.17.9)(@milaboratories/pl-model-common@1.47.1)(@milaboratories/pl-model-middle-layer@1.30.13) - '@milaboratories/pl-client': 3.14.2 - '@milaboratories/pl-deployments': 3.0.12 - '@milaboratories/pl-drivers': 1.16.10 - '@milaboratories/pl-errors': 1.4.31 + '@milaboratories/pl-middle-layer@1.66.10(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1)': + dependencies: + '@milaboratories/columns-collection-driver': 0.2.3 + '@milaboratories/computable': 2.9.8 + '@milaboratories/helpers': 1.14.5 + '@milaboratories/pf-driver': 1.8.5(@bytecodealliance/preview2-shim@0.17.9) + '@milaboratories/pf-spec-driver': 1.4.24(@bytecodealliance/preview2-shim@0.17.9) + '@milaboratories/pframes-rs-node': 1.1.56 + '@milaboratories/pframes-rs-wasm': 1.1.56(@bytecodealliance/preview2-shim@0.17.9)(@milaboratories/pl-model-common@1.47.3)(@milaboratories/pl-model-middle-layer@1.30.15) + '@milaboratories/pl-client': 3.14.4 + '@milaboratories/pl-deployments': 3.0.14 + '@milaboratories/pl-drivers': 1.16.12 + '@milaboratories/pl-errors': 1.4.33 '@milaboratories/pl-http': 1.2.4 - '@milaboratories/pl-model-backend': 1.4.16 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/pl-model-middle-layer': 1.30.13 - '@milaboratories/pl-tree': 1.13.1 + '@milaboratories/pl-model-backend': 1.4.18 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/pl-model-middle-layer': 1.30.15 + '@milaboratories/pl-tree': 1.13.3 '@milaboratories/resolve-helper': 1.1.3 - '@milaboratories/ts-helpers': 1.8.5 - '@platforma-sdk/block-tools': 2.12.7(@types/node@25.9.1) - '@platforma-sdk/model': 1.80.2 - '@platforma-sdk/workflow-tengo': 6.7.2 + '@milaboratories/ts-helpers': 1.8.6 + '@platforma-sdk/block-tools': 2.12.9(@types/node@25.9.1) + '@platforma-sdk/model': 1.80.10 + '@platforma-sdk/workflow-tengo': 6.8.2 canonicalize: 2.1.0 denque: 2.1.0 es-toolkit: 1.47.0 @@ -6317,9 +6307,9 @@ snapshots: - react-native-b4a - supports-color - '@milaboratories/pl-model-backend@1.4.16': + '@milaboratories/pl-model-backend@1.4.18': dependencies: - '@milaboratories/pl-client': 3.14.2 + '@milaboratories/pl-client': 3.14.4 canonicalize: 2.1.0 zod: 3.25.76 @@ -6330,18 +6320,18 @@ snapshots: canonicalize: 2.1.0 zod: 3.25.76 - '@milaboratories/pl-model-common@1.47.1': + '@milaboratories/pl-model-common@1.47.3': dependencies: - '@milaboratories/helpers': 1.14.4 + '@milaboratories/helpers': 1.14.5 '@milaboratories/pl-error-like': 1.12.10 canonicalize: 2.1.0 es-toolkit: 1.47.0 zod: 3.25.76 - '@milaboratories/pl-model-middle-layer@1.30.13': + '@milaboratories/pl-model-middle-layer@1.30.15': dependencies: - '@milaboratories/helpers': 1.14.4 - '@milaboratories/pl-model-common': 1.47.1 + '@milaboratories/helpers': 1.14.5 + '@milaboratories/pl-model-common': 1.47.3 es-toolkit: 1.47.0 utility-types: 3.11.0 zod: 3.25.76 @@ -6354,19 +6344,19 @@ snapshots: utility-types: 3.11.0 zod: 3.25.76 - '@milaboratories/pl-tree@1.13.1': + '@milaboratories/pl-tree@1.13.3': dependencies: - '@milaboratories/computable': 2.9.7 - '@milaboratories/pl-client': 3.14.2 - '@milaboratories/pl-errors': 1.4.31 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/computable': 2.9.8 + '@milaboratories/pl-client': 