diff --git a/.changeset/bump-package-builder.md b/.changeset/bump-package-builder.md new file mode 100644 index 0000000..4c7d80b --- /dev/null +++ b/.changeset/bump-package-builder.md @@ -0,0 +1,5 @@ +--- +'@platforma-open/milaboratories.samples-and-data': patch +--- + +Bump package-builder to 3.11.4 diff --git a/.changeset/dash-dependency.md b/.changeset/dash-dependency.md new file mode 100644 index 0000000..44c5e38 --- /dev/null +++ b/.changeset/dash-dependency.md @@ -0,0 +1,5 @@ +--- +'@platforma-open/milaboratories.samples-and-data': patch +--- + +Adds dash system dependency diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 6a2a1e4..f47af58 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -7,16 +7,16 @@ settings: catalogs: default: '@changesets/cli': - specifier: ^2.29.7 + specifier: ~2.29.7 version: 2.29.7 '@milaboratories/helpers': specifier: 1.13.0 version: 1.13.0 '@platforma-open/milaboratories.runenv-python-3': - specifier: ^1.7.5 + specifier: ~1.7.5 version: 1.7.5 '@platforma-open/milaboratories.runenv-r-samples-and-data': - 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Please update. 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supports-color - '@babel/generator@7.28.5': + '@babel/generator@7.29.1': dependencies: - '@babel/parser': 7.28.5 - '@babel/types': 7.28.5 + '@babel/parser': 7.29.0 + '@babel/types': 7.29.0 '@jridgewell/gen-mapping': 0.3.13 '@jridgewell/trace-mapping': 0.3.31 jsesc: 3.1.0 - '@babel/helper-compilation-targets@7.27.2': + '@babel/helper-compilation-targets@7.28.6': dependencies: - '@babel/compat-data': 7.28.5 + '@babel/compat-data': 7.29.0 '@babel/helper-validator-option': 7.27.1 browserslist: 4.28.1 lru-cache: 5.1.1 @@ -4551,19 +4570,19 @@ snapshots: '@babel/helper-globals@7.28.0': {} - '@babel/helper-module-imports@7.27.1': + '@babel/helper-module-imports@7.28.6': dependencies: - '@babel/traverse': 7.28.5 - '@babel/types': 7.28.5 + '@babel/traverse': 7.29.0 + '@babel/types': 7.29.0 transitivePeerDependencies: - supports-color - '@babel/helper-module-transforms@7.28.3(@babel/core@7.28.5)': + '@babel/helper-module-transforms@7.28.6(@babel/core@7.29.0)': dependencies: - '@babel/core': 7.28.5 - '@babel/helper-module-imports': 7.27.1 + '@babel/core': 7.29.0 + '@babel/helper-module-imports': 7.28.6 '@babel/helper-validator-identifier': 7.28.5 - '@babel/traverse': 7.28.5 + '@babel/traverse': 7.29.0 transitivePeerDependencies: - supports-color @@ -4573,33 +4592,37 @@ snapshots: '@babel/helper-validator-option@7.27.1': {} - '@babel/helpers@7.28.4': + '@babel/helpers@7.28.6': dependencies: - '@babel/template': 7.27.2 - '@babel/types': 7.28.5 + '@babel/template': 7.28.6 + '@babel/types': 7.29.0 '@babel/parser@7.28.5': dependencies: '@babel/types': 7.28.5 + '@babel/parser@7.29.0': + dependencies: + '@babel/types': 7.29.0 + '@babel/runtime@7.26.0': dependencies: regenerator-runtime: 0.14.1 - '@babel/template@7.27.2': + '@babel/template@7.28.6': dependencies: - '@babel/code-frame': 7.27.1 - '@babel/parser': 7.28.5 - '@babel/types': 7.28.5 + '@babel/code-frame': 7.29.0 + '@babel/parser': 7.29.0 + '@babel/types': 