From 59ff4650a246a48691ba207bdbaa745261638a2a Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 30 Jan 2025 07:46:46 +0000 Subject: [PATCH] [update docs] v3.0.1 --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 12 ++-- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 6 +- packages/sv-core/package.json | 6 +- packages/text-indexing/package.json | 10 +-- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 16 ++--- plugins/arc/package.json | 8 +-- plugins/authentication/package.json | 6 +- plugins/bed/package.json | 4 +- plugins/breakpoint-split-view/package.json | 8 +-- plugins/circular-view/package.json | 6 +- plugins/comparative-adapters/package.json | 10 +-- plugins/config/package.json | 6 +- plugins/data-management/package.json | 16 ++--- plugins/dotplot-view/package.json | 8 +-- plugins/gccontent/package.json | 10 +-- plugins/gff3/package.json | 8 +-- plugins/grid-bookmark/package.json | 12 ++-- plugins/gtf/package.json | 8 +-- plugins/hic/package.json | 8 +-- plugins/jobs-management/package.json | 6 +- plugins/legacy-jbrowse/package.json | 8 +-- plugins/linear-comparative-view/package.json | 10 +-- plugins/linear-genome-view/package.json | 6 +- plugins/lollipop/package.json | 6 +- plugins/menus/package.json | 10 +-- plugins/rdf/package.json | 8 +-- plugins/sequence/package.json | 8 +-- plugins/spreadsheet-view/package.json | 8 +-- plugins/sv-inspector/package.json | 10 +-- plugins/svg/package.json | 4 +- plugins/text-indexing/package.json | 6 +- plugins/trix/package.json | 4 +- plugins/variants/package.json | 12 ++-- plugins/wiggle/package.json | 14 ++-- products/jbrowse-cli/README.md | 26 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 304 insertions(+), 304 deletions(-) diff --git a/lerna.json b/lerna.json index 59b5cfded5..e472f05fe1 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "3.0.0", + "version": "3.0.1", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index f33f2195ff..f15563ed5c 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^3.0.0", + "@jbrowse/product-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index 509c781dc3..738a019205 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", @@ -35,6 +35,7 @@ "@gmod/bgzf-filehandle": "^2.0.1", "@gmod/http-range-fetcher": "^4.0.0", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "canvas-sequencer": "^3.1.0", "canvas2svg": "^1.0.16", @@ -50,15 +51,14 @@ "librpc-web-mod": "^1.1.5", "load-script": "^2.0.0", "material-ui-popup-state": "^5.0.0", - "rbush": "^3.0.1", - "react-draggable": "^4.4.5", - "serialize-error": "^8.0.0", - "source-map-js": "^1.0.2", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", + "rbush": "^3.0.1", + "react-draggable": "^4.4.5", "rxjs": "^7.0.0", + "serialize-error": "^8.0.0", + "source-map-js": "^1.0.2", "tss-react": "^4.0.0" }, "peerDependencies": { diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index 6c2d4e2781..4560f6525c 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index 9925013089..72f9e60b4e 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "3.0.0", + "version": "3.0.1", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,16 +43,16 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", "librpc-web-mod": "^1.0.0", - "serialize-error": "^8.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", "rxjs": "^7.0.0", + "serialize-error": "^8.0.0", "tss-react": "^4.0.0" }, "peerDependencies": { diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index bb1ad077da..667a7fdd52 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@gmod/vcf": "^6.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.0.0", diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index 8e28ade308..ae1d9b5070 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,14 +42,14 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "ixixx": "^2.0.1", - "node-fetch": "^2.6.0", - "sanitize-filename": "^1.6.3", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", - "rxjs": "^7.0.0" + "node-fetch": "^2.6.0", + "rxjs": "^7.0.0", + "sanitize-filename": "^1.6.3" }, "peerDependencies": { "react": ">=18.0.0", diff --git a/packages/web-core/package.json b/packages/web-core/package.json index d49b98808e..1e74a50dba 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", + "@jbrowse/app-core": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index f833f692ac..ffdd91a471 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,21 +38,21 @@ "dependencies": { "@gmod/bam": "^5.0.0", "@gmod/cram": "^4.0.1", - "@jbrowse/sv-core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", + "@jbrowse/sv-core": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "canvas2svg": "^1.0.16", "copy-to-clipboard": "^3.3.1", "fast-deep-equal": "^3.1.3", "generic-filehandle2": "^1.