build: use renv to manage dependencies

.Rbuildignore

@@ -1,2 +1,10 @@
 ^.*\.Rproj$
+^HISTORY\.rst$
+^LICENSE\.md$
 ^\.Rproj\.user$
+^\.github$
+^\.pre-commit-config\.yaml$
+^codemeta\.json$
+^renv$
+^renv\.lock$
+^utilities$

.Rprofile

@@ -0,0 +1,7 @@
+rprofile <- file.path(Sys.getenv("HOME"), ".Rprofile")
+
+if (file.exists(rprofile) & interactive()) {
+    source(rprofile)
+}
+
+source("renv/activate.R")

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/create_github_release.yaml

@@ -0,0 +1,89 @@
+on:
+  push:
+    branches:
+      - devel
+      - RELEASE*
+
+name: Create Github Release
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  optimize_ci:
+      runs-on: ubuntu-latest
+      outputs:
+        skip: ${{ steps.check_skip.outputs.skip }}
+      steps:
+        - name: Optimize CI
+          id: check_skip
+          uses: withgraphite/graphite-ci-action@main
+          with:
+            graphite_token: ${{secrets.GRAPHITE_TOKEN}}
+  create-release:
+    runs-on: ubuntu-latest
+    needs: [optimize_ci]
+    if: needs.optimize_ci.outputs.skip == 'false'
+    permissions:
+      contents: write
+    outputs:
+      tag_version: ${{ steps.create_release.outputs.tag_version }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        with:
+          fetch-depth: 0
+      - name: Get most recent tag
+        id: get_tag
+        run: echo "TAG_VERSION=$(git describe --tags $(git rev-list --tags --max-count=1))" >> "$GITHUB_ENV"
+      - name: Create Release
+        id: create_release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          echo "Creating release for tag $TAG_VERSION"
+          gh release create $TAG_VERSION --title "Release $TAG_VERSION" --notes "Release $TAG_VERSION" --target ${{ github.ref }}
+          echo "tag_version=$TAG_VERSION" >> "$GITHUB_OUTPUT"
+  create_release_artifacts:
+    needs: [create-release]
+    permissions:
+      contents: write
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ['release', 'devel']
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      - name: Update system repositories
+        run: sudo apt-get update
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install -y libxml2-dev \
+          libssl-dev libcurl4-openssl-dev \
+          libharfbuzz-dev libfribidi-dev \
+          pandoc
+      - name: Setup R
+        uses: r-lib/actions/setup-r@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2.10.1
+        with:
+          r-version: ${{ matrix.r_version }}
+          use-public-rspm: true
+        id: r
+      - name: Install dependencies
+        uses: r-lib/actions/setup-renv@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2.10.1
+      - name: Build Package
+        run: R CMD build .
+      - name: Rename Package
+        run: echo "NEWNAME=$(./utilities/rename-package.R *.tar.gz)" >> "$GITHUB_ENV"
+      - name: debug
+        run: |
+          echo "R version: ${{ steps.r.outputs.installed-r-version }}"
+          echo "Current Tag: ${{ needs.create-release.outputs.tag_version }}"
+          echo "Release File Name: ${{ env.NEWNAME }}"
+      - name: Upload Release Artifact
+        env:
+          RELEASE_TAG: ${{ needs.create-release.outputs.tag_version }}
+          GH_TOKEN: ${{ github.token }}
+        run: gh release upload ${{ env.RELEASE_TAG }} ${{ env.NEWNAME }}

.github/workflows/rworkflows.yml

@@ -0,0 +1,68 @@
+name: Continuous Integration / R Workflows
+on:
+  workflow_dispatch:
+  push:
+    branches-ignore:
+    - master
+    - main
+    - RELEASE_**
+    - graphite-**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  optimize_ci:
+      runs-on: ubuntu-latest
+      outputs:
+        skip: ${{ steps.check_skip.outputs.skip }}
+      steps:
+        - name: Optimize CI
+          id: check_skip
+          uses: withgraphite/graphite-ci-action@main
+          with:
+            graphite_token: ${{secrets.GRAPHITE_TOKEN}}
+  rworkflows:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    needs: [optimize_ci]
+    if: needs.optimize_ci.outputs.skip == 'false'
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+        - os: windows-latest
+          bioc: devel
+          r: auto
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN:  ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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, devel]
+  pull_request:
+    branches: [main, master, devel]
+
+name: test-coverage
+
+jobs:
+  optimize_ci:
+      runs-on: ubuntu-latest
+      outputs:
+        skip: ${{ steps.check_skip.outputs.skip }}
+      steps:
+        - name: Optimize CI
+          id: check_skip
+          uses: withgraphite/graphite-ci-action@main
+          with:
+            graphite_token: ${{secrets.GRAPHITE_TOKEN}}
+  test-coverage:
+    runs-on: ubuntu-latest
+    needs: [optimize_ci]
+    if: needs.optimize_ci.outputs.skip == 'false'
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+
+      - uses: r-lib/actions/setup-r@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.lintr

@@ -0,0 +1,12 @@
+linters: linters_with_tags(
+    tags = c("default", "style", "misc", "potential-bug", "performance", "documentation", "risky", "package_development"),
+    line_length_linter(length = 80L),
+    indentation_linter(indent = 4L, hanging_indent_style = "never"),
+    undesirable_function_linter(modify_defaults(
+        defaults = default_undesirable_functions, library = NULL)),
+    object_usage_linter = NULL,
+    object_name_linter(styles = c("camelCase")))
+encoding: "UTF-8"
+exclusions: list(
+    "renv/activate.R",
+    "doc/")

.markdownlint.json

@@ -0,0 +1,16 @@
+{
+    "MD003": {
+        "style": "atx"
+    },
+    "MD007": {
+        "indent": 2
+    },
+    "MD013": false,
+    "MD024": false,
+    "MD033": false,
+    "MD041": false,
+    "MD036": false,
+    "default": true,
+    "no-hard-tabs": true,
+    "whitespace": false
+}

.markdownlintignore

@@ -0,0 +1,3 @@
+^LICENSE
+.github/**/*
+meta/LICENSE-HEADER