Add npm script to regenerate the package-lock.json (#21)

Adds a new npm script called `regen-package-lock` to the root
`package.json`. This script removes all `node_modules` and
`package-lock.json` files from the root and all workspaces, then
reinstalls dependencies and runs `npm audit:fix` to ensure a clean and
secure dependency tree.

Author: AlexJSully

.github/ISSUE_TEMPLATE/bug_report.md

@@ -22,16 +22,16 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
 
--   OS: [e.g. iOS]
--   Browser [e.g. chrome, safari]
--   Version [e.g. 22]
+- OS: [e.g. iOS]
+- Browser [e.g. chrome, safari]
+- Version [e.g. 22]
 
 **Smartphone (please complete the following information):**
 
--   Device: [e.g. iPhone6]
--   OS: [e.g. iOS8.1]
--   Browser [e.g. stock browser, safari]
--   Version [e.g. 22]
+- Device: [e.g. iPhone6]
+- OS: [e.g. iOS8.1]
+- Browser [e.g. stock browser, safari]
+- Version [e.g. 22]
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/security_report.md

@@ -22,16 +22,16 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
 
--   OS: [e.g. iOS]
--   Browser [e.g. chrome, safari]
--   Version [e.g. 22]
+- OS: [e.g. iOS]
+- Browser [e.g. chrome, safari]
+- Version [e.g. 22]
 
 **Smartphone (please complete the following information):**
 
--   Device: [e.g. iPhone6]
--   OS: [e.g. iOS8.1]
--   Browser [e.g. stock browser, safari]
--   Version [e.g. 22]
+- Device: [e.g. iPhone6]
+- OS: [e.g. iOS8.1]
+- Browser [e.g. stock browser, safari]
+- Version [e.g. 22]
 
 **Additional context**
 Add any other context about the problem here.

.github/workflows/code-qa.yml

@@ -1,16 +1,18 @@
 # This workflow will do a clean install of node dependencies, build the source code and run tests across different versions of node
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions
 
-name: Node.js CI
+name: Code Quality Assurance
 
 on:
     push:
         branches: [master]
     pull_request:
         branches: [master]
 
+permissions:
+    contents: read
 jobs:
-    build:
+    code-quality:
         runs-on: ubuntu-latest
 
         strategy:
@@ -20,7 +22,7 @@ jobs:
 
         steps:
             - name: Checkout repository
-              uses: actions/checkout@v4
+              uses: actions/checkout@v5
             - name: Use Node.js ${{ matrix.node-version }}
               uses: actions/setup-node@v4
               with:

.github/workflows/codeql-analysis.yml

@@ -13,27 +13,40 @@ name: "CodeQL"
 
 on:
     push:
-        branches: [master]
+        branches: ["master"]
     pull_request:
-        # The branches below must be a subset of the branches above
-        branches: [master]
+        branches: ["master"]
 
 jobs:
     analyze:
         name: Analyze
-        runs-on: ubuntu-latest
+        # Runner size impacts CodeQL analysis time. To learn more, please see:
+        #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+        #   - https://gh.io/supported-runners-and-hardware-resources
+        #   - https://gh.io/using-larger-runners
+        # Consider using larger runners for possible analysis time improvements.
+        runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+        timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+        permissions:
+            # required for all workflows
+            security-events: write
+
+            # only required for workflows in private repositories
+            actions: read
+            contents: read
 
         strategy:
             fail-fast: false
             matrix:
-                language: ["javascript"]
-                # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
-                # Learn more:
-                # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+                language: ["javascript-typescript", "actions"]
+                # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+                # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
+                # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+                # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 
         steps:
             - name: Checkout repository
-              uses: actions/checkout@v4
+              uses: actions/checkout@v5
 
             # Initializes the CodeQL tools for scanning.
             - name: Initialize CodeQL
@@ -43,23 +56,30 @@ jobs:
                   # If you wish to specify custom queries, you can do so here or in a config file.
                   # By default, queries listed here will override any specified in a config file.
                   # Prefix the list here with "+" to use these queries and those in the config file.
-                  # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
-            # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+                  # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+                  # queries: security-extended,security-and-quality
+
+            # This workflow runs CodeQL analysis on the codebase to find security vulnerabilities.
+            # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+            # queries: security-extended,security-and-quality
+
+            # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
             # If this step fails, then you should remove it and run the build manually (see below)
             - name: Autobuild
               uses: github/codeql-action/autobuild@v3
 
             # ℹ️ Command-line programs to run using the OS shell.
-            # 📚 https://git.io/JvXDl
+            # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
 
-            # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-            #    and modify them (or add more) to build your code if your project
-            #    uses a compiled language
+            #   If the Autobuild fails above, remove it and uncomment the following three lines.
+            #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
 
-            #- run: |
-            #   make bootstrap
-            #   make release
+            # - run: |
+            #     echo "Run, Build Application using script"
+            #     ./location_of_script_within_repo/buildscript.sh
 
             - name: Perform CodeQL Analysis
               uses: github/codeql-action/analyze@v3
+              with:
+                  category: "/language:${{matrix.language}}"