7.29.0 - '@babel/traverse@7.28.5': + '@babel/traverse@7.29.0': dependencies: - '@babel/code-frame': 7.27.1 - '@babel/generator': 7.28.5 + '@babel/code-frame': 7.29.0 + '@babel/generator': 7.29.1 '@babel/helper-globals': 7.28.0 - '@babel/parser': 7.28.5 - '@babel/template': 7.27.2 - '@babel/types': 7.28.5 + '@babel/parser': 7.29.0 + '@babel/template': 7.28.6 + '@babel/types': 7.29.0 debug: 4.4.3(supports-color@8.1.1) transitivePeerDependencies: - supports-color @@ -4609,6 +4632,11 @@ snapshots: '@babel/helper-string-parser': 7.27.1 '@babel/helper-validator-identifier': 7.28.5 + '@babel/types@7.29.0': + dependencies: + '@babel/helper-string-parser': 7.27.1 + '@babel/helper-validator-identifier': 7.28.5 + '@bufbuild/protobuf@2.6.2': {} '@bufbuild/protoplugin@2.6.2': @@ -4957,7 +4985,7 @@ snapshots: '@jridgewell/gen-mapping@0.3.13': dependencies: - '@jridgewell/sourcemap-codec': 1.5.5 + '@jridgewell/sourcemap-codec': 1.5.0 '@jridgewell/trace-mapping': 0.3.31 '@jridgewell/remapping@2.3.5': @@ -4967,12 +4995,14 @@ snapshots: '@jridgewell/resolve-uri@3.1.2': {} + '@jridgewell/sourcemap-codec@1.5.0': {} + '@jridgewell/sourcemap-codec@1.5.5': {} '@jridgewell/trace-mapping@0.3.31': dependencies: '@jridgewell/resolve-uri': 3.1.2 - '@jridgewell/sourcemap-codec': 1.5.5 + '@jridgewell/sourcemap-codec': 1.5.0 '@js-sdsl/ordered-map@4.4.2': {} @@ -5562,17 +5592,15 @@ snapshots: utility-types: 3.11.0 zod: 3.23.8 - '@platforma-sdk/package-builder@3.10.7': + '@platforma-sdk/package-builder@3.11.4': dependencies: '@aws-sdk/client-s3': 3.859.0 '@aws-sdk/lib-storage': 3.859.0(@aws-sdk/client-s3@3.859.0) - '@milaboratories/resolve-helper': 1.1.1 + '@milaboratories/resolve-helper': 1.1.2 '@oclif/core': 4.0.37 '@types/archiver': 6.0.4 '@types/node': 24.5.2 archiver: 7.0.1 - canonicalize: 2.1.0 - tar: 7.4.3 undici: 7.16.0 winston: 3.17.0 yaml: 2.8.1 @@ -5601,9 +5629,9 @@ snapshots: '@milaboratories/pl-tree': 1.8.28 '@milaboratories/ts-helpers': 1.5.4 '@platforma-sdk/model': 1.51.2 - '@vitest/coverage-istanbul': 4.0.16(vitest@4.0.16(@types/node@24.5.2)(yaml@2.8.1)) + '@vitest/coverage-istanbul': 4.0.18(vitest@4.0.18(@types/node@24.5.2)(yaml@2.8.1)) eslint: 9.37.0 - vitest: 4.0.16(@types/node@24.5.2)(yaml@2.8.1) + vitest: 4.0.18(@types/node@24.5.2)(yaml@2.8.1) transitivePeerDependencies: - '@edge-runtime/vm' - '@eslint/js' @@ -6335,7 +6363,7 @@ snapshots: vite: 6.2.3(@types/node@20.16.15)(yaml@2.8.1) vue: 3.5.25(typescript@5.6.3) - '@vitest/coverage-istanbul@4.0.16(vitest@4.0.16(@types/node@24.5.2)(yaml@2.8.1))': + '@vitest/coverage-istanbul@4.0.18(vitest@4.0.18(@types/node@24.5.2)(yaml@2.8.1))': dependencies: '@istanbuljs/schema': 0.1.3 '@jridgewell/gen-mapping': 0.3.13 @@ -6343,12 +6371,11 @@ snapshots: istanbul-lib-coverage: 3.2.2 istanbul-lib-instrument: 6.0.3 istanbul-lib-report: 3.0.1 - istanbul-lib-source-maps: 5.0.6 istanbul-reports: 3.2.0 - magicast: 0.5.1 + magicast: 0.5.2 obug: 2.1.1 tinyrainbow: 3.0.3 - vitest: 4.0.16(@types/node@24.5.2)(yaml@2.8.1) + vitest: 4.0.18(@types/node@24.5.2)(yaml@2.8.1) transitivePeerDependencies: - supports-color @@ -6361,12 +6388,12 @@ snapshots: chai: 6.2.1 tinyrainbow: 3.0.3 - '@vitest/expect@4.0.16': + '@vitest/expect@4.0.18': dependencies: '@standard-schema/spec': 1.0.0 '@types/chai': 5.2.3 - '@vitest/spy': 4.0.16 - '@vitest/utils': 4.0.16 + '@vitest/spy': 4.0.18 + '@vitest/utils': 4.0.18 chai: 6.2.1 tinyrainbow: 3.0.3 @@ -6386,9 +6413,9 @@ snapshots: optionalDependencies: vite: 6.2.3(@types/node@24.5.2)(yaml@2.8.1) - '@vitest/mocker@4.0.16(vite@6.2.3(@types/node@24.5.2)(yaml@2.8.1))': + '@vitest/mocker@4.0.18(vite@6.2.3(@types/node@24.5.2)(yaml@2.8.1))': dependencies: - '@vitest/spy': 4.0.16 + '@vitest/spy': 4.0.18 estree-walker: 3.0.3 magic-string: 0.30.21 optionalDependencies: @@ -6398,7 +6425,7 @@ snapshots: dependencies: tinyrainbow: 3.0.3 - '@vitest/pretty-format@4.0.16': + '@vitest/pretty-format@4.0.18': dependencies: tinyrainbow: 3.0.3 @@ -6407,9 +6434,9 @@ snapshots: '@vitest/utils': 4.0.10 pathe: 2.0.3 - '@vitest/runner@4.0.16': + '@vitest/runner@4.0.18': dependencies: - '@vitest/utils': 4.0.16 + '@vitest/utils': 4.0.18 pathe: 2.0.3 '@vitest/snapshot@4.0.10': @@ -6418,24 +6445,24 @@ snapshots: magic-string: 0.30.21 pathe: 2.0.3 - '@vitest/snapshot@4.0.16': + '@vitest/snapshot@4.0.18': dependencies: - '@vitest/pretty-format': 4.0.16 + '@vitest/pretty-format': 4.0.18 magic-string: 0.30.21 pathe: 2.0.3 '@vitest/spy@4.0.10': {} - '@vitest/spy@4.0.16': {} + '@vitest/spy@4.0.18': {} '@vitest/utils@4.0.10': dependencies: '@vitest/pretty-format': 4.0.10 tinyrainbow: 3.0.3 - '@vitest/utils@4.0.16': + '@vitest/utils@4.0.18': dependencies: - '@vitest/pretty-format': 4.0.16 + '@vitest/pretty-format': 4.0.18 tinyrainbow: 3.0.3 '@volar/language-core@2.4.11': @@ -6744,7 +6771,7 @@ snapshots: base64-js@1.5.1: {} - baseline-browser-mapping@2.9.11: {} + baseline-browser-mapping@2.10.0: {} bcrypt-pbkdf@1.0.2: dependencies: @@ -6778,9 +6805,9 @@ snapshots: browserslist@4.28.1: dependencies: - baseline-browser-mapping: 2.9.11 - caniuse-lite: 1.0.30001761 - electron-to-chromium: 1.5.267 + baseline-browser-mapping: 2.10.0 + caniuse-lite: 1.0.30001775 + electron-to-chromium: 1.5.302 node-releases: 2.0.27 update-browserslist-db: 1.2.3(browserslist@4.28.1) @@ -6824,7 +6851,7 @@ snapshots: callsites@3.1.0: {} - caniuse-lite@1.0.30001761: {} + caniuse-lite@1.0.30001775: {} canonicalize@2.1.0: {} @@ -6978,6 +7005,10 @@ snapshots: de-indent@1.0.2: {} + debug@4.4.0: + dependencies: + ms: 2.1.3 + debug@4.4.3(supports-color@8.1.1): dependencies: ms: 2.1.3 @@ -7047,7 +7078,7 @@ snapshots: dependencies: jake: 10.9.2 - electron-to-chromium@1.5.267: {} + electron-to-chromium@1.5.302: {} emoji-regex@8.0.0: {} @@ -7506,7 +7537,7 @@ snapshots: istanbul-lib-instrument@6.0.3: dependencies: - '@babel/core': 7.28.5 + '@babel/core': 7.29.0 '@babel/parser': 7.28.5 '@istanbuljs/schema': 0.1.3 istanbul-lib-coverage: 3.2.2 @@ -7520,14 +7551,6 @@ snapshots: make-dir: 4.0.0 supports-color: 7.2.0 - istanbul-lib-source-maps@5.0.6: - dependencies: - '@jridgewell/trace-mapping': 0.3.31 - debug: 4.4.3(supports-color@8.1.1) - istanbul-lib-coverage: 3.2.2 - transitivePeerDependencies: - - supports-color - istanbul-reports@3.2.0: dependencies: html-escaper: 2.0.2 @@ -7665,10 +7688,10 @@ snapshots: dependencies: '@jridgewell/sourcemap-codec': 1.5.5 - magicast@0.5.1: + magicast@0.5.2: dependencies: - '@babel/parser': 7.28.5 - '@babel/types': 7.28.5 + '@babel/parser': 7.29.0 + '@babel/types': 7.29.0 source-map-js: 1.2.1 make-dir@1.3.0: @@ -8316,7 +8339,7 @@ snapshots: cac: 6.7.14 chokidar: 4.0.3 consola: 3.4.2 - debug: 4.4.3(supports-color@8.1.1) + debug: 4.4.0 esbuild: 0.25.1 joycon: 3.1.1 picocolors: 1.1.1 @@ -8529,15 +8552,15 @@ snapshots: - tsx - yaml - vitest@4.0.16(@types/node@24.5.2)(yaml@2.8.1): + vitest@4.0.18(@types/node@24.5.2)(yaml@2.8.1): dependencies: - '@vitest/expect': 4.0.16 - '@vitest/mocker': 4.0.16(vite@6.2.3(@types/node@24.5.2)(yaml@2.8.1)) - '@vitest/pretty-format': 4.0.16 - '@vitest/runner': 4.0.16 - '@vitest/snapshot': 4.0.16 - '@vitest/spy': 4.0.16 - '@vitest/utils': 4.0.16 + '@vitest/expect': 4.0.18 + '@vitest/mocker': 4.0.18(vite@6.2.3(@types/node@24.5.2)(yaml@2.8.1)) + '@vitest/pretty-format': 4.0.18 + '@vitest/runner': 4.0.18 + '@vitest/snapshot': 4.0.18 + '@vitest/spy': 4.0.18 + '@vitest/utils': 4.0.18 es-module-lexer: 1.7.0 expect-type: 1.2.2 magic-string: 0.30.21 diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml index d0559e9..c97fdc3 100644 --- a/pnpm-workspace.yaml +++ b/pnpm-workspace.yaml @@ -14,37 +14,37 @@ catalog: '@platforma-sdk/tengo-builder': 2.4.8 '@platforma-sdk/workflow-tengo': 5.8.0 "@platforma-sdk/blocks-deps-updater": 2.0.0 - "@platforma-sdk/eslint-config": ^1.2.0 - '@platforma-sdk/package-builder': 3.10.7 + "@platforma-sdk/eslint-config": ~1.2.0 + '@platforma-sdk/package-builder': ~3.11.4 - '@platforma-open/milaboratories.runenv-python-3': ^1.7.5 - '@platforma-open/milaboratories.runenv-r-samples-and-data': ^1.0.1 + '@platforma-open/milaboratories.runenv-python-3': ~1.7.5 + '@platforma-open/milaboratories.runenv-r-samples-and-data': ~1.0.1 '@platforma-sdk/test': 1.51.3 '@milaboratories/helpers': 1.13.0 - 'vue': ^3.5.24 - 'vue-tsc': ^2.2.8 + 'vue': ~3.5.24 + 'vue-tsc': ~2.2.8 'zod': ~3.23.8 - 'radashi': ^12.7.0 - 'utility-types': ^3.11.0 + 'radashi': ~12.7.0 + 'utility-types': ~3.11.0 'typescript': ~5.6.3 'tsup': ~8.4.0 - 'turbo': ^2.6.1 + 'turbo': ~2.6.1 - 'vite': ^6.0.6 - 'vitest': ^4.0.10 - '@vitejs/plugin-vue': ^5.2.1 - 'vite-plugin-dts': ^4.3.0 - 'shx': ^0.4.0 + 'vite': ~6.2.3 + 'vitest': ~4.0.10 + '@vitejs/plugin-vue': ~5.2.1 + 'vite-plugin-dts': ~4.3.0 + 'shx': ~0.4.0 - '@vueuse/core': ^12.2.0 + '@vueuse/core': ~12.8.2 - 'ag-grid-enterprise': &ag-grid ^34.1.2 + 'ag-grid-enterprise': &ag-grid ~34.1.2 'ag-grid-vue3': *ag-grid - '@changesets/cli': ^2.29.7 + '@changesets/cli': ~2.29.7 '@types/node': ~20.16.15 diff --git a/software/parse-seurat/Dockerfile b/software/parse-seurat/Dockerfile index bdc1178..ca10a5d 100644 --- a/software/parse-seurat/Dockerfile +++ b/software/parse-seurat/Dockerfile @@ -8,6 +8,7 @@ ENV RENV_CONFIG_REPOS_OVERRIDE=https://cloud.r-project.org # Install system dependencies required for R packages RUN apt-get update && apt-get install -y \ + dash \ libcurl4-openssl-dev \ libssl-dev \ libxml2-dev \