Update deps

LICENSE.md

@@ -1,8 +1,6 @@
-Apache License
-==============
+# Apache License
 
-_Version 2.0, January 2004_
-_&lt;<http://www.apache.org/licenses/>&gt;_
+_Version 2.0, January 2004_ _&lt;<http://www.apache.org/licenses/>&gt;_
 
 ### Terms and Conditions for use, reproduction, and distribution
 
@@ -16,10 +14,10 @@ owner that is granting the License.
 
 “Legal Entity” shall mean the union of the acting entity and all other entities
 that control, are controlled by, or are under common control with that entity.
-For the purposes of this definition, “control” means **(i)** the power, direct or
-indirect, to cause the direction or management of such entity, whether by
-contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of the
-outstanding shares, or **(iii)** beneficial ownership of such entity.
+For the purposes of this definition, “control” means **(i)** the power, direct
+or indirect, to cause the direction or management of such entity, whether by
+contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of
+the outstanding shares, or **(iii)** beneficial ownership of such entity.
 
 “You” (or “Your”) shall mean an individual or Legal Entity exercising
 permissions granted by this License.
@@ -89,27 +87,27 @@ You may reproduce and distribute copies of the Work or Derivative Works thereof
 in any medium, with or without modifications, and in Source or Object form,
 provided that You meet the following conditions:
 
-* **(a)** You must give any other recipients of the Work or Derivative Works a copy of
-this License; and
-* **(b)** You must cause any modified files to carry prominent notices stating that You
-changed the files; and
-* **(c)** You must retain, in the Source form of any Derivative Works that You distribute,
-all copyright, patent, trademark, and attribution notices from the Source form
-of the Work, excluding those notices that do not pertain to any part of the
-Derivative Works; and
-* **(d)** If the Work includes a “NOTICE” text file as part of its distribution, then any
-Derivative Works that You distribute must include a readable copy of the
-attribution notices contained within such NOTICE file, excluding those notices
-that do not pertain to any part of the Derivative Works, in at least one of the
-following places: within a NOTICE text file distributed as part of the
-Derivative Works; within the Source form or documentation, if provided along
-with the Derivative Works; or, within a display generated by the Derivative
-Works, if and wherever such third-party notices normally appear. The contents of
-the NOTICE file are for informational purposes only and do not modify the
-License. You may add Your own attribution notices within Derivative Works that
-You distribute, alongside or as an addendum to the NOTICE text from the Work,
-provided that such additional attribution notices cannot be construed as
-modifying the License.
+- **(a)** You must give any other recipients of the Work or Derivative Works a
+  copy of this License; and
+- **(b)** You must cause any modified files to carry prominent notices stating
+  that You changed the files; and
+- **(c)** You must retain, in the Source form of any Derivative Works that You
+  distribute, all copyright, patent, trademark, and attribution notices from the
+  Source form of the Work, excluding those notices that do not pertain to any
+  part of the Derivative Works; and
+- **(d)** If the Work includes a “NOTICE” text file as part of its distribution,
+  then any Derivative Works that You distribute must include a readable copy of
+  the attribution notices contained within such NOTICE file, excluding those
+  notices that do not pertain to any part of the Derivative Works, in at least
+  one of the following places: within a NOTICE text file distributed as part of
+  the Derivative Works; within the Source form or documentation, if provided
+  along with the Derivative Works; or, within a display generated by the
+  Derivative Works, if and wherever such third-party notices normally appear.
+  The contents of the NOTICE file are for informational purposes only and do not
+  modify the License. You may add Your own attribution notices within Derivative
+  Works that You distribute, alongside or as an addendum to the NOTICE text from
+  the Work, provided that such additional attribution notices cannot be
+  construed as modifying the License.
 
 You may add Your own copyright statement to Your modifications and may provide
 additional or different license terms and conditions for use, reproduction, or

README.md

@@ -4,42 +4,43 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-
-
 # JBrowseR <img src='man/figures/logo.png' align="right" height="136" />
 
 <!-- badges: start -->
+
 [![R-CMD-check](https://github.com/GMOD/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/gmod/JBrowseR/actions)
 [![CRAN status](https://www.r-pkg.org/badges/version/JBrowseR)](https://CRAN.R-project.org/package=JBrowseR)
+
 <!-- badges: end -->
 
-JBrowseR is an R package that provides a simple and clean interface to [JBrowse 2](https://jbrowse.org/jb2/) for R users.
-Using JBrowseR, you can:
+JBrowseR is an R package that provides a simple and clean interface to
+[JBrowse 2](https://jbrowse.org/jb2/) for R users. Using JBrowseR, you can:
 
-- Embed the JBrowse 2 genome browser in **R Markdown** documents and **Shiny applications**
+- Embed the JBrowse 2 genome browser in **R Markdown** documents and **Shiny
+  applications**
 - Deploy a genome browser directly from the R console to view your data
 - Customize your genome browser to display your own data
 
-
 ## Installation
 
-You can install the released version of JBrowseR from [CRAN](https://CRAN.R-project.org) with:
+You can install the released version of JBrowseR from
+[CRAN](https://CRAN.R-project.org) with:
 
