[r] Prepare package for CRAN

.github/workflows/check-standard-test.yaml

@@ -0,0 +1,105 @@
+name: R-CMD-check
+
+on:
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }}
+    timeout-minutes: 120
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      ENABLE_INSTALL_COUNTING: no
+      _R_CHECK_BUILD_VIGNETTES_: false
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install binary dependencies on ubuntu
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libhdf5-dev libhwy-dev
+          sudo apt-get isntall -y libhwy-dev || true
+
+      - name: Install binary dependencies on macOS
+        if: matrix.os == 'macos-latest' || matrix.os == 'macos-13'
+        shell: bash
+        run: |
+          brew update
+          brew install hdf5 pkg-config highway
+
+      - name: Configure compilation flags
+        shell: bash
+        run: |
+          cat <<'MAKEVARS' > "$GITHUB_WORKSPACE/Makevars.user"
+          MAKEFLAGS=--jobs=3
+          MAKEVARS
+          echo "R_MAKEVARS_USER=$GITHUB_WORKSPACE/Makevars.user" >> "$GITHUB_ENV"
+
+      - name: Install Highway on Windows (MSYS2 UCRT64)
+        if: matrix.os == 'windows-latest'
+        uses: msys2/setup-msys2@v2
+        with:
+          release: false
+          update: true
+          cache: true
+          install: >-
+            base-devel
+            git
+            mingw-w64-ucrt-x86_64-toolchain
+            mingw-w64-ucrt-x86_64-pkgconf
+            mingw-w64-ucrt-x86_64-highway
+          msystem: UCRT64
+          path-type: minimal
+
+      - name: Expose UCRT64 pkg-config to PATH (Windows)
+        if: matrix.os == 'windows-latest'
+        shell: bash
+        run: |
+          echo "C:/msys64/ucrt64/bin" >> $GITHUB_PATH
+          # Ensure pkg-config finds the .pc files for UCRT64
+          echo "PKG_CONFIG_PATH=C:/msys64/ucrt64/lib/pkgconfig" >> $GITHUB_ENV
+          echo "PKG_CONFIG=C:/msys64/ucrt64/bin/pkg-config.exe" >> $GITHUB_ENV
+
+      - name: Handle Windows big object files
+        if: matrix.os == 'windows-latest'
+        shell: bash
+        run: |
+          echo "CXXFLAGS += -Wa,-mbig-obj" >> "$GITHUB_WORKSPACE/Makevars.user"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          Ncpus: '3'
+          use-public-rspm: true
+          extra-repositories: |
+            https://bioconductor.org/packages/release/data/annotation
+            https://bpcells.github.io/drat
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            any::testthat
+            any::decor
+          working-directory: 'r'
+          needs: check
+      - name: Check package
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: r
+          build_args: c("--no-build-vignettes")
+          upload-snapshots: false
+          error-on: '"error"'
+
+

.github/workflows/deploy-docs.yml

@@ -18,6 +18,12 @@ jobs:
       run: bash -c 'echo -e "MAKEFLAGS=--jobs=3\nCXXFLAGS += -O1 -UNDEBUG" > "$GITHUB_WORKSPACE/Makevars.user" && echo "R_MAKEVARS_USER=$GITHUB_WORKSPACE/Makevars.user" >> "$GITHUB_ENV"'
     - name: Setup R
       uses: r-lib/actions/setup-r@v2
+      with:
+        Ncpus: '3'
+        use-public-rspm: true
+        extra-repositories: |
+            https://bioconductor.org/packages/release/data/annotation
+            https://bpcells.github.io/drat
     - name: Install R dependencies
       uses: r-lib/actions/setup-r-dependencies@v2
       with: 

.github/workflows/deploy-full-website.yml

@@ -16,6 +16,12 @@ jobs:
       run: bash -c 'echo -e "MAKEFLAGS=--jobs=3\nCXXFLAGS += -O1 -UNDEBUG" > "$GITHUB_WORKSPACE/Makevars.user" && echo "R_MAKEVARS_USER=$GITHUB_WORKSPACE/Makevars.user" >> "$GITHUB_ENV"'
     - name: Setup R
       uses: r-lib/actions/setup-r@v2
+      with:
+        Ncpus: '3'
+        use-public-rspm: true
+        extra-repositories: |
+            https://bioconductor.org/packages/release/data/annotation
+            https://bpcells.github.io/drat
     - name: Install R dependencies
       uses: r-lib/actions/setup-r-dependencies@v2
       with: 

.github/workflows/r-test.yml

@@ -38,6 +38,9 @@ jobs:
         with:
           Ncpus: '3'
           use-public-rspm: true
+          extra-repositories: |
+            https://bioconductor.org/packages/release/data/annotation
+            https://bpcells.github.io/drat
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache-version: 1

