[update docs] v3.0.0

cmdcolin · cmdcolin · commit 2c6897f1fa73 · 2025-01-29T22:49:51.000Z
diff --git a/lerna.json b/lerna.json
@@ -1,5 +1,5 @@
 {
-  "version": "2.18.0",
+  "version": "3.0.0",
   "npmClient": "yarn",
   "$schema": "node_modules/lerna/schemas/lerna-schema.json"
 }
diff --git a/packages/app-core/package.json b/packages/app-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "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": "^2.18.0",
+    "@jbrowse/product-core": "^3.0.0",
     "@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
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/embedded-core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 code shared between embedded products",
   "keywords": [
     "jbrowse",
@@ -42,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.18.0",
-    "@jbrowse/product-core": "^2.18.0",
+    "@jbrowse/core": "^3.0.0",
+    "@jbrowse/product-core": "^3.0.0",
     "@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
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
   "keywords": [
@@ -43,7 +43,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.18.0",
+    "@jbrowse/core": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1",
diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/sv-core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 code shared between sv type code",
   "keywords": [
     "jbrowse",
@@ -42,8 +42,8 @@
   },
   "dependencies": {
     "@gmod/vcf": "^6.0.0",
-    "@jbrowse/core": "^2.18.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.18.0",
+    "@jbrowse/core": "^3.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0"
   },
diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.18.0",
+    "@jbrowse/core": "^3.0.0",
     "ixixx": "^2.0.1",
     "node-fetch": "^2.6.0",
     "sanitize-filename": "^1.6.3"
diff --git a/packages/web-core/package.json b/packages/web-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/web-core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "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": "^2.18.0",
-    "@jbrowse/product-core": "^2.18.0",
+    "@jbrowse/app-core": "^3.0.0",
+    "@jbrowse/product-core": "^3.0.0",
     "@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
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   "dependencies": {
     "@gmod/bam": "^5.0.0",
     "@gmod/cram": "^4.0.1",
-    "@jbrowse/sv-core": "^2.18.0",
+    "@jbrowse/sv-core": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
     "copy-to-clipboard": "^3.3.1",
diff --git a/plugins/arc/package.json b/plugins/arc/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-authentication",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 Authentication",
   "keywords": [
     "jbrowse",
diff --git a/plugins/bed/package.json b/plugins/bed/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
diff --git 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": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-circular-view",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 circular view",
   "keywords": [
     "jbrowse",
diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
diff --git a/plugins/config/package.json b/plugins/config/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-dotplot-view",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 dotplot view",
   "keywords": [
     "jbrowse",
diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gccontent",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 gccontent concepts",
   "keywords": [
     "jbrowse",
diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-grid-bookmark",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 grid bookmark widget",
   "keywords": [
     "jbrowse",
diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
diff --git a/plugins/hic/package.json b/plugins/hic/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-jobs-management",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 jobs management",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/text-indexing": "^2.18.0",
+    "@jbrowse/text-indexing": "^3.0.0",
     "@mui/icons-material": "^6.0.0"
   },
   "peerDependencies": {
diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
diff --git 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": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
diff --git 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": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-lollipop",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 plugin for lollipops",
   "keywords": [
     "jbrowse",
diff --git a/plugins/menus/package.json b/plugins/menus/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-menus",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 basic menus",
   "keywords": [
     "jbrowse",
diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
     "jbrowse",
diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-spreadsheet-view",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 spreadsheet view",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^2.0.1",
     "@gmod/vcf": "^6.0.0",
-    "@jbrowse/plugin-variants": "^2.18.0",
+    "@jbrowse/plugin-variants": "^3.0.0",
     "@mui/icons-material": "^6.0.0"
   },
   "peerDependencies": {
diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sv-inspector",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 SV inspector view",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/sv-core": "^2.18.0",
+    "@jbrowse/sv-core": "^3.0.0",
     "@mui/icons-material": "^6.0.0"
   },
   "peerDependencies": {
diff --git a/plugins/svg/package.json b/plugins/svg/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-svg",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 plugin for svg features",
   "keywords": [
     "jbrowse",
diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-text-indexing",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 text indexing rpc method",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/text-indexing": "^2.18.0"
+    "@jbrowse/text-indexing": "^3.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
diff --git a/plugins/trix/package.json b/plugins/trix/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
     "jbrowse",
diff --git a/plugins/variants/package.json b/plugins/variants/package.json
diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json
diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json
diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json
diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json
diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json
diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json
diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json
diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json
diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "version": "2.18.0",`
	`2`	`+ "version": "3.0.0",`
`3`	`3`	`"npmClient": "yarn",`
`4`	`4`	`"$schema": "node_modules/lerna/schemas/lerna-schema.json"`
`5`	`5`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/core",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 core libraries used by plugins",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-arc",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 arc adapters, tracks, etc.",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-authentication",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 Authentication",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-bed",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 bed adapters, tracks, etc.",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-breakpoint-split-view",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 breakpoint detail split view",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-circular-view",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 circular view",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-comparative-adapters",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 comparative adapters",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-config",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 config utilities",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "@jbrowse/plugin-data-management",`
`3`		`- "version": "2.18.0",`
	`3`	`+ "version": "3.0.0",`
`4`	`4`	`"description": "JBrowse 2 linear genome view",`
`5`	`5`	`"keywords": [`
`6`	`6`	`"jbrowse",`