Adding standard templates and GHA

.github/ISSUE_TEMPLATE

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+<!-- Inspiration from https://github.com/angular-translate/angular-translate/blob/master/.github/ISSUE_TEMPLATE.md --> 
+
+### Issue Description 
+Please provide a brief description of the issue here.
+
+### Inputs
+Please describe your experimental/sequencing strategy (e.g. pgPEN library and screening data, sequenced with an Illumina MiSeq, etc.)
+
+### Your environment
+Describe how you ran the pipeline (e.g. high-performance computing [HPC] cluster, linux/shell interface (Ubuntu, MacOS terminal, Windows powershell, etc.)
+
+### Steps to reproduce
+Please include relevant commands and steps taken. If your counts table was generated outside of the Berger Lab's pgPEN analysis workflow, please also describe the steps taken to pre-process your data. 
+
+### Pipeline behavior and error messages
+Please include relevant screenshots or codeblocks with any relevant error messages. If your code ran up to a certain point before encountering an error, please include this information as well.

.github/pull_request_template.md

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+<!-- From https://axolo.co/blog/p/part-3-github-pull-request-template--> 
+
+# Description
+
+<!-- Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change. --> 
+
+Fixes # (issue)
+
+## Type of change
+
+<!-- Please delete options that are not relevant. --> 
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+# How Has This Been Tested?
+
+<!-- Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration --> 
+
+- [ ] Test A
+- [ ] Test B
+
+# Checklist:
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published in downstream modules

.github/workflows/R-CMD-check.yaml

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+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Check testthat
+        if: runner.os != 'Windows'
+        id: check_check
+        run: |
+            error_num=$(Rscript --vanilla '.github/workflows/check_testthat.R')
+            echo "error_num=$error_num" >> $GITHUB_OUTPUT
+
+      - name: Stop if there are errors!
+        if: ${{ steps.check_check.outputs.error_num != '0' }}
+        run: exit 1
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/check_testthat.R

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+# Check up on the testthat results
+# C. Savonen
+# Nov 2023
+
+library(magrittr)
+
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+out_file <- list.files(pattern = "testthat.Rout$|Rout.fail$", file.path(root_dir, "check"),
+ recursive = TRUE, full.names = TRUE)
+
+check_content <- readLines(out_file)
+test_result <- grep("\\[ FAIL", check_content, value = TRUE)[1]
+test_result <- unlist(strsplit(test_result, "\\||\\[|\\]"))
+
+# Format the data into a dataframe
+test_result_df <- data.frame(result = trimws(test_result)) %>%
+  dplyr::filter(result != "") %>%
+  tidyr::separate(result, sep = " ", into = c("test_name", "num")) %>%
+  dplyr::mutate(num = as.numeric(num))
+
+fail_num <- test_result_df %>%
+  dplyr::filter(test_name %in% c("FAIL", "WARN")) %>%
+  dplyr::summarize(total = sum(num))
+
+fail_num <- as.character(fail_num$total)
+
+# Spit the number out
+writeLines(fail_num, con = stdout())

.github/workflows/pkgdown.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:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/style-code.yml

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+# Candace Savonen 2024
+
+name: Style Code
+
+on:
+  pull_request:
+    branches: [ main, staging ]
+
+jobs:
+
+  style-code:
+    name: Style code
+    runs-on: ubuntu-latest
+    container:
+      image: cansav09/gimap
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Login as jhudsl-robot
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
+
+      - name: Run styler
+        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+
+      - name: Commit styled files
+        run: |
+          git config --system --add safe.directory "$GITHUB_WORKSPACE"
+          git add \*.Rmd
+          git commit -m 'Style Rmds' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"