Merge origin/main

.github/workflows/release.yml

@@ -56,6 +56,12 @@ jobs:
       - uses: actions/checkout@v4
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
+      - name: Setup java
+        uses: actions/setup-java@v4
+        with:
+          # eclipse 'temurin' openjdk https://github.com/actions/setup-java/blob/main/docs/advanced-usage.md#Selecting-a-Java-distribution
+          distribution: 'temurin'
+          java-version: '21'
       - name: Install wine
         # https://wiki.debian.org/Wine
         run: |
@@ -65,15 +71,29 @@ jobs:
       - name: Install build deps
         run: |
           apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
+      # We are just cloning the esigner repo instead of calling their github
+      # action directly https://github.com/SSLcom/esigner-codesign
+      - name: Get ssl.com esigner zip file and unzip
+        run: |
+          mkdir products/jbrowse-desktop/code_signer
+          cd products/jbrowse-desktop/code_signer
+          wget  https://www.ssl.com/download/codesigntool-for-linux-and-macos -O out.zip
+          unzip out.zip
+          chmod +x CodeSignTool.sh
+          cd ../../../
+
       - name: Build app
         env:
-          WIN_CSC_LINK: ${{ secrets.WIN_CSC_LINK }}
-          WIN_CSC_KEY_PASSWORD: ${{ secrets.WIN_CSC_KEY_PASSWORD }}
+          WINDOWS_SIGN_USER_NAME: ${{ secrets.WINDOWS_SIGN_USER_NAME }}
+          WINDOWS_SIGN_USER_PASSWORD: ${{ secrets.WINDOWS_SIGN_USER_PASSWORD }}
+          WINDOWS_SIGN_CREDENTIAL_ID: ${{ secrets.WINDOWS_SIGN_CREDENTIAL_ID }}
+          WINDOWS_SIGN_USER_TOTP: ${{ secrets.WINDOWS_SIGN_USER_TOTP }}
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           chown --recursive root:root /github/home
           yarn build-electron:win --publish always
         working-directory: products/jbrowse-desktop
+
   buildmac:
     needs: createrelease
     name: Build Mac desktop app

CHANGELOG.md

@@ -1,3 +1,50 @@
+yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.4
+
+## 2.15.4 (2024-09-20)
+
+#### :bug: Bug Fix
+
+- Other
+  - [#4582](https://github.com/GMOD/jbrowse-components/pull/4582) Fix text
+    indexing on Windows ([@cmdcolin](https://github.com/cmdcolin))
+- `text-indexing`
+  - [#4580](https://github.com/GMOD/jbrowse-components/pull/4580) Fix indexing
+    plaintext gff/vcf on desktop ([@cmdcolin](https://github.com/cmdcolin))
+
+#### Committers: 1
+
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.22s.
+
+yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3
+
+Done in 0.57s.
+
+yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2
+
+## 2.15.2 (2024-09-18)
+
+#### :rocket: Enhancement
+
+- [#4573](https://github.com/GMOD/jbrowse-components/pull/4573) Add pif.gz
+  option to synteny import form ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :bug: Bug Fix
+
+- [#4571](https://github.com/GMOD/jbrowse-components/pull/4571) Fix code signing
+  on the windows for jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin))
+- [#4566](https://github.com/GMOD/jbrowse-components/pull/4566) Fix handling of
+  "." in VCF ALT field ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :house: Internal
+
+- [#4569](https://github.com/GMOD/jbrowse-components/pull/4569) Refactor GFF3
+  parser to avoid returning internal \_linehash variable
+  ([@cmdcolin](https://github.com/cmdcolin))
+
+#### Committers: 1
+
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s.
+
 yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.1
 
 ## 2.15.1 (2024-09-12)

PUBLISHING.md

@@ -93,16 +93,9 @@ mac, windows, and linux desktop builds) have been added to the release, click
 workflows will refuse to add them to the published release since it looks for
 draft releases)
 