DESCRIPTION

@@ -2,5 +2,5 @@ Package: BPCells.installation.moved
 Title: Dummy package to provide new BPCells installation location
 Version: 0.0.0.9000
 Description: This package prints an error message upon attempted installation
-License: Apache-2.0 or MIT
+License: Apache License (== 2.0) | MIT + file LICENSE
 Encoding: UTF-8

python/docs/source/notebooks/fragment_basics.md

@@ -108,7 +108,7 @@ cluster_order = sorted(set(clusters))
 cell_groups_array = bpcells.experimental.build_cell_groups(fragments_bpcells_path, barcodes, clusters, cluster_order)
 
 # We could provide a dict or local file path, but URL is easier
-chrom_sizes = "http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes"
+chrom_sizes = "https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes"
 
 insertions_matrix_path = os.path.join(tmpdir.name, "bpcells_insertions_matrix")
 

python/tests/test_real_data.py

@@ -40,7 +40,7 @@ def test_500_pbmc_matrix(tmp_path, fetch_cached_file):
     peaks_path = fetch_cached_file("https://cf.10xgenomics.com/samples/cell-atac/2.0.0/atac_pbmc_500_nextgem/atac_pbmc_500_nextgem_peaks.bed")
     peak_matrix_path = fetch_cached_file("https://cf.10xgenomics.com/samples/cell-atac/2.0.0/atac_pbmc_500_nextgem/atac_pbmc_500_nextgem_raw_peak_bc_matrix.h5")
     barcode_metrics_path = fetch_cached_file("https://cf.10xgenomics.com/samples/cell-atac/2.0.0/atac_pbmc_500_nextgem/atac_pbmc_500_nextgem_singlecell.csv")
-    chrom_sizes_path = fetch_cached_file("http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes")
+    chrom_sizes_path = fetch_cached_file("https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes")
 
 
     # Convert BPCells fragments

r/.Rbuildignore

@@ -1,11 +1,18 @@
 ^_pkgdown\.yml$
+^compile_commands\.json$
+^index\.md$
 ^docs$
+^scripts$
+^data-raw$
 ^pkgdown$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^tools/highway$
 
 ^\.idea
+^\.cache$
 ^bench$
+^vignettes$
 
 .*\.o$
 .*\.so$
@@ -15,4 +22,6 @@
 build/$
 cmake-build-debug/
 \.vscode/
-\.snakemake/
+\.snakemake/
+
+^cran-comments\.md$

r/DESCRIPTION

@@ -1,31 +1,34 @@
 Package: BPCells
 Title: Single Cell Counts Matrices to PCA
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: c(
     person(given = "Benjamin",
            family = "Parks",
            role = c("aut", "cre", "cph"),
            email = "bparks@alumni.stanford.edu",
            comment = c(ORCID = "0000-0002-0261-7472")),
-    person("Immanuel", "Abdi", role = "aut"),
+    person("Immanuel", "Abdi", email = "immanuelazn@berkeley.edu", role = "aut"),
     person("Stanford University", role=c("cph", "fnd")),
     person("Genentech, Inc.", role=c("cph", "fnd")))
-Description: > Efficient operations for single cell ATAC-seq fragments and
+Description: Efficient operations for single cell ATAC-seq fragments and
     RNA counts matrices. Interoperable with standard file formats, and introduces
     efficient bit-packed formats that allow large storage savings and increased
     read speeds.
-License: Apache-2.0 or MIT
+License: Apache License (>= 2) | MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
-URL: https://bnprks.github.io/BPCells, https://github.com/bnprks/BPCells
+URL: https://bnprks.github.io/BPCells/, https://github.com/bnprks/BPCells
 LinkingTo: 
     Rcpp,
     RcppEigen
-Imports: 
+Imports:
     methods,
     grDevices,
+    graphics,
+    stats,
+    utils,
     magrittr,
     Matrix,
     Rcpp,
@@ -36,22 +39,48 @@ Imports:
     stringr,
     tibble,
     dplyr (>= 1.0.0),
-    tidyr,
     readr,
     ggplot2 (>= 3.4.0),
     scales,
     patchwork,
+    ragg,
+    purrr,
     scattermore,
     ggrepel,
-    RColorBrewer,
-    hexbin
+    RColorBrewer
 Suggests:
     IRanges,
+    tidyr,
+    hexbin,
     GenomicRanges,
+    GenomeInfoDb,
+    S4Vectors,
     matrixStats,
+    MatrixGenerics,
+    RSpectra,
     igraph,
     RcppHNSW,
-    RcppAnnoy
+    RcppAnnoy,
+    Seurat,
+    pkgdown,
+    devtools,
+    uwot,
+    irlba,
+    BiocManager,
+    BSgenome.Hsapiens.UCSC.hg38,
+    TFMPvalue (>= 0.0.5),
+    motifmatchr,
+    chromVARmotifs,
+    png,
+    testthat (>= 3.0.0)
+Additional_repositories: 
+    https://bioconductor.org/packages/release/data/annotation,
+    https://bpcells.github.io/drat
 Depends: 
     R (>= 4.0.0)
-Config/Needs/website: pkgdown, devtools, uwot, irlba, RcppHNSW, igraph, BiocManager, bioc::BSgenome.Hsapiens.UCSC.hg38, github::GreenleafLab/motifmatchr, github::GreenleafLab/chromVARmotifs, png, magrittr
+SystemRequirements: C++17,
+    HDF5 (>= 1.10) [optional; detected via pkg-config 'hdf5' or 'h5cc'; 
+        else set HDF5_CFLAGS/HDF5_LIBS],
+    Highway (>= 1.0.5) [optional; detected via pkg-config 'libhwy'/'hwy'; 
+        falls back to vendored build if not found]
+Config/Needs/website: pkgdown, devtools, uwot, irlba, RcppHNSW, igraph, BiocManager, bioc::BSgenome.Hsapiens.UCSC.hg38, github::GreenleafLab/motifmatchr, github::GreenleafLab/chromVARmotifs, png

