From d95d72a4976b8d2d7c45d274b069d102c4ab07a2 Mon Sep 17 00:00:00 2001 From: sara castellano Date: Tue, 14 Nov 2023 12:26:35 +0100 Subject: [PATCH 1/5] update documentation for dimensionality reduction Signed-off-by: sara castellano --- src/utils/upload/fileUploadSpecifications.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/utils/upload/fileUploadSpecifications.js b/src/utils/upload/fileUploadSpecifications.js index 166df8fe5c..11eb4d7a25 100644 --- a/src/utils/upload/fileUploadSpecifications.js +++ b/src/utils/upload/fileUploadSpecifications.js @@ -55,7 +55,8 @@ const fileUploadSpecifications = { inputInfo: [ ['scdata$samples: sample assignment. If absent, treated as unisample.'], ['scdata[[\'RNA\']]@counts: raw feature counts.'], - ['scdata@reductions: contains the embbedings for pca as well as either umap or tsne.'], + ['scdata@reductions: contains the embeddings for pca, as well as either umap or tsne.'], + ['Important notes on dimensionality reductions: ensure the default dimensionality reduction in your Seurat object is named exactly umap or tsne. If the default reduction name includes umap or tsne (e.g., ref.umap), it will be automatically renamed. If the default reduction is different and does not contain these names, the upload will not be successful.'], ['\uD83D\uDCA1cluster metadata in scdata@meta.data is auto-detected.'], ['\uD83D\uDCA1sample level metadata in scdata@meta.data that groups samples in scdata$samples is auto-detected for downstream analysis.'], ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'], From be3f3e4d4f9c24bf6d2170233caf9ac2fbd966f7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Nov 2023 10:07:25 +0000 Subject: [PATCH 2/5] Bump mathjs from 11.12.0 to 12.1.0 Bumps [mathjs](https://github.com/josdejong/mathjs) from 11.12.0 to 12.1.0. - [Changelog](https://github.com/josdejong/mathjs/blob/develop/HISTORY.md) - [Commits](https://github.com/josdejong/mathjs/compare/v11.12.0...v12.1.0) --- updated-dependencies: - dependency-name: mathjs dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0745c4a56b..c200336674 100644 --- a/package-lock.json +++ b/package-lock.json @@ -19599,9 +19599,9 @@ } }, "mathjs": { - "version": "11.12.0", - "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-11.12.0.tgz", - "integrity": "sha512-UGhVw8rS1AyedyI55DGz9q1qZ0p98kyKPyc9vherBkoueLntPfKtPBh14x+V4cdUWK0NZV2TBwqRFlvadscSuw==", + "version": "12.1.0", + "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-12.1.0.tgz", + "integrity": "sha512-x5wUkWo3CfXMl4mf/jHsbVNuMcUwN2m4qbj+tR/jYr9fdiIrlsexQbKYav8Uwfe+E5he30CyVaABNLmAlTFO3w==", "requires": { "@babel/runtime": "^7.23.2", "complex.js": "^2.1.1", diff --git a/package.json b/package.json index 35d1322a8d..6c83499a4f 100644 --- a/package.json +++ b/package.json @@ -77,7 +77,7 @@ "localforage": "^1.7.4", "lodash": "^4.17.13", "lru-memoize": "^1.1.0", - "mathjs": "^11.0.1", + "mathjs": "^12.1.0", "next": "^12.3.4", "next-images": "^1.4.0", "next-plugin-antd-less": "^1.8.0", From a4cb7617be9e985b92e13058ea4c4a7b6d9c301d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Nov 2023 10:37:55 +0000 Subject: [PATCH 3/5] Bump axios from 0.21.4 to 1.6.2 Bumps [axios](https://github.com/axios/axios) from 0.21.4 to 1.6.2. - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](https://github.com/axios/axios/compare/v0.21.4...v1.6.2) --- updated-dependencies: - dependency-name: axios dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- package-lock.json | 22 ++++++++++++++++++---- package.json | 2 +- 2 files changed, 19 insertions(+), 5 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0745c4a56b..2dba53a114 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13123,11 +13123,25 @@ "dev": true }, "axios": { - "version": "0.21.4", - "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.4.tgz", - "integrity": "sha512-ut5vewkiu8jjGBdqpM44XxjuCjq9LAKeHVmoVfHVzy8eHgxxq8SbAVQNovDA8mVi05kP0Ea/n/UzcSHcTJQfNg==", + "version": "1.6.2", + "resolved": "https://registry.npmjs.org/axios/-/axios-1.6.2.tgz", + "integrity": "sha512-7i24Ri4pmDRfJTR7LDBhsOTtcm+9kjX5WiY1X3wIisx6G9So3pfMkEiU7emUBe46oceVImccTEM3k6C5dbVW8A==", "requires": { - "follow-redirects": "^1.14.0" + "follow-redirects": "^1.15.0", + "form-data": "^4.0.0", + "proxy-from-env": "^1.1.0" + }, + "dependencies": { + "form-data": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.0.tgz", + "integrity": "sha512-ETEklSGi5t0QMZuiXoA/Q6vcnxcLQP5vdugSpuAyi6SVGi2clPPp+xgEhuMaHC+zGgn31Kd235W35f7Hykkaww==", + "requires": { + "asynckit": "^0.4.0", + "combined-stream": "^1.0.8", + "mime-types": "^2.1.12" + } + } } }, "axobject-query": { diff --git a/package.json b/package.json index 35d1322a8d..c80c551d6c 100644 --- a/package.json +++ b/package.json @@ -57,7 +57,7 @@ "@vitessce/scatterplot": "^3.2.2", "antd": "^4.24.8", "aws-amplify": "^5.3.11", - "axios": "^0.21.2", + "axios": "^1.6.2", "babel-plugin-add-module-exports": "^1.0.4", "babel-plugin-dynamic-import-node": "^2.3.3", "babel-plugin-import": "^1.13.6", From 26613329cc45cd59fafbc97cdf22b234b9f1510a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Nov 2023 10:39:23 +0000 Subject: [PATCH 4/5] Bump @next/bundle-analyzer from 10.2.3 to 14.0.3 Bumps [@next/bundle-analyzer](https://github.com/vercel/next.js/tree/HEAD/packages/next-bundle-analyzer) from 10.2.3 to 14.0.3. - [Release notes](https://github.com/vercel/next.js/releases) - [Changelog](https://github.com/vercel/next.js/blob/canary/release.js) - [Commits](https://github.com/vercel/next.js/commits/v14.0.3/packages/next-bundle-analyzer) --- updated-dependencies: - dependency-name: "@next/bundle-analyzer" dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- package-lock.json | 21 +++++++++++++-------- package.json | 2 +- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0745c4a56b..42637e4802 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8956,11 +8956,11 @@ } }, "@next/bundle-analyzer": { - "version": "10.2.3", - "resolved": "https://registry.npmjs.org/@next/bundle-analyzer/-/bundle-analyzer-10.2.3.tgz", - "integrity": "sha512-vEfQhGWgJugZOlSUlj3DZWs/KsK0SO2SPKoHSZ7KkzpruKzc/e45G0oUh0rffzdhasMQZM1TuSBkxO+1UcnDNw==", + "version": "14.0.3", + "resolved": "https://registry.npmjs.org/@next/bundle-analyzer/-/bundle-analyzer-14.0.3.tgz", + "integrity": "sha512-+UriXNEn2vGR2IxTiiuen45G7lXUbtMh0hgS/UH2o2E4TnScwjEEepqT76pY8fdpa5JEZ+gvBy6aSnrw4G2P2w==", "requires": { - "webpack-bundle-analyzer": "4.3.0" + "webpack-bundle-analyzer": "4.7.0" }, "dependencies": { "ansi-styles": { @@ -8993,6 +8993,11 @@ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz", "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==" }, + "commander": { + "version": "7.2.0", + "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz", + "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==" + }, "has-flag": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz", @@ -9007,14 +9012,14 @@ } }, "webpack-bundle-analyzer": { - "version": "4.3.0", - "resolved": "https://registry.npmjs.org/webpack-bundle-analyzer/-/webpack-bundle-analyzer-4.3.0.tgz", - "integrity": "sha512-J3TPm54bPARx6QG8z4cKBszahnUglcv70+N+8gUqv2I5KOFHJbzBiLx+pAp606so0X004fxM7hqRu10MLjJifA==", + "version": "4.7.0", + "resolved": "https://registry.npmjs.org/webpack-bundle-analyzer/-/webpack-bundle-analyzer-4.7.0.tgz", + "integrity": "sha512-j9b8ynpJS4K+zfO5GGwsAcQX4ZHpWV+yRiHDiL+bE0XHJ8NiPYLTNVQdlFYWxtpg9lfAQNlwJg16J9AJtFSXRg==", "requires": { "acorn": "^8.0.4", "acorn-walk": "^8.0.0", "chalk": "^4.1.0", - "commander": "^6.2.0", + "commander": "^7.2.0", "gzip-size": "^6.0.0", "lodash": "^4.17.20", "opener": "^1.5.2", diff --git a/package.json b/package.json index 35d1322a8d..37d40349f2 100644 --- a/package.json +++ b/package.json @@ -51,7 +51,7 @@ "@babel/core": "^7.21.0", "@babel/plugin-transform-runtime": "^7.21.0", "@babel/polyfill": "^7.8.7", - "@next/bundle-analyzer": "^10.0.9", + "@next/bundle-analyzer": "^14.0.3", "@socialgouv/matomo-next": "^1.2.2", "@vitessce/heatmap": "^3.2.2", "@vitessce/scatterplot": "^3.2.2", From f072dbdd4189d76a257d747254ac55f2d15aa1a0 Mon Sep 17 00:00:00 2001 From: Alex Pickering Date: Mon, 20 Nov 2023 09:30:57 -0800 Subject: [PATCH 5/5] add safe to run to dependabot PRs Signed-off-by: Alex Pickering --- .github/dependabot.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 70ff415707..eda6d1a820 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -9,4 +9,5 @@ updates: directory: "/" # Location of package manifests schedule: interval: "weekly" - + labels: + - "safe to run" \ No newline at end of file