Add TileDB

.Rbuildignore

@@ -15,3 +15,4 @@
 ^Dockerfile$
 ^Apptainer\.def$
 ^README\.Rmd$
+^README\.html$

.circleci/config.yml

@@ -11,10 +11,24 @@ commands:
               r-cran-devtools \
               r-bioc-rhdf5 \
               r-bioc-delayedarray \
+              r-cran-tiledb \
+              r-cran-jsonlite \
               pandoc
       - run:
           name: Install package dependencies
           command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
+      - run:
+          # TileDBArray is Bioconductor-only, so install_deps() cannot resolve
+          # it from CRAN. Without this the TileDB tests skip silently and the
+          # backend reads as covered when it is not.
+          name: Install TileDBArray (Bioconductor)
+          command: |
+            R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
+            R -e 'BiocManager::install("TileDBArray", ask = FALSE, update = FALSE)'
+      - run:
+          name: Verify optional TileDB stack is installed
+          command: |
+            R -q -e 'for (p in c("tiledb", "TileDBArray", "jsonlite")) if (!requireNamespace(p, quietly = TRUE)) stop("TileDB test dependency missing: ", p)'
 
 jobs:
   check_package:

.gitignore

@@ -143,6 +143,9 @@ ReadingMaterial/
 vignettes/*.html
 vignettes/*.pdf
 
+# knitted README (README.md is the committed artifact)
+/README.html
+
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 

Apptainer.def

@@ -1,5 +1,5 @@
 Bootstrap: docker
-From: rocker/r2u:jammy
+From: rocker/r2u:noble
 
 %help
     ModelArray - an R package for statistical analysis of fixel-wise data and beyond
@@ -12,10 +12,11 @@ From: rocker/r2u:jammy
     org.label-schema.schema-version "1.0"
 
 %environment
-    export DEBIAN_FRONTEND=noninteractive
+    export PATH="/opt/modelarrayio/bin:${PATH}"
 
 %post
     set -e
+    sed -i 's#https://cloud.r-project.org#https://cran.r-project.org#' /etc/apt/sources.list.d/cran.sources
     apt-get update \
         && apt-get install -y --no-install-recommends \
             r-bioc-delayedarray \
@@ -37,12 +38,20 @@ From: rocker/r2u:jammy
             r-cran-tibble \
             r-cran-tidyr \
             r-cran-tidyverse \
+            git \
+            python3-venv \
         && apt-get clean \
-        && echo 'options(bspm.sudo = TRUE)' >> /etc/R/Rprofile.site \
         && rm -rf /var/lib/apt/lists/*
 
+    R -e 'install.packages(c("jsonlite", "tiledb", "BiocManager"))'
+    R -e 'BiocManager::install("TileDBArray", ask = FALSE, update = FALSE)'
+    python3 -m venv /opt/modelarrayio
+    /opt/modelarrayio/bin/pip install --no-cache-dir git+https://github.com/PennLINC/ModelArrayIO.git
+
     cd /ModelArray
     R -e 'devtools::install()'
+    R -e 'library(ModelArray); stopifnot(requireNamespace("tiledb", quietly = TRUE)); stopifnot(requireNamespace("TileDBArray", quietly = TRUE))'
+    /opt/modelarrayio/bin/modelarrayio --version
 
 %files
     . /ModelArray
@@ -55,5 +64,3 @@ From: rocker/r2u:jammy
     else
         exec R
     fi
-
-

DESCRIPTION

@@ -42,12 +42,15 @@ Imports:
 RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 Suggests:
+    jsonlite,
     rmarkdown,
     knitr,
     testthat (>= 3.0.0),
     styler (>= 1.6.2),
     lintr,
-    stringr
+    stringr,
+    tiledb,
+    TileDBArray
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 URL: https://pennlinc.github.io/ModelArray, https://pennlinc.github.io/ModelArray/

Dockerfile

@@ -1,18 +1,53 @@
-FROM rocker/r2u:jammy
+FROM rocker/r2u:noble
 
 # Install tricky bioconductor packages and minimal LaTeX for PDF generation
-RUN apt update \
-        && apt install -y --no-install-recommends \
- 		 r-cran-devtools \
-         r-bioc-rhdf5 \
-         r-bioc-delayedarray
+RUN sed -i 's#https://cloud.r-project.org#https://cran.r-project.org#' /etc/apt/sources.list.d/cran.sources \
+        && apt-get update \
+        && apt-get install -y --no-install-recommends \
+            r-bioc-delayedarray \
+            r-bioc-hdf5array \
+            r-cran-broom \
+            r-cran-crayon \
+            r-cran-devtools \
+            r-cran-doparallel \
+            r-cran