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", - "tss-react": "^4.0.0", - "rxjs": "^7.0.0" + "rxjs": "^7.0.0", + "tss-react": "^4.0.0" }, "peerDependencies": { "react": ">=18.0.0" diff --git a/plugins/arc/package.json b/plugins/arc/package.json index c4da877205..014a9ac82f 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -36,9 +36,9 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index bb7c77fb97..abd9e5f052 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", @@ -36,10 +36,10 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", + "@mui/material": "^6.0.0", "crypto-js": "^4.2.0", "generic-filehandle2": "^1.0.0", - "@jbrowse/core": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 169219040c..dab0ccd031 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "@gmod/bed": "^2.1.2", "@gmod/bgzf-filehandle": "^2.0.1", "@gmod/tabix": "^2.0.0", - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index 82845a0ed2..e71bfd0080 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", @@ -37,12 +37,12 @@ }, "dependencies": { "@gmod/vcf": "^6.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@types/file-saver": "^2.0.1", "file-saver": "^2.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index 5cd6be0513..f3000d2efb 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", @@ -36,11 +36,11 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@types/file-saver": "^2.0.0", "file-saver": "^2.0.0", - "@jbrowse/core": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 0de40a65c0..ebd99253a8 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", @@ -38,11 +38,11 @@ "dependencies": { "@gmod/bgzf-filehandle": "^2.0.1", "@gmod/tabix": "^2.0.0", - "generic-filehandle2": "^1.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/material": "^6.0.0", + "generic-filehandle2": "^1.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/config/package.json b/plugins/config/package.json index 68e569d8a6..916ca83cec 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", @@ -36,13 +36,13 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", "@mui/icons-material": "^6.0.0", - "pluralize": "^8.0.0", - "@jbrowse/core": "^3.0.0", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", + "pluralize": "^8.0.0", "rxjs": "^7.0.0", "tss-react": "^4.0.0" }, diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index db96501a9a..2c14475d3b 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", @@ -37,19 +37,19 @@ }, "dependencies": { "@gmod/ucsc-hub": "^1.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "deepmerge": "^4.3.1", - "react-virtualized-auto-sizer": "^1.0.2", - "react-vtree": "^3.0.0-beta.1", - "react-window": "^1.8.6", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", + "react-virtualized-auto-sizer": "^1.0.2", + "react-vtree": "^3.0.0-beta.1", + "react-window": "^1.8.6", "tss-react": "^4.0.0" }, "peerDependencies": { diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 4d1a6ca4cf..1965e0d4ba 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", @@ -36,13 +36,13 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "@types/file-saver": "^2.0.1", "file-saver": "^2.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index aefa4363aa..c8907625e2 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", @@ -36,10 +36,10 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-sequence": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-sequence": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index 2f004e67b9..a3822b58c5 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", @@ -39,10 +39,10 @@ "@flatten-js/interval-tree": "^1.0.15", "@gmod/bgzf-filehandle": "^2.0.1", "@gmod/tabix": "^2.0.0", - "gff-nostream": "^1.3.3", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/material": "^6.0.0", + "gff-nostream": "^1.3.3", "mobx": "^6.0.0", "mobx-state-tree": "^5.0.0", "rxjs": "^7.0.0" diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index 727a3d3c4d..f4a3389e8e 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", @@ -36,15 +36,15 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", + "@mui/x-data-grid": "^7.0.0", "@types/file-saver": "^2.0.1", "copy-to-clipboard": "^3.3.1", "file-saver": "^2.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@mui/material": "^6.0.0", - "@mui/x-data-grid": "^7.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index f2f1f21248..056e0d9054 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", @@ -38,10 +38,10 @@ "dependencies": { "@flatten-js/interval-tree": "^1.0.15", "@gmod/bgzf-filehandle": "^2.0.1", - "gtf-nostream": "^1.