[update docs] v3.0.1

GMOD · Jan 30, 2025 · 59ff465 · 59ff465
1 parent 94923fa
commit 59ff465
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Showing 47 changed files with 304 additions and 304 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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": {