Restructure package to repo root for devtools::install_github compati…

.Rbuildignore

@@ -0,0 +1,7 @@
+^\.github$
+^data-raw$
+^environment\.yml$
+^\.git$
+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$

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

@@ -0,0 +1,49 @@
+on:
+  push:
+    branches: [main, master, restructure]
+  pull_request:
+    branches: [main, master, restructure]
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel'}
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"warning"'
+          upload-snapshots: true

.github/workflows/release.yaml

@@ -0,0 +1,63 @@
+on:
+  push:
+    tags:
+      - 'v*'
+
+name: Release
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Check package
+        shell: Rscript {0}
+        run: |
+          rcmdcheck::rcmdcheck(
+            args     = c("--no-manual", "--as-cran"),
+            error_on = "warning"
+          )
+
+      - name: Build source tarball
+        run: R CMD build .
+
+      - name: Get package version and tarball name
+        id: pkg
+        run: |
+          VERSION=$(grep "^Version:" DESCRIPTION | sed 's/Version:[[:space:]]*//')
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+          echo "tarball=DeOPUS_${VERSION}.tar.gz" >> "$GITHUB_OUTPUT"
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: "DeOPUS ${{ steps.pkg.outputs.version }}"
+          body: |
+            ## DeOPUS ${{ steps.pkg.outputs.version }}
+
+            See [NEWS.md](https://github.com/tinnlab/DeOPUS/blob/main/NEWS.md) for a full list of changes.
+
+            ### Installation
+
+            ```r
+            devtools::install_github("tinnlab/DeOPUS@${{ github.ref_name }}")
+            ```
+          files: ${{ steps.pkg.outputs.tarball }}
+          fail_on_unmatched_files: true

.gitignore

@@ -1 +1,8 @@
 .DS_Store
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.Rproj
+/doc/
+/Meta/

DeOPUS/DESCRIPTION → DESCRIPTION

@@ -5,27 +5,28 @@ Version: 1.0.0
 Authors@R: c(
     person("Ha", "Nguyen", email = "hvn0006@wayne.edu", role = c("aut", "cre"))
     )
-Description: A reference-based cellular deconvolution method that employs 
-    hierarchical shrinkage transformation to robustly estimate cell-type 
-    proportions from bulk RNA sequencing data. DeOPUS applies a multi-level 
-    adaptive transformation combining local and global shrinkage priors, 
-    variance-stabilizing power transformation, and quantile normalization 
+Description: A reference-based cellular deconvolution method that employs
+    hierarchical shrinkage transformation to robustly estimate cell-type
+    proportions from bulk RNA sequencing data. DeOPUS applies a multi-level
+    adaptive transformation combining local and global shrinkage priors,
+    variance-stabilizing power transformation, and quantile normalization
     to minimize the influence of outliers and high-variance genes.
 License: MIT + file LICENSE
 Encoding: UTF-8
+Depends: R (>= 3.5.0)
 LazyData: true
-RoxygenNote: 7.2.3
+LazyDataCompression: xz
+RoxygenNote: 7.3.3
 Imports:
     Matrix,
-    dplyr,
     parallel,
     stats
 Suggests:
     testthat (>= 3.0.0),
     knitr,
     rmarkdown,
-    ggplot2,
-    tidyverse
+    ggplot2
 VignetteBuilder: knitr
-URL: https://github.com/tinnlab/DeOPUS/DeOPUS
+Config/testthat/edition: 3
+URL: https://github.com/tinnlab/DeOPUS
 BugReports: https://github.com/tinnlab/DeOPUS/issues