-``` r
+```r
 install.packages("JBrowseR")
 ```
 
 And the development version from [GitHub](https://github.com/) with:
 
-``` r
+```r
 # install.packages("devtools")
 devtools::install_github("gmod/JBrowseR")
 ```
+
 ## Example
 
 This line of code can be used to launch a genome browser from your R console:
 
-
 ```r
 library(JBrowseR)
 JBrowseR("ViewHg19", location = "10:29,838,737..29,838,819")
@@ -49,7 +50,8 @@ JBrowseR("ViewHg19", location = "10:29,838,737..29,838,819")
 
 ## Getting started
 
-In order to get started with JBrowseR, please refer to the vignette that best suits your needs:
+In order to get started with JBrowseR, please refer to the vignette that best
+suits your needs:
 
 - [Introduction](https://gmod.github.io/JBrowseR/articles/JBrowseR.html)
 - [Custom browser tutorial](https://gmod.github.io/JBrowseR/articles/custom-browser-tutorial.html)
@@ -58,49 +60,54 @@ In order to get started with JBrowseR, please refer to the vignette that best su
 
 ## Live demos
 
-
 ### Basic usage including text search index
 
 Allows you to search by gene name
 
 - Link demo: https://gmod.shinyapps.io/basic_usage_with_text_index
-- Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/basic_usage_with_text_index/app.R
+- Source code:
+  https://github.com/GMOD/JBrowseR/blob/main/example_apps/basic_usage_with_text_index/app.R
 
 ### Multi purpose demo app
 
-Shows a "bookmark" type feature, loading data from data frame, and buttons to navigate to genes of interest
+Shows a "bookmark" type feature, loading data from data frame, and buttons to
+navigate to genes of interest
 
 - Live link: https://gmod.shinyapps.io/bookmarks_demo
-- Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/bookmarks_demo/app.R
+- Source code:
+  https://github.com/GMOD/JBrowseR/blob/main/example_apps/bookmarks_demo/app.R
 
 ### Load config.json file
 
 Shows loading a config.json file
 
 - Live link: https://gmod.shinyapps.io/load_config_json
-- Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/load_config_json/app.R
+- Source code:
+  https://github.com/GMOD/JBrowseR/blob/main/example_apps/load_config_json/app.R
 
 ### Load data frame
 
 Simple example showing a data frame as a track
 
 - Live link: https://gmod.shinyapps.io/load_data_frame
-- Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/load_data_frame/app.R
+- Source code:
+  https://github.com/GMOD/JBrowseR/blob/main/example_apps/load_data_frame/app.R
 
 ### Gene fusion example
 
 Shows putative gene fusions in the SKBR3 breast cancer cell line
 
 - Live link: https://gmod.shinyapps.io/skbr3_gene_fusions
-- Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/skbr3_gene_fusions/app.R
+- Source code:
+  https://github.com/GMOD/JBrowseR/blob/main/example_apps/skbr3_gene_fusions/app.R
 
 ### Using plugins
 
 Uses the config.json loading method
 
 - Live link: not yet online
-- Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/using_plugins/app.R
-
+- Source code:
+  https://github.com/GMOD/JBrowseR/blob/main/example_apps/using_plugins/app.R
 
 ## Citation
 

package.json

@@ -5,27 +5,27 @@
     "lint": "eslint srcjs"
   },
   "dependencies": {
-    "@jbrowse/react-linear-genome-view": "^2.5.0",
+    "@jbrowse/react-linear-genome-view": "^2.10.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0"
   },
   "devDependencies": {
-    "@babel/core": "^7.22.1",
-    "@babel/preset-env": "^7.22.4",
+    "@babel/core": "^7.24.0",
+    "@babel/preset-env": "^7.24.0",
     "@babel/preset-react": "^7.22.3",
     "@babel/preset-typescript": "^7.23.0",
-    "@typescript-eslint/eslint-plugin": "^6.7.0",
-    "@typescript-eslint/parser": "^6.7.0",
+    "@typescript-eslint/eslint-plugin": "^7.1.0",
+    "@typescript-eslint/parser": "^7.1.0",
     "babel-loader": "^9.1.2",
-    "eslint": "^8.49.0",
+    "eslint": "^8.57.0",
     "eslint-plugin-react": "^7.33.2",
     "eslint-plugin-react-hooks": "^4.6.0",
     "eslint-plugin-react-refresh": "^0.4.3",
-    "eslint-plugin-unicorn": "^49.0.0",
+    "eslint-plugin-unicorn": "^51.0.1",
     "node-polyfill-webpack-plugin": "^3.0.0",
-    "prettier": "^3.0.3",
+    "prettier": "^3.2.5",
     "typescript": "^5.2.2",
-    "webpack": "^5.85.0",
+    "webpack": "^5.90.3",
     "webpack-cli": "^5.1.1"
   }
 }

srcjs/components/ViewHg38.tsx

@@ -87,7 +87,7 @@ const defaultSession = {
   },
 }
 
-export default function ViewHg38({location}:{location:string}) {
+export default function ViewHg38({ location }: { location: string }) {
   const state = createViewState({
     assembly,
     tracks,

tsconfig.json

@@ -14,5 +14,5 @@
     "strict": true,
     "noFallthroughCasesInSwitch": true
   },
-  "include": ["srcjs"],
+  "include": ["srcjs"]
 }