.github/workflows/ossar.yml

@@ -10,26 +10,26 @@ To see tags and releases, please go to [Tags](https://github.com/BioAnalyticReso
 
 Optimization:
 
--   Addressed client-side caching for faster loading
--   Improved performance of mouse hover listeners
--   Optimized images
+- Addressed client-side caching for faster loading
+- Improved performance of mouse hover listeners
+- Optimized images
 
 Update:
 
--   Added ESLint
--   No longer supporting Internet Explorer
--   Updated packages
+- Added ESLint
+- No longer supporting Internet Explorer
+- Updated packages
 
 Documentation:
 
--   Fixed links in markdown files
--   Updated README's examples
+- Fixed links in markdown files
+- Updated README's examples
 
 Bug fix:
 
--   Fixed `localStorage` failing to initialize and store/call data
--   Fixed issue where cannot call `generateSVG`
--   Fixed issue with favicons, now uses BAR's favicon over local (same for web manifest)
+- Fixed `localStorage` failing to initialize and store/call data
+- Fixed issue where cannot call `generateSVG`
+- Fixed issue with favicons, now uses BAR's favicon over local (same for web manifest)
 
 ## [1.0.19] - 2022-11-03
 

CHANGELOG.md

@@ -17,24 +17,24 @@ diverse, inclusive, and healthy community.
 Examples of behavior that contributes to a positive environment for our
 community include:
 
--   Demonstrating empathy and kindness toward other people
--   Being respectful of differing opinions, viewpoints, and experiences
--   Giving and gracefully accepting constructive feedback
--   Accepting responsibility and apologizing to those affected by our mistakes,
-    and learning from the experience
--   Focusing on what is best not just for us as individuals, but for the
-    overall community
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the
+  overall community
 
 Examples of unacceptable behavior include:
 
--   The use of sexualized language or imagery, and sexual attention or
-    advances of any kind
--   Trolling, insulting or derogatory comments, and personal or political attacks
--   Public or private harassment
--   Publishing others' private information, such as a physical or email
-    address, without their explicit permission
--   Other conduct which could reasonably be considered inappropriate in a
-    professional setting
+- The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Enforcement Responsibilities
 

CODE_OF_CONDUCT.md

@@ -21,19 +21,19 @@ In the interest of fostering an open and welcoming environment, we as contributo
 
 Examples of behavior that contributes to creating a positive environment include:
 
--   Using welcoming and inclusive language
--   Being respectful of differing viewpoints and experiences
--   Gracefully accepting constructive criticism
--   Focusing on what is best for the community
--   Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
--   The use of sexualized language or imagery and unwelcome sexual attention or advances
--   Trolling, insulting/derogatory comments, and personal or political attacks
--   Public or private harassment
--   Publishing others' private information, such as a physical or electronic address, without explicit permission
--   Other conduct which could reasonably be considered inappropriate in a professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
 
 ### Our Responsibilities
 

CONTRIBUTING.md

@@ -56,7 +56,7 @@ This will display the visualized and coloured tissue expression data within the
 
 We aim to make the ePlant Plant eFP as perfect as possible but unfortunately, there may be some unforeseen bugs. If you manage to find one that is not here, feel free to create a [bug report](https://github.com/BioAnalyticResource/ePlant_Plant_eFP/issues/new/choose) so we can fix it.
 
--   None at the moment... Help us find some!
+- None at the moment... Help us find some!
 
 ## Contributing
 
@@ -68,7 +68,7 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for more details.
 
 ## Authors
 
--   Alexander Sullivan - [GitHub](https://github.com/AlexJSully), [Twitter](https://twitter.com/alexjsully), [ORCiD](https://orcid.org/0000-0002-4463-4473), [LinkedIn](https://www.linkedin.com/in/alexanderjsullivan/), [Website](https://alexjsully.me/)
--   Asher Pasha - [Github](https://github.com/asherpasha), [Twitter](https://twitter.com/AsherPasha), [ORCiD](https://orcid.org/0000-0002-9315-0520)
--   Youyang Li - [Github](https://github.com/lyy321)
--   Nicholas J. Provart - [Github](https://github.com/BioAnalyticResource), [Twitter](https://twitter.com/BAR_PlantBio), [Website](https://bar.utoronto.ca)
+- Alexander Sullivan - [GitHub](https://github.com/AlexJSully), [Twitter](https://twitter.com/alexjsully), [ORCiD](https://orcid.org/0000-0002-4463-4473), [LinkedIn](https://www.linkedin.com/in/alexanderjsullivan/), [Website](https://alexjsully.me/)
+- Asher Pasha - [Github](https://github.com/asherpasha), [Twitter](https://twitter.com/AsherPasha), [ORCiD](https://orcid.org/0000-0002-9315-0520)
+- Youyang Li - [Github](https://github.com/lyy321)
+- Nicholas J. Provart - [Github](https://github.com/BioAnalyticResource), [Twitter](https://twitter.com/BAR_PlantBio), [Website](https://bar.utoronto.ca)