3.14.4 + '@milaboratories/pl-errors': 1.4.33 + '@milaboratories/ts-helpers': 1.8.6 denque: 2.1.0 utility-types: 3.11.0 zod: 3.25.76 - '@milaboratories/ptabler-expression-js@1.2.35': + '@milaboratories/ptabler-expression-js@1.2.37': dependencies: - '@platforma-open/milaboratories.software-ptabler.schema': 1.15.19 + '@platforma-open/milaboratories.software-ptabler.schema': 1.15.21 '@milaboratories/resolve-helper@1.1.3': {} @@ -6374,9 +6364,9 @@ snapshots: '@milaboratories/tengo-tester@1.6.4': {} - '@milaboratories/ts-builder@1.6.0(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.24(typescript@6.0.3))(yaml@2.9.0)': + '@milaboratories/ts-builder@1.6.1(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.24(typescript@6.0.3))(yaml@2.9.0)': dependencies: - '@milaboratories/ts-configs': 1.3.0 + '@milaboratories/ts-configs': 1.3.1 '@vitejs/plugin-vue': 6.0.7(vite@8.0.16(@types/node@25.9.1)(esbuild@0.27.7)(yaml@2.9.0))(vue@3.5.24(typescript@6.0.3)) commander: 15.0.0 jsonc-parser: 3.3.1 @@ -6415,9 +6405,9 @@ snapshots: - vue - yaml - '@milaboratories/ts-builder@1.6.0(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@5.9.3))(yaml@2.9.0)': + '@milaboratories/ts-builder@1.6.1(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@5.9.3))(yaml@2.9.0)': dependencies: - '@milaboratories/ts-configs': 1.3.0 + '@milaboratories/ts-configs': 1.3.1 '@vitejs/plugin-vue': 6.0.7(vite@8.0.16(@types/node@25.9.1)(esbuild@0.27.7)(yaml@2.9.0))(vue@3.5.35(typescript@5.9.3)) commander: 15.0.0 jsonc-parser: 3.3.1 @@ -6456,9 +6446,9 @@ snapshots: - vue - yaml - '@milaboratories/ts-builder@1.6.0(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@6.0.3))(yaml@2.9.0)': + '@milaboratories/ts-builder@1.6.1(@types/node@25.9.1)(esbuild@0.27.7)(rollup@4.61.0)(vue@3.5.35(typescript@6.0.3))(yaml@2.9.0)': dependencies: - '@milaboratories/ts-configs': 1.3.0 + '@milaboratories/ts-configs': 1.3.1 '@vitejs/plugin-vue': 6.0.7(vite@8.0.16(@types/node@25.9.1)(esbuild@0.27.7)(yaml@2.9.0))(vue@3.5.35(typescript@6.0.3)) commander: 15.0.0 jsonc-parser: 3.3.1 @@ -6497,18 +6487,18 @@ snapshots: - vue - yaml - '@milaboratories/ts-configs@1.3.0': {} + '@milaboratories/ts-configs@1.3.1': {} - '@milaboratories/ts-helpers@1.8.5': + '@milaboratories/ts-helpers@1.8.6': dependencies: - '@milaboratories/helpers': 1.14.4 + '@milaboratories/helpers': 1.14.5 canonicalize: 2.1.0 denque: 2.1.0 - '@milaboratories/uikit@2.15.16(@vue/compiler-dom@3.5.35)(@vue/server-renderer@3.5.35(vue@3.5.24(typescript@6.0.3)))(typescript@6.0.3)': + '@milaboratories/uikit@2.15.18(@vue/compiler-dom@3.5.35)(@vue/server-renderer@3.5.35(vue@3.5.24(typescript@6.0.3)))(typescript@6.0.3)': dependencies: - '@milaboratories/helpers': 1.14.4 - '@platforma-sdk/model': 1.80.2 + '@milaboratories/helpers': 1.14.5 + '@platforma-sdk/model': 1.80.10 '@types/d3-array': 3.2.2 '@types/d3-axis': 3.0.6 '@types/d3-scale': 4.0.9 @@ -6962,13 +6952,13 @@ snapshots: '@platforma-open/milaboratories.runenv-python-3.12.10-scientific-slim': 1.1.0 '@platforma-open/milaboratories.runenv-python-3.12.10-torch-cuda': 0.2.0 - '@platforma-open/milaboratories.software-ptabler.schema@1.15.19': + '@platforma-open/milaboratories.software-ptabler.schema@1.15.21': dependencies: - '@milaboratories/pl-model-common': 1.47.1 + '@milaboratories/pl-model-common': 1.47.3 - '@platforma-open/milaboratories.software-ptabler@2.1.6': {} + '@platforma-open/milaboratories.software-ptabler@2.1.8': {} - '@platforma-open/milaboratories.software-ptexter@1.2.3': {} + '@platforma-open/milaboratories.software-ptexter@1.2.4': {} '@platforma-open/milaboratories.software-small-binaries.hello-world-py@1.0.10': {} @@ -6988,19 +6978,19 @@ snapshots: '@platforma-open/milaboratories.software-small-binaries.mnz-client': 1.6.5 '@platforma-open/milaboratories.software-small-binaries.table-converter': 1.3.5 - '@platforma-sdk/block-tools@2.12.7(@types/node@25.9.1)': + '@platforma-sdk/block-tools@2.12.9(@types/node@25.9.1)': dependencies: '@aws-sdk/client-ecr-public': 3.859.0 '@aws-sdk/client-s3': 3.859.0 '@inquirer/prompts': 7.10.1(@types/node@25.9.1) '@milaboratories/pl-http': 1.2.4 - '@milaboratories/pl-model-backend': 1.4.16 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/pl-model-middle-layer': 1.30.13 + '@milaboratories/pl-model-backend': 1.4.18 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/pl-model-middle-layer': 1.30.15 '@milaboratories/resolve-helper': 1.1.3 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/ts-helpers': 1.8.6 '@platforma-sdk/blocks-deps-updater': 2.2.0 - '@platforma-sdk/package-builder-lib': 1.2.0 + '@platforma-sdk/package-builder-lib': 1.2.1 canonicalize: 2.1.0 commander: 15.0.0 lru-cache: 11.5.1 @@ -7020,13 +7010,13 @@ snapshots: dependencies: yaml: 2.9.0 - '@platforma-sdk/model@1.80.2': + '@platforma-sdk/model@1.80.10': dependencies: - '@milaboratories/helpers': 1.14.4 + '@milaboratories/helpers': 1.14.5 '@milaboratories/pl-error-like': 1.12.10 - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/pl-model-middle-layer': 1.30.13 - '@milaboratories/ptabler-expression-js': 1.2.35 + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/pl-model-middle-layer': 1.30.15 + '@milaboratories/ptabler-expression-js': 1.2.37 canonicalize: 2.1.0 es-toolkit: 1.47.0 fast-json-patch: 3.1.1 @@ -7034,7 +7024,7 @@ snapshots: utility-types: 3.11.0 zod: 3.25.76 - '@platforma-sdk/package-builder-lib@1.2.0': + '@platforma-sdk/package-builder-lib@1.2.1': dependencies: '@aws-sdk/client-s3': 3.859.0 '@aws-sdk/lib-storage': 3.859.0(@aws-sdk/client-s3@3.859.0) @@ -7050,33 +7040,22 @@ snapshots: - bare-buffer - react-native-b4a - '@platforma-sdk/package-builder@3.14.1': - dependencies: - '@platforma-sdk/package-builder-lib': 1.2.0 - commander: 15.0.0 - winston: 3.19.0 - transitivePeerDependencies: - - aws-crt - - bare-abort-controller - - bare-buffer - - react-native-b4a - - '@platforma-sdk/tengo-builder@4.0.18': + '@platforma-sdk/tengo-builder@4.0.20': dependencies: - '@milaboratories/pl-model-backend': 1.4.16 + '@milaboratories/pl-model-backend': 1.4.18 '@milaboratories/resolve-helper': 1.1.3 '@milaboratories/tengo-tester': 1.6.4 - '@milaboratories/ts-helpers': 1.8.5 + '@milaboratories/ts-helpers': 1.8.6 commander: 15.0.0 winston: 3.19.0 - '@platforma-sdk/test@1.80.5(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1)(vite@7.3.5(@types/node@25.9.1)(lightningcss@1.32.0)(yaml@2.9.0))': + '@platforma-sdk/test@1.80.11(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1)(vite@7.3.5(@types/node@25.9.1)(lightningcss@1.32.0)(yaml@2.9.0))': dependencies: - '@milaboratories/computable': 2.9.7 - '@milaboratories/pl-client': 3.14.2 - '@milaboratories/pl-middle-layer': 1.66.4(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1) - '@milaboratories/pl-tree': 1.13.1 - '@platforma-sdk/model': 1.80.2 + '@milaboratories/computable': 2.9.8 + '@milaboratories/pl-client': 3.14.4 + '@milaboratories/pl-middle-layer': 1.66.10(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1) + '@milaboratories/pl-tree': 1.13.3 + '@platforma-sdk/model': 1.80.10 '@vitest/coverage-istanbul': 4.1.8(vitest@4.0.18(@types/node@25.9.1)(lightningcss@1.32.0)(yaml@2.9.0)) vitest: 4.1.8(@types/node@25.9.1)(@vitest/coverage-istanbul@4.1.8)(vite@7.3.5(@types/node@25.9.1)(lightningcss@1.32.0)(yaml@2.9.0)) transitivePeerDependencies: @@ -7100,13 +7079,13 @@ snapshots: - supports-color - vite - '@platforma-sdk/test@1.80.5(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1)(vite@8.0.16(@types/node@25.9.1)(esbuild@0.27.7)(yaml@2.9.0))': + '@platforma-sdk/test@1.80.11(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1)(vite@8.0.16(@types/node@25.9.1)(esbuild@0.27.7)(yaml@2.9.0))': dependencies: - '@milaboratories/computable': 2.9.7 - '@milaboratories/pl-client': 3.14.2 - '@milaboratories/pl-middle-layer': 1.66.4(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1) - '@milaboratories/pl-tree': 1.13.1 - '@platforma-sdk/model': 1.80.2 + '@milaboratories/computable': 2.9.8 + '@milaboratories/pl-client': 3.14.4 + '@milaboratories/pl-middle-layer': 1.66.10(@bytecodealliance/preview2-shim@0.17.9)(@types/node@25.9.1) + '@milaboratories/pl-tree': 1.13.3 + '@platforma-sdk/model': 1.80.10 '@vitest/coverage-istanbul': 4.1.8(vitest@4.1.8) vitest: 4.1.8(@types/node@25.9.1)(@vitest/coverage-istanbul@4.1.8)(vite@8.0.16(@types/node@25.9.1)(esbuild@0.27.7)(yaml@2.9.0)) transitivePeerDependencies: @@ -7130,13 +7109,13 @@ snapshots: - supports-color - vite - '@platforma-sdk/ui-vue@1.80.4(@bytecodealliance/preview2-shim@0.17.9)(@vue/compiler-dom@3.5.35)(@vue/server-renderer@3.5.35(vue@3.5.24(typescript@6.0.3)))(typescript@6.0.3)': + '@platforma-sdk/ui-vue@1.80.10(@bytecodealliance/preview2-shim@0.17.9)(@vue/compiler-dom@3.5.35)(@vue/server-renderer@3.5.35(vue@3.5.24(typescript@6.0.3)))(typescript@6.0.3)': dependencies: - '@milaboratories/columns-collection-driver': 0.2.1 - '@milaboratories/pf-spec-driver': 1.4.21(@bytecodealliance/preview2-shim@0.17.9) - '@milaboratories/pl-model-common': 1.47.1 - '@milaboratories/uikit': 2.15.16(@vue/compiler-dom@3.5.35)(@vue/server-renderer@3.5.35(vue@3.5.24(typescript@6.0.3)))(typescript@6.0.3) - '@platforma-sdk/model': 1.80.2 + '@milaboratories/columns-collection-driver': 0.2.3 + '@milaboratories/pf-spec-driver': 1.4.24(@bytecodealliance/preview2-shim@0.17.9) + '@milaboratories/pl-model-common': 1.47.3 + '@milaboratories/uikit': 2.15.18(@vue/compiler-dom@3.5.35)(@vue/server-renderer@3.5.35(vue@3.5.24(typescript@6.0.3)))(typescript@6.0.3) + '@platforma-sdk/model': 