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/material": "^6.0.0", + "gtf-nostream": "^1.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index ac7c715944..9f27b6d79d 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -36,11 +36,11 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@mui/material": "^6.0.0", "@mui/x-charts-vendor": "^7.12.0", "hic-straw": "^2.0.3", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index 948d26a90b..40478e3235 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,9 +36,9 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/text-indexing": "^3.0.1", "@mui/icons-material": "^6.0.0", - "@jbrowse/core": "^3.0.0", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index 6eda4ae7e1..cb99bf59cf 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", @@ -37,15 +37,15 @@ }, "dependencies": { "@gmod/nclist": "^2.0.0", + "@jbrowse/core": "^3.0.1", "crc": "^4.0.0", "generic-filehandle2": "^1.0.0", "get-value": "^3.0.0", - "set-value": "^4.0.1", - "@jbrowse/core": "^3.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", - "rxjs": "^7.0.0" + "rxjs": "^7.0.0", + "set-value": "^4.0.1" }, "publishConfig": { "access": "public" diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 0e2f62b7e1..60f722a7f2 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", @@ -36,13 +36,13 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", "file-saver": "^2.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index a1fc6b8b61..be186fb7fa 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", @@ -38,13 +38,13 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@types/file-saver": "^2.0.1", "copy-to-clipboard": "^3.3.1", "file-saver": "^2.0.0", "material-ui-popup-state": "^5.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 21b7737858..14b2c89832 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", @@ -36,8 +36,8 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index a71a34d378..6954159496 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", @@ -36,15 +36,15 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "@jbrowse/core": "^3.0.1", "@mui/icons-material": "^6.0.0", - "date-fns": "^4.1.0", - "pluralize": "^8.0.0", - "react-dropzone": "^14.2.1", - "@jbrowse/core": "^3.0.0", "@mui/material": "^6.0.0", + "date-fns": "^4.1.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", + "pluralize": "^8.0.0", + "react-dropzone": "^14.2.1", "tss-react": "^4.0.0" }, "peerDependencies": { diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index fa6d31ecb1..abd6fca711 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", @@ -36,12 +36,12 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "string-template": "^1.0.0", - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", - "rxjs": "^7.0.0" + "rxjs": "^7.0.0", + "string-template": "^1.0.0" }, "distModule": "esm/index.js", "srcModule": "src/index.ts", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index 259ae5ce23..5c811a693b 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -39,9 +39,9 @@ "@gmod/abortable-promise-cache": "^2.0.0", "@gmod/indexedfasta": "^3.0.0", "@gmod/twobit": "^4.0.1", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index ebef93efbb..f13a82ddf3 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,10 +38,10 @@ "dependencies": { "@gmod/bgzf-filehandle": "^2.0.1", "@gmod/vcf": "^6.0.0", - "@jbrowse/plugin-variants": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-variants": "^3.0.1", "@mui/icons-material": "^6.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "mobx": "^6.0.0", diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index cd40eb5aa6..600bce17fd 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", @@ -36,11 +36,11 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/sv-core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-spreadsheet-view": "^3.0.1", + "@jbrowse/sv-core": "^3.0.1", "@mui/icons-material": "^6.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-spreadsheet-view": "^3.0.0", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index d6ac1015e8..daf1446ed1 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index e9631b1510..e448fa4ec2 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,8 +36,8 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^3.0.0", - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/text-indexing": "^3.0.1", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0" diff --git a/plugins/trix/package.json b/plugins/trix/package.json index 8f508180f3..f32ddfbd2c 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ }, "dependencies": { "@gmod/trix": "^3.0.0", - "@jbrowse/core": "^3.0.0", + "@jbrowse/core": "^3.0.1", "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index 0d858239a2..37786e5054 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,13 +40,13 @@ "@gmod/bgzf-filehandle": "^2.0.1", "@gmod/tabix": "^2.0.0", "@gmod/vcf": "^6.0.0", - "@jbrowse/sv-core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/sv-core": "^3.0.1", "@mui/icons-material": "^6.0.0", - "@mui/x-data-grid": "^7.