Update JRaviLab .github Repository

.Rbuildignore

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+^\.github$

.github/.gitignore

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+*.html

.github/CONTRIBUTING.md

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+# Contribution guide
+
+This outlines how to propose a change to this repo.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file.
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file.
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+- Fork the repository and clone onto your computer. If you haven't done this before, we recommend using `usethis`.
+
+- Install and load the `usethis` package with:
+
+  ```
+  install.packages("usethis")
+
+  library("usethis")
+  ```
+
+- If you are outside our group and the repo is public, please fork this repo using:
+
+  ```
+  usethis::create_from_github("JRaviLab/REPONAME", fork = TRUE)
+  ```
+- Install BiocManager from Bioconductor:
+
+  ```
+  if (!require("BiocManager", quietly = TRUE))
+      install.packages("BiocManager")
+  BiocManager::install(version = "3.19")
+  ```
+
+- If this repository is a package, install other development dependencies and then ensure that the package passes R CMD check using `devtools`:
+
+  ```
+  install.packages("devtools")
+
+  library("devtools")
+
+  devtools::install_dev_deps()
+
+  devtools::check()
+  ```
+
+  _If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing._
+
+- Create a Git branch for your pull request (PR). We recommend using:
+
+  ```
+  usethis::pr_init("brief-description-of-change")
+  ```
+
+- Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+  The title of your PR should briefly describe the change.
+  The body of your PR should contain `Fixes #issue-number`.
+
+### Code style
+
+- New code should follow the tidyverse [style guide](https://style.tidyverse.org).
+  You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
+- Lint Your Code: Ensure your code adheres to our style guidelines by using [lintr](https://lintr.r-lib.org/):
+
+  ```
+  install.packages("lintr")
+
+  library("lintr")
+
+  lintr::lint("path/to/your/file.R")
+  ```
+
+- We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for package documentation.
+
+- We use [testthat](https://cran.r-project.org/package=testthat) for unit tests.
+  Contributions with test cases included are easier to accept.
+
+## Code of Conduct
+
+Please note that the this project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: "\U0001F41E[BUG]"
+labels: bug
+assignees: jananiravi
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Use code '...' (or add hyperlink)
+2. Click on '...'
+3. Scroll down to '...'
+4. See error/issue
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+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]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g., iPhone16]
+ - OS: [e.g., iOS8.1]
+ - Browser [e.g., stock browser, safari]
+ - Version [e.g., 22]
+
+**Additional context**
+Please add any other context about the problem here, along with screenshots, code snippets, possible fixes, and relevant information to help troubleshoot.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: "\U0001F195 [FEAT]"
+labels: enhancement
+assignees: jananiravi
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. E.g., I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen and how you envision this. If you already have a solution, awesome 🙌 -- link to the branch/PR here.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/pull_request_template.md

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+<!-- _modified from [EmbeddedArtistry](https://embeddedartistry.com/blog/2017/08/04/a-github-pull-request-template-for-your-projects/)_
+_referenced with modifications from [pycytominer](https://github.com/cytomining/pycytominer/blob/master/.github/PULL_REQUEST_TEMPLATE.md)_ -->
+
+# Description
+
+<!--
+Thank you so much for your contribution to <NewPackage>!
+
+Please _succinctly_ summarize your proposed change.
+Namely, consider addressing the following questions:
+
+- What motivated you to open this pull request?
+- Were there any special adjustments you had to make to complete the work?
+- Are there any issues, which are related to this pull request (you may use a `#<digit>` to reference GitHub issues as links within this description)?
+
+GHA exist for linting and styling
+- https://github.com/r-lib/actions/blob/v2/examples/lint-project.yaml
+- https://github.com/r-lib/actions/blob/v2/examples/style.yaml
+-->
+
+## What kind of change(s) are included?
+
+- [ ] Feature (adds or updates new capabilities)
+- [ ] Bug fix (fixes an issue).
+- [ ] Enhancement (adds functionality).
+- [ ] Breaking change (these changes would cause existing functionality to not work as expected).
+
+# Checklist
+
+Please ensure that all boxes are checked before indicating that this pull request is ready for review.
+
+- [ ] I have read and followed the [CONTRIBUTING.md](CONTRIBUTING.md) guidelines.
+- [ ] I have searched for existing content to ensure this is not a duplicate. I have deduplicated my codebase.
+- [ ] I have performed a self-review of these additions (including spelling, grammar, and related).
+- [ ] I have implemented basic code linting, styling, and indentation (e.g., with lintr, styler).
+- [ ] I have added comments to my code to help provide understanding.
+- [ ] I have added a test which covers the code changes found within this PR.
+- [ ] I have added necessary data (or sample data) to test run these scripts.
+- [ ] **Reviewer assignment**: Tag a relevant team member to review and approve the changes.

.github/workflows/lint-project.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: lint-project.yaml
+
+permissions: read-all
+
+jobs:
+  lint-project:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install lintr
+        run: install.packages("lintr")
+        shell: Rscript {0}
+
+      - name: Lint root directory
+        run: lintr::lint_dir()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/style.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: style.yaml
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "**.[rR]"
+      - "**.[qrR]md"
+      - "**.[rR]markdown"
+      - "**.[rR]nw"
+      - "**.[rR]profile"
+
+  pull_request:
+    paths:
+      - "**.[rR]"
+      - "**.[qrR]md"
+      - "**.[rR]markdown"
+      - "**.[rR]nw"
+      - "**.[rR]profile"
+
+permissions: read-all
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref || github.ref_name }}
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install styler, biocthis, and roxygen2
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: styler, biocthis, roxygen2
+
+      - name: Enable styler cache
+        run: styler::cache_activate()
+        shell: Rscript {0}
+
+      - name: Determine cache location
+        id: styler-location
+        run: |
+          cat(
+            "location=",
+            styler::cache_info(format = "tabular")$location,
+            "\n",
+            file = Sys.getenv("GITHUB_OUTPUT"),
+            append = TRUE,
+            sep = ""
+          )
+        shell: Rscript {0}
+
+      - name: Cache styler
+        uses: actions/cache@v4
+        with:
+          path: ${{ steps.styler-location.outputs.location }}
+          key: ${{ runner.os }}-styler-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-styler-
+            ${{ runner.os }}-
+
+      - name: Style
+        run: styler::style_dir(transformers = biocthis::bioc_style())
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          FILES_TO_COMMIT=$(git diff --name-only | egrep -i '\.(r|[qr]md|rmarkdown|rnw|rprofile)$' || true)
+          if [ -n "$FILES_TO_COMMIT" ]; then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git add $FILES_TO_COMMIT
+            git commit -m "Style code (GHA)"
+            git push origin HEAD:${{ github.head_ref || github.ref_name }}
+          else
+            echo "No changes to commit."
+          fi