1.80.10 '@types/d3-format': 3.0.4 '@types/node': 24.5.2 '@types/semver': 7.7.1 @@ -7169,20 +7148,12 @@ snapshots: - typescript - universal-cookie - '@platforma-sdk/workflow-tengo@6.7.2': - dependencies: - '@milaboratories/pframes-rs-wasip2': 1.1.55 - '@milaboratories/software-pframes-conv': 2.2.9 - '@platforma-open/milaboratories.software-ptabler': 2.1.6 - '@platforma-open/milaboratories.software-ptexter': 1.2.3 - '@platforma-open/milaboratories.software-small-binaries': 2.1.1 - - '@platforma-sdk/workflow-tengo@6.8.0': + '@platforma-sdk/workflow-tengo@6.8.2': dependencies: - '@milaboratories/pframes-rs-wasip2': 1.1.55 + '@milaboratories/pframes-rs-wasip2': 1.1.56 '@milaboratories/software-pframes-conv': 2.2.9 - '@platforma-open/milaboratories.software-ptabler': 2.1.6 - '@platforma-open/milaboratories.software-ptexter': 1.2.3 + '@platforma-open/milaboratories.software-ptabler': 2.1.8 + '@platforma-open/milaboratories.software-ptexter': 1.2.4 '@platforma-open/milaboratories.software-small-binaries': 2.1.1 '@protobuf-ts/grpc-transport@2.11.1(@grpc/grpc-js@1.13.5)': diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml index 08f3c3d..0a1018a 100644 --- a/pnpm-workspace.yaml +++ b/pnpm-workspace.yaml @@ -7,16 +7,16 @@ packages: - workflow catalog: - "@milaboratories/ts-builder": 1.6.0 - "@milaboratories/ts-configs": 1.3.0 + "@milaboratories/ts-builder": 1.6.1 + "@milaboratories/ts-configs": 1.3.1 "typescript": ~5.9.3 - "@platforma-sdk/workflow-tengo": 6.8.0 - "@platforma-sdk/block-tools": 2.12.7 - "@platforma-sdk/model": 1.80.2 - "@platforma-sdk/ui-vue": 1.80.4 - "@platforma-sdk/test": 1.80.5 - "@platforma-sdk/tengo-builder": 4.0.18 - "@platforma-sdk/package-builder": 3.14.1 + "@platforma-sdk/workflow-tengo": 6.8.2 + "@platforma-sdk/block-tools": 2.12.9 + "@platforma-sdk/model": 1.80.10 + "@platforma-sdk/ui-vue": 1.80.10 + "@platforma-sdk/test": 1.80.11 + "@platforma-sdk/tengo-builder": 4.0.20 + "@platforma-sdk/package-builder": 3.14.2 "@platforma-sdk/blocks-deps-updater": 2.2.0 "vue": 3.5.24 @@ -32,3 +32,4 @@ catalog: "shx": 0.4.0 "@changesets/cli": 2.29.8 vitest: ~4.0.18 + "@milaboratories/helpers": 1.14.5 diff --git a/software/package.json b/software/package.json index fb5ace3..c1e2b69 100644 --- a/software/package.json +++ b/software/package.json @@ -7,15 +7,14 @@ ], "type": "module", "scripts": { - "do-pack": "shx rm -f *.tgz && pl-pkg build && pnpm pack && shx mv platforma-open*.tgz package.tgz", + "do-pack": "shx rm -f *.tgz && block-tools software build && pnpm pack && shx mv platforma-open*.tgz package.tgz", "changeset": "changeset", "version-packages": "changeset version", - "build": "pl-pkg build", - "prepublishOnly": "pl-pkg prepublish" + "build": "block-tools software build" }, "devDependencies": { "@platforma-open/milaboratories.runenv-python-3": "catalog:", - "@platforma-sdk/package-builder": "catalog:" + "@platforma-sdk/block-tools": "catalog:" }, "block-software": { "artifacts": { diff --git a/test/.oxfmtrc.json b/test/.oxfmtrc.json index 7eff5e7..6f74854 100644 --- a/test/.oxfmtrc.json +++ b/test/.oxfmtrc.json @@ -1,4 +1,4 @@ { "extends": ["node_modules/@milaboratories/ts-builder/configs/oxfmt.json"], - "ignorePatterns": ["dist", "coverage", "CHANGELOG.md"] + "ignorePatterns": ["dist", "coverage", "CHANGELOG.md", ".test_auth.json"] } diff --git a/turbo.json b/turbo.json index 47032ac..d079cd3 100644 --- a/turbo.json +++ b/turbo.json @@ -12,13 +12,23 @@ "build": { "dependsOn": ["^build", "check"], "inputs": ["$TURBO_DEFAULT$"], - "env": ["PL_PKG_DEV", "PL_PKG_FULL_HASH", "PL_DOCKER_REGISTRY", "PL_DOCKER_BUILD", "PL_DOCKER_NO_BUILD", "PL_DOCKER_AUTOPUSH", "PL_DOCKER_NO_AUTOPUSH", "PL_DOCKER_REGISTRY_PUSH_TO"], + "env": [ + "PL_DOCKER_REGISTRY_PUSH_TO", + "PL_BUILD_CHANNEL", + "PL_BUILD_VARIANT", + "PL_BUILD_LOCATION", + "PL_BUILD_USE_PUBLISHED", + "PL_DEV_DOCKER_PUSH_URL", + "PL_DEV_DOCKER_PULL_URL", + "PL_DEV_BINARY_UPLOAD_URL", + "PL_RELEASE_DOCKER_PUSH_URL", + "PL_RELEASE_DOCKER_PULL_URL", + "PL_RELEASE_BINARY_UPLOAD_URL", + "PL_REGISTRY_PLATFORMA_OPEN_UPLOAD_URL" + ], + "passThroughEnv": ["AWS_*", "PL_AWS_*"], "outputs": ["./dist/**", "./block-pack/**", "./pkg-*.tgz"] }, - "build:dev": { - "dependsOn": ["build"], - "outputs": ["./dist/**"] - }, "do-pack": { "dependsOn": ["build"], "outputs": ["package.tgz"] From 511b0a5fa13ddc076246bfdd0c6ab3468acf8579 Mon Sep 17 00:00:00 2001 From: Mariia Zueva Date: Fri, 24 Jul 2026 16:48:26 +0200 Subject: [PATCH 2/3] Adapt embedding to DMS data (peptide mode only), SDK update --- .changeset/embed-amplicon-sequence.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.changeset/embed-amplicon-sequence.md b/.changeset/embed-amplicon-sequence.md index ce8b89b..d434025 100644 --- a/.changeset/embed-amplicon-sequence.md +++ b/.changeset/embed-amplicon-sequence.md @@ -1,6 +1,8 @@ --- -'@platforma-open/milaboratories.sequence-embeddings.model': minor -'@platforma-open/milaboratories.sequence-embeddings': minor +'@platforma-open/milaboratories.sequence-embeddings.model': patch +'@platforma-open/milaboratories.sequence-embeddings.workflow': patch +'@platforma-open/milaboratories.sequence-embeddings.ui': patch +'@platforma-open/milaboratories.sequence-embeddings': patch --- Recognize synthetic-repertoire-profiler variant sequences: the peptide-family sequence selector now also matches `pl7.app/sequence` columns with the `amplicon-sequence` feature (in addition to `peptide`), so profiler outputs become embeddable via the peptide scope. From ce4ded8b7670dd26f4538e2c5b9dd447e785ed67 Mon Sep 17 00:00:00 2001 From: Mariia Zueva Date: Fri, 24 Jul 2026 18:31:05 +0200 Subject: [PATCH 3/3] Fix changeset --- .changeset/embed-amplicon-sequence.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.changeset/embed-amplicon-sequence.md b/.changeset/embed-amplicon-sequence.md index d434025..bc4ac6e 100644 --- a/.changeset/embed-amplicon-sequence.md +++ b/.changeset/embed-amplicon-sequence.md @@ -2,6 +2,7 @@ '@platforma-open/milaboratories.sequence-embeddings.model': patch '@platforma-open/milaboratories.sequence-embeddings.workflow': patch '@platforma-open/milaboratories.sequence-embeddings.ui': patch +'@platforma-open/milaboratories.sequence-embeddings.software': patch '@platforma-open/milaboratories.sequence-embeddings': patch ---