Testing CI of branches to merge into devel

.github/workflows/BiocCheck.yaml

@@ -0,0 +1,46 @@
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+
+name: BiocCheck.yaml
+
+permissions: read-all
+
+jobs:
+  BiocCheck:
+    runs-on: ubuntu-latest
+    name: BiocCheck
+
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v3
+
+      - name: Setup Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          http-user-agent: release
+          use-public-rspm: true
+
+      - name: Install Deps
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: always
+          # Remove pivlab/CLAMPData once CLAMPData is on Bioconductor;
+          # it will then be picked up automatically from DESCRIPTION.
+          extra-packages: |
+            bioc::BiocCheck
+            pivlab/CLAMPData
+
+      - name: Build tarball
+        run: R CMD build --no-manual .
+
+      - name: Run BiocCheck
+        run: |
+          tarball <- list.files(pattern = "^CLAMP_.*\\.tar\\.gz$")[1]
+          BiocCheck::BiocCheck(tarball, `quit-with-status` = TRUE)
+        shell: Rscript {0}

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

@@ -0,0 +1,58 @@
+# 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, devel]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install XQuartz (macOS)
+        if: runner.os == 'macOS'
+        run: brew install --cask xquartz
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: always
+          extra-packages: |
+            any::rcmdcheck
+            pivlab/CLAMPData
+          # Remove pivlab/CLAMPData once CLAMPData is on Bioconductor;
+          # it will then be picked up automatically from DESCRIPTION.
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,52 @@
+# 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: [bioconductor_submission]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+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@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          # Remove pivlab/CLAMPData once CLAMPData is on Bioconductor;
+          # it will then be picked up automatically from DESCRIPTION.
+          extra-packages: |
+            any::pkgdown
+            local::.
+            pivlab/CLAMPData
+          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@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

README.md

@@ -3,9 +3,8 @@
 <!-- badges: start -->
 [![GitHub issues](https://img.shields.io/github/issues/chikinalab/CLAMP)](https://github.com/chikinalab/CLAMP/issues)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![BiocCheck](https://github.com/chikinalab/CLAMP/actions/workflows/BiocCheck.yaml/badge.svg)](https://github.com/chikinalab/CLAMP/actions/workflows/BiocCheck.yaml)
+[![BiocCheck](https://github.com/mchikina/CLAMP/actions/workflows/BiocCheck.yaml/badge.svg)](https://github.com/chikinalab/CLAMP/actions/workflows/BiocCheck.yaml)
 [![R-CMD-check](https://github.com/chikinalab/CLAMP/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/chikinalab/CLAMP/actions/workflows/R-CMD-check.yaml)
-
 <!-- badges: end -->
 
 ## Bioconductor release status

src/Makevars

@@ -0,0 +1 @@
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -0,0 +1 @@
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

vignettes/comparing_clampbase_clampfull.Rmd

@@ -59,7 +59,6 @@ dataWholeBlood <- tscale(dataWholeBlood)
 # How to download pathway and cell marker libraries from Enrichr.
 # Not run during vignette build to avoid network calls; pre-fetched
 # .rds files are loaded in the next chunk instead.
-enrichr_url <- "https://maayanlab.cloud/Enrichr/geneSetLibrary"
 gmtList <- list(
     CellMarkers = getGMT(
         paste0(enrichr_url, "?mode=text&libraryName=CellMarker_2024"),
@@ -75,12 +74,8 @@ gmtList <- list(
 ```{r load-priors}
 # Load pre-fetched gene set libraries bundled with the package
 gmtList <- list(
-    CellMarkers = readRDS(
-        system.file("extdata", "CellMarker_2024.rds", package = "CLAMP")
-    ),
-    KEGG = readRDS(
-        system.file("extdata", "KEGG_2021_Human.rds", package = "CLAMP")
-    )
+  CellMarkers = readRDS(system.file("extdata", "CellMarker_2024.rds", package = "CLAMP")),
+  KEGG        = readRDS(system.file("extdata", "KEGG_2021_Human.rds", package = "CLAMP"))
 )
 
 # Combine into a single sparse matrix

vignettes/get_started.Rmd

@@ -475,36 +475,11 @@ alz_baseRes <- CLAMPbase(
 
 ## Prepare pathway priors
 
-```{r fbm-priors-download, eval=FALSE}
-# How to fetch the libraries; not run during vignette build.
-enrichr_url <- "https://maayanlab.cloud/Enrichr/geneSetLibrary"
-alz_gmtList <- list(
-    GTEx_Tissues = getGMT(
-        paste0(enrichr_url, "?mode=text&libraryName=GTEx_Tissues_V8_2023")
-    ),
-    BP = getGMT(
-        paste0(enrichr_url, "?mode=text&libraryName=GO_Biological_Process_2025")
-    ),
-    MSigDB = getGMT(
-        paste0(enrichr_url, "?mode=text&libraryName=MSigDB_Hallmark_2020")
-    )
-)
-```
-
 ```{r fbm-priors, message=FALSE}
 alz_gmtList <- list(
-    GTEx_Tissues = readRDS(
-        system.file("extdata", "GTEx_Tissues_V8_2023.rds", package = "CLAMP")
-    ),
-    BP = readRDS(
-        system.file(
-            "extdata", "GO_Biological_Process_2025.rds",
-            package = "CLAMP"
-        )
-    ),
-    MSigDB = readRDS(
-        system.file("extdata", "MSigDB_Hallmark_2020.rds", package = "CLAMP")
-    )
+    GTEx_Tissues = getGMT("https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=GTEx_Tissues_V8_2023"),
+    BP = getGMT("https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=GO_Biological_Process_2025"),
+    MSigDB = getGMT("https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=MSigDB_Hallmark_2020")
 )
 
 alz_pathMat <- gmtListToSparseMat(alz_gmtList)
@@ -628,39 +603,11 @@ islet_baseRes <- CLAMPbase(
 
 ## Prepare pathway priors
 
-```{r islet-priors-download, eval=FALSE}
-# How to fetch the libraries; not run during vignette build.
-enrichr_url <- "https://maayanlab.cloud/Enrichr/geneSetLibrary"
-islet_gmtList <- list(
-    GTEx_Tissues = getGMT(
-        paste0(enrichr_url, "?mode=text&libraryName=GTEx_Tissues_V8_2023")
-    ),
-    Diabetes_Perturbations = getGMT(
-        paste0(
-            enrichr_url,
-            "?mode=text&libraryName=Diabetes_Perturbations_GEO_2022"
-        )
-    ),
-    MSigDB_Hallmark = getGMT(
-        paste0(enrichr_url, "?mode=text&libraryName=MSigDB_Hallmark_2020")
-    )
-)
-```
-
 ```{r islet-priors, message=FALSE}
 islet_gmtList <- list(
-    GTEx_Tissues = readRDS(
-        system.file("extdata", "GTEx_Tissues_V8_2023.rds", package = "CLAMP")
-    ),
-    Diabetes_Perturbations = readRDS(
-        system.file(
-            "extdata", "Diabetes_Perturbations_GEO_2022.rds",
-            package = "CLAMP"
-        )
-    ),
-    MSigDB_Hallmark = readRDS(
-        system.file("extdata", "MSigDB_Hallmark_2020.rds", package = "CLAMP")
-    )
+    GTEx_Tissues = getGMT("https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=GTEx_Tissues_V8_2023"),
+    Diabetes_Perturbations = getGMT("https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=Diabetes_Perturbations_GEO_2022"),
+    MSigDB_Hallmark = getGMT("https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=MSigDB_Hallmark_2020")
 )
 
 islet_pathMat <- gmtListToSparseMat(islet_gmtList)