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", "@mui/material": "^6.0.0", + "@mui/x-data-grid": "^7.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index b6ba55ce62..6557d5e499 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -37,19 +37,19 @@ }, "dependencies": { "@gmod/bbi": "^6.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-data-management": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", "@mui/icons-material": "^6.0.0", + "@mui/material": "^6.0.0", "@mui/x-charts-vendor": "^7.12.0", "@mui/x-data-grid": "^7.0.0", "fast-deep-equal": "^3.1.3", - "react-d3-axis-mod": "^0.1.9", - "react-draggable": "^4.4.5", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-data-management": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@mui/material": "^6.0.0", "mobx": "^6.0.0", "mobx-react": "^9.0.0", "mobx-state-tree": "^5.0.0", + "react-d3-axis-mod": "^0.1.9", + "react-draggable": "^4.4.5", "rxjs": "^7.0.0", "tss-react": "^4.0.0" }, diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index 6c04a1ee60..2a5226a8f6 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -206,7 +206,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -257,7 +257,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -338,7 +338,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -368,7 +368,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -400,7 +400,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -457,7 +457,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -508,7 +508,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -536,7 +536,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -578,7 +578,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-bed FILE` @@ -609,7 +609,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-bed.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/sort-bed.ts)_ +[src/commands/sort-bed.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/sort-bed.ts)_ ## `jbrowse sort-gff FILE` @@ -640,7 +640,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -707,7 +707,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -770,7 +770,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.0/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v3.0.1/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 5989d7b4f3..358f774a92 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "3.0.0", + "version": "3.0.1", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index e35891d81a..9cd329dfde 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^3.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@jbrowse/plugin-arc": "^3.0.0", - "@jbrowse/plugin-authentication": "^3.0.0", - "@jbrowse/plugin-bed": "^3.0.0", - "@jbrowse/plugin-breakpoint-split-view": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-comparative-adapters": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/plugin-data-management": "^3.0.0", - "@jbrowse/plugin-dotplot-view": "^3.0.0", - "@jbrowse/plugin-gccontent": "^3.0.0", - "@jbrowse/plugin-gff3": "^3.0.0", - "@jbrowse/plugin-grid-bookmark": "^3.0.0", - "@jbrowse/plugin-gtf": "^3.0.0", - "@jbrowse/plugin-hic": "^3.0.0", - "@jbrowse/plugin-jobs-management": "^3.0.0", - "@jbrowse/plugin-legacy-jbrowse": "^3.0.0", - "@jbrowse/plugin-linear-comparative-view": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-lollipop": "^3.0.0", - "@jbrowse/plugin-menus": "^3.0.0", - "@jbrowse/plugin-rdf": "^3.0.0", - "@jbrowse/plugin-sequence": "^3.0.0", - "@jbrowse/plugin-spreadsheet-view": "^3.0.0", - "@jbrowse/plugin-sv-inspector": "^3.0.0", - "@jbrowse/plugin-svg": "^3.0.0", - "@jbrowse/plugin-text-indexing": "^3.0.0", - "@jbrowse/plugin-trix": "^3.0.0", - "@jbrowse/plugin-variants": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", - "@jbrowse/text-indexing": "^3.0.0", + "@jbrowse/app-core": "^3.0.1", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", + "@jbrowse/plugin-arc": "^3.0.1", + "@jbrowse/plugin-authentication": "^3.0.1", + "@jbrowse/plugin-bed": "^3.0.1", + "@jbrowse/plugin-breakpoint-split-view": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-comparative-adapters": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/plugin-data-management": "^3.0.1", + "@jbrowse/plugin-dotplot-view": "^3.0.1", + "@jbrowse/plugin-gccontent": "^3.0.1", + "@jbrowse/plugin-gff3": "^3.0.1", + "@jbrowse/plugin-grid-bookmark": "^3.0.1", + "@jbrowse/plugin-gtf": "^3.0.1", + "@jbrowse/plugin-hic": "^3.0.1", + "@jbrowse/plugin-jobs-management": "^3.0.1", + "@jbrowse/plugin-legacy-jbrowse": "^3.0.1", + "@jbrowse/plugin-linear-comparative-view": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-lollipop": "^3.0.1", + "@jbrowse/plugin-menus": "^3.0.1", + "@jbrowse/plugin-rdf": "^3.0.1", + "@jbrowse/plugin-sequence": "^3.0.1", + "@jbrowse/plugin-spreadsheet-view": "^3.0.1", + "@jbrowse/plugin-sv-inspector": "^3.0.1", + "@jbrowse/plugin-svg": "^3.0.1", + "@jbrowse/plugin-text-indexing": "^3.0.1", + "@jbrowse/plugin-trix": "^3.0.1", + "@jbrowse/plugin-variants": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", + "@jbrowse/text-indexing": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index 9d1353f1f5..eb9769ac10 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "3.0.0", + "version": "3.0.1", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/react-linear-genome-view": "^3.0.0", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/react-linear-genome-view": "^3.0.1", "canvas": "^3.0.0", "jsdom": "^26.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 0497d17468..e75aa6d4bc 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "3.0.0", + "version": "3.0.1", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index 545953ea89..7f09ec5fdc 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -46,38 +46,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^3.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@jbrowse/plugin-arc": "^3.0.0", - "@jbrowse/plugin-authentication": "^3.0.0", - "@jbrowse/plugin-bed": "^3.0.0", - "@jbrowse/plugin-breakpoint-split-view": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-comparative-adapters": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/plugin-data-management": "^3.0.0", - "@jbrowse/plugin-dotplot-view": "^3.0.0", - "@jbrowse/plugin-gccontent": "^3.0.0", - "@jbrowse/plugin-gff3": "^3.0.0", - "@jbrowse/plugin-grid-bookmark": "^3.0.0", - "@jbrowse/plugin-gtf": "^3.0.0", - "@jbrowse/plugin-hic": "^3.0.0", - "@jbrowse/plugin-legacy-jbrowse": "^3.0.0", - "@jbrowse/plugin-linear-comparative-view": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-lollipop": "^3.0.0", - "@jbrowse/plugin-menus": "^3.0.0", - "@jbrowse/plugin-rdf": "^3.0.0", - "@jbrowse/plugin-sequence": "^3.0.0", - "@jbrowse/plugin-spreadsheet-view": "^3.0.0", - "@jbrowse/plugin-sv-inspector": "^3.0.0", - "@jbrowse/plugin-svg": "^3.0.0", - "@jbrowse/plugin-trix": "^3.0.0", - "@jbrowse/plugin-variants": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", - "@jbrowse/web-core": "^3.0.0", + "@jbrowse/app-core": "^3.0.1", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", + "@jbrowse/plugin-arc": "^3.0.1", + "@jbrowse/plugin-authentication": "^3.0.1", + "@jbrowse/plugin-bed": "^3.0.1", + "@jbrowse/plugin-breakpoint-split-view": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-comparative-adapters": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/plugin-data-management": "^3.0.1", + "@jbrowse/plugin-dotplot-view": "^3.0.1", + "@jbrowse/plugin-gccontent": "^3.0.1", + "@jbrowse/plugin-gff3": "^3.0.1", + "@jbrowse/plugin-grid-bookmark": "^3.0.1", + "@jbrowse/plugin-gtf": "^3.0.1", + "@jbrowse/plugin-hic": "^3.0.1", + "@jbrowse/plugin-legacy-jbrowse": "^3.0.1", + "@jbrowse/plugin-linear-comparative-view": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-lollipop": "^3.0.1", + "@jbrowse/plugin-menus": "^3.0.1", + "@jbrowse/plugin-rdf": "^3.0.1", + "@jbrowse/plugin-sequence": "^3.0.1", + "@jbrowse/plugin-spreadsheet-view": "^3.0.1", + "@jbrowse/plugin-sv-inspector": "^3.0.1", + "@jbrowse/plugin-svg": "^3.0.1", + "@jbrowse/plugin-trix": "^3.0.1", + "@jbrowse/plugin-variants": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", + "@jbrowse/web-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index d11e2ee0fd..691fe53ff0 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -39,17 +39,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^3.0.0", - "@jbrowse/embedded-core": "^3.0.0", - "@jbrowse/plugin-authentication": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/plugin-data-management": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-sequence": "^3.0.0", - "@jbrowse/plugin-variants": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/embedded-core": "^3.0.1", + "@jbrowse/plugin-authentication": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/plugin-data-management": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-sequence": "^3.0.1", + "@jbrowse/plugin-variants": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index 