r/LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2025
+COPYRIGHT HOLDER: BPCells contributors

r/NAMESPACE

@@ -27,15 +27,12 @@ export(cluster_graph_louvain)
 export(cluster_graph_seurat)
 export(colMaxs)
 export(colMaxs.IterableMatrix)
-export(colMaxs.default)
 export(colMeans)
 export(colQuantiles)
 export(colQuantiles.IterableMatrix)
-export(colQuantiles.default)
 export(colSums)
 export(colVars)
 export(colVars.IterableMatrix)
-export(colVars.default)
 export(collect_features)
 export(continuous_palette)
 export(convert_matrix_type)
@@ -92,6 +89,7 @@ export(plot_tss_scatter)
 export(prefix_cell_names)
 export(pseudobulk_matrix)
 export(qc_scATAC)
+export(ragg_wrap)
 export(range_distance_to_nearest)
 export(read_bed)
 export(read_encode_blacklist)
@@ -104,15 +102,13 @@ export(remove_demo_data)
 export(rotate_x_labels)
 export(rowMaxs)
 export(rowMaxs.IterableMatrix)
-export(rowMaxs.default)
 export(rowMeans)
 export(rowQuantiles)
 export(rowQuantiles.IterableMatrix)
-export(rowQuantiles.default)
 export(rowSums)
 export(rowVars)
 export(rowVars.IterableMatrix)
-export(rowVars.default)
+export(scale_next_plot_height)
 export(sctransform_pearson)
 export(select_cells)
 export(select_chromosomes)
@@ -144,6 +140,7 @@ export(write_matrix_anndata_hdf5_dense)
 export(write_matrix_dir)
 export(write_matrix_hdf5)
 export(write_matrix_memory)
+exportMethods("dimnames<-")
 exportMethods(as.data.frame)
 exportMethods(as.matrix)
 exportMethods(t)
@@ -154,6 +151,9 @@ importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
 importFrom(Matrix,t)
 importFrom(Rcpp,sourceCpp)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,theme)
+importFrom(graphics,text)
 importFrom(magrittr,"%>%")
 importFrom(methods,.hasSlot)
 importFrom(methods,Arith)
@@ -162,6 +162,7 @@ importFrom(methods,Math)
 importFrom(methods,Math2)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
+importFrom(methods,canCoerce)
 importFrom(methods,cbind2)
 importFrom(methods,is)
 importFrom(methods,new)
@@ -171,6 +172,19 @@ importFrom(methods,setClass)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,show)
+importFrom(ragg,agg_png)
+importFrom(stats,as.formula)
+importFrom(stats,end)
+importFrom(stats,model.matrix)
+importFrom(stats,p.adjust)
+importFrom(stats,ppois)
+importFrom(stats,qpois)
+importFrom(stats,quantile)
+importFrom(stats,start)
+importFrom(utils,download.file)
+importFrom(utils,head)
+importFrom(utils,tail)
+importFrom(utils,untar)
 importMethodsFrom(Matrix,colMeans)
 importMethodsFrom(Matrix,colSums)
 importMethodsFrom(Matrix,rowMeans)