-Once the draft release has been created (you can look for it
-[here](https://github.com/GMOD/jbrowse-components/releases)), go to the release
-and click "Edit," then add a description to the release. Usually you can copy
-the content of the blog post that was generated (it will be named something like
-`website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the "Downloads"
-section.
-
-Note also that I edit the .prettierrc.json file to change "proseWrap":"always"
-to "proseWrap":"never", format the blogpost, then copy to the github release,
-because they make markdown newlines into actual newlines in these release notes
+Then run `yarn --silent releasenotes|pbcopy` to get the release notes in a
+copy-and-pasteable way for the github release (it is slightly different than the
+blogpost format)
 
 ### Step 5. Update embedded demos
 
@@ -111,12 +104,9 @@ automated, but you can run each step and check that there aren't any errors
 
 ```bash
 cd embedded_demos
-export NODE_OPTIONS=--openssl-legacy-provider # needed to deploy the CRA4 demos
-export JB2TMP=~/jb2tmp # the embedded demo repos are cloned to this folder instead of the embedded_demos folder to avoid typescript and eslint complaining about ../ related weirdness
-./clone_demos.sh # clones embedded demo repos to local folder
-./update_demos.sh # runs yarn upgrade in each embedded demo to get latest jbrowse code
-./deploy_demos.sh # runs build and uploads to amazon s3 bucket
-./push_demos.sh # pushes updated yarn.locks to the github repos so consumers get same lock file
+export JB2TMP=~/jb2tmp
+./clone_demos.sh
+./update_all.sh
 ```
 
 Then you can manually check e.g. https://jbrowse.org/demos/lgv and see that the

eslint.config.mjs

@@ -61,6 +61,7 @@ export default tseslint.config(
   },
   {
     rules: {
+      'no-restricted-globals': ['error', 'Buffer'],
       'no-empty': 'off',
       'no-console': [
         'warn',
@@ -169,6 +170,7 @@ export default tseslint.config(
       'products/jbrowse-img/**/*',
       'products/jbrowse-web/scripts/*',
       'products/jbrowse-desktop/scripts/*',
+      'products/jbrowse-desktop/sign.js',
       'products/jbrowse-desktop/linux-sandbox-fix.js',
       'products/jbrowse-aws-lambda-functions/**/*.js',
       'plugins/data-management/scripts/*.js',
@@ -179,6 +181,7 @@ export default tseslint.config(
       },
     },
     rules: {
+      'no-restricted-globals': ['off'],
       '@typescript-eslint/no-require-imports': 'off',
       'no-console': 'off',
     },

lerna.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.15.1",
+  "version": "2.15.4",
   "npmClient": "yarn",
   "$schema": "node_modules/lerna/schemas/lerna-schema.json"
 }

package.json

@@ -23,7 +23,8 @@
     "prepare": "husky",
     "configdocs": "rm -rf website/docs/config && mkdir website/docs/config && yarn tsx docs/generateConfigDocs.ts",
     "statedocs": "rm -rf website/docs/models && mkdir website/docs/models && yarn tsx docs/generateStateModelDocs.ts",
-    "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website"
+    "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website",
+    "releasenotes": "npx prettier --prose-wrap never website/blog/$(ls -Art website/blog/ | tail -n 1)|sed -e '/## Downloads/,+7d'|tail -n +7"
   },
   "devDependencies": {
     "@babel/core": "^7.3.4",

packages/app-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "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": "^2.15.1",
+    "@jbrowse/product-core": "^2.15.4",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1",

packages/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",

packages/core/util/index.ts

@@ -1,6 +1,7 @@
 import React, { useEffect, useRef, useState } from 'react'
 import isObject from 'is-object'
 import PluginManager from '../PluginManager'
+import type { Buffer } from 'buffer'
 import {
   addDisposer,
   getParent,
@@ -1426,8 +1427,7 @@ export function gatherOverlaps(regions: BasicFeature[], w = 5000) {
 }
 
 export function stripAlpha(str: string) {
-  const c = colord(str)
-  return c.alpha(1).toHex()
+  return colord(str).alpha(1).toHex()
 }
 