3e0b72c758..e8af188b1b 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "3.0.0", + "version": "3.0.1", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -46,25 +46,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^3.0.0", - "@jbrowse/embedded-core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@jbrowse/plugin-arc": "^3.0.0", - "@jbrowse/plugin-authentication": "^3.0.0", - "@jbrowse/plugin-bed": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/plugin-data-management": "^3.0.0", - "@jbrowse/plugin-gccontent": "^3.0.0", - "@jbrowse/plugin-gff3": "^3.0.0", - "@jbrowse/plugin-legacy-jbrowse": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-sequence": "^3.0.0", - "@jbrowse/plugin-svg": "^3.0.0", - "@jbrowse/plugin-trix": "^3.0.0", - "@jbrowse/plugin-variants": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", + "@jbrowse/core": "^3.0.1", + "@jbrowse/embedded-core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", + "@jbrowse/plugin-arc": "^3.0.1", + "@jbrowse/plugin-authentication": "^3.0.1", + "@jbrowse/plugin-bed": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/plugin-data-management": "^3.0.1", + "@jbrowse/plugin-gccontent": "^3.0.1", + "@jbrowse/plugin-gff3": "^3.0.1", + "@jbrowse/plugin-legacy-jbrowse": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-sequence": "^3.0.1", + "@jbrowse/plugin-svg": "^3.0.1", + "@jbrowse/plugin-trix": "^3.0.1", + "@jbrowse/plugin-variants": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index 31be631886..19688c23b3 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "3.0.0", + "version": "3.0.1", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -13,38 +13,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^3.0.0", - "@jbrowse/core": "^3.0.0", - "@jbrowse/plugin-alignments": "^3.0.0", - "@jbrowse/plugin-arc": "^3.0.0", - "@jbrowse/plugin-authentication": "^3.0.0", - "@jbrowse/plugin-bed": "^3.0.0", - "@jbrowse/plugin-breakpoint-split-view": "^3.0.0", - "@jbrowse/plugin-circular-view": "^3.0.0", - "@jbrowse/plugin-comparative-adapters": "^3.0.0", - "@jbrowse/plugin-config": "^3.0.0", - "@jbrowse/plugin-data-management": "^3.0.0", - "@jbrowse/plugin-dotplot-view": "^3.0.0", - "@jbrowse/plugin-gccontent": "^3.0.0", - "@jbrowse/plugin-gff3": "^3.0.0", - "@jbrowse/plugin-grid-bookmark": "^3.0.0", - "@jbrowse/plugin-gtf": "^3.0.0", - "@jbrowse/plugin-hic": "^3.0.0", - "@jbrowse/plugin-legacy-jbrowse": "^3.0.0", - "@jbrowse/plugin-linear-comparative-view": "^3.0.0", - "@jbrowse/plugin-linear-genome-view": "^3.0.0", - "@jbrowse/plugin-lollipop": "^3.0.0", - "@jbrowse/plugin-menus": "^3.0.0", - "@jbrowse/plugin-rdf": "^3.0.0", - "@jbrowse/plugin-sequence": "^3.0.0", - "@jbrowse/plugin-spreadsheet-view": "^3.0.0", - "@jbrowse/plugin-sv-inspector": "^3.0.0", - "@jbrowse/plugin-svg": "^3.0.0", - "@jbrowse/plugin-trix": "^3.0.0", - "@jbrowse/plugin-variants": "^3.0.0", - "@jbrowse/plugin-wiggle": "^3.0.0", - "@jbrowse/product-core": "^3.0.0", - "@jbrowse/web-core": "^3.0.0", + "@jbrowse/app-core": "^3.0.1", + "@jbrowse/core": "^3.0.1", + "@jbrowse/plugin-alignments": "^3.0.1", + "@jbrowse/plugin-arc": "^3.0.1", + "@jbrowse/plugin-authentication": "^3.0.1", + "@jbrowse/plugin-bed": "^3.0.1", + "@jbrowse/plugin-breakpoint-split-view": "^3.0.1", + "@jbrowse/plugin-circular-view": "^3.0.1", + "@jbrowse/plugin-comparative-adapters": "^3.0.1", + "@jbrowse/plugin-config": "^3.0.1", + "@jbrowse/plugin-data-management": "^3.0.1", + "@jbrowse/plugin-dotplot-view": "^3.0.1", + "@jbrowse/plugin-gccontent": "^3.0.1", + "@jbrowse/plugin-gff3": "^3.0.1", + "@jbrowse/plugin-grid-bookmark": "^3.0.1", + "@jbrowse/plugin-gtf": "^3.0.1", + "@jbrowse/plugin-hic": "^3.0.1", + "@jbrowse/plugin-legacy-jbrowse": "^3.0.1", + "@jbrowse/plugin-linear-comparative-view": "^3.0.1", + "@jbrowse/plugin-linear-genome-view": "^3.0.1", + "@jbrowse/plugin-lollipop": "^3.0.1", + "@jbrowse/plugin-menus": "^3.0.1", + "@jbrowse/plugin-rdf": "^3.0.1", + "@jbrowse/plugin-sequence": "^3.0.1", + "@jbrowse/plugin-spreadsheet-view": "^3.0.1", + "@jbrowse/plugin-sv-inspector": "^3.0.1", + "@jbrowse/plugin-svg": "^3.0.1", + "@jbrowse/plugin-trix": "^3.0.1", + "@jbrowse/plugin-variants": "^3.0.1", + "@jbrowse/plugin-wiggle": "^3.0.1", + "@jbrowse/product-core": "^3.0.1", + "@jbrowse/web-core": "^3.0.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0",