 export function getStrokeProps(str: string) {

packages/embedded-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/embedded-core",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "description": "JBrowse 2 code shared between embedded products",
   "keywords": [
     "jbrowse",
@@ -42,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.15.1",
-    "@jbrowse/product-core": "^2.15.1",
+    "@jbrowse/core": "^2.15.4",
+    "@jbrowse/product-core": "^2.15.4",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1",

packages/product-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "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": "^2.15.1",
+    "@jbrowse/core": "^2.15.4",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1",

packages/sv-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/sv-core",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "description": "JBrowse 2 code shared between sv type code",
   "keywords": [
     "jbrowse",
@@ -41,9 +41,9 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
+    "@jbrowse/plugin-linear-genome-view": "^2.15.4",
     "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.0.0"
+    "@mui/material": "^6.0.0"
   },
   "peerDependencies": {
     "mobx": "^6.0.0",

packages/text-indexing/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.15.1",
+    "@jbrowse/core": "^2.15.4",
     "ixixx": "^2.0.1",
     "node-fetch": "^2.6.0",
     "sanitize-filename": "^1.6.3"

packages/text-indexing/src/TextIndexing.ts

@@ -215,7 +215,22 @@ async function* indexFiles({
       indexingAttributes: attributesToIndex = idx1,
     } = textSearching || {}
     let myTotalBytes: number | undefined
-    if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
+    if (type === 'Gff3Adapter') {
+      yield* indexGff3({
+        config: track,
+        attributesToIndex,
+        inLocation: getLoc('gffLocation', track),
+        outDir,
+        featureTypesToExclude,
+        onStart: totalBytes => {
+          myTotalBytes = totalBytes
+        },
+        onUpdate: progressBytes => {
+          statusCallback(`${progressBytes}/${myTotalBytes}`)
+        },
+      })
+    }
+    if (type === 'Gff3TabixAdapter') {
       yield* indexGff3({
         config: track,
         attributesToIndex,
@@ -229,7 +244,20 @@ async function* indexFiles({
           statusCallback(`${progressBytes}/${myTotalBytes}`)
         },
       })
-    } else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
+    } else if (type === 'VcfAdapter') {
+      yield* indexVcf({
+        config: track,
+        attributesToIndex,
+        inLocation: getLoc('vcfLocation', track),
+        outDir,
+        onStart: totalBytes => {
+          myTotalBytes = totalBytes
+        },
+        onUpdate: progressBytes => {
+          statusCallback(`${progressBytes}/${myTotalBytes}`)
+        },
+      })
+    } else if (type === 'VcfTabixAdapter') {
       yield* indexVcf({
         config: track,
         attributesToIndex,
@@ -252,7 +280,9 @@ function getLoc(attr: string, config: Track) {
     | { uri: string; localPath: string }
     | undefined
   if (!elt) {
-    throw new Error('none')
+    throw new Error(
+      `can't get find ${attr} from ${config.adapter} for text indexing`,
+    )
   }
   return elt.uri || elt.localPath
 }

packages/web-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/web-core",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "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": "^2.15.1",
-    "@jbrowse/product-core": "^2.15.1",
+    "@jbrowse/app-core": "^2.15.4",
+    "@jbrowse/product-core": "^2.15.4",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "clone": "^2.0.0",

plugins/alignments/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   "dependencies": {
     "@gmod/bam": "^2.0.0",
     "@gmod/cram": "^3.0.3",
-    "@jbrowse/sv-core": "^2.15.1",
+    "@jbrowse/sv-core": "^2.15.4",
     "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",

plugins/alignments/src/MismatchParser/index.ts

@@ -1,4 +1,5 @@
 import { revcom, Feature } from '@jbrowse/core/util'
+import type { Buffer } from 'buffer'
 import { getTagAlt } from '../util'
 
 export interface Mismatch {

plugins/arc/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "2.15.1",
+  "version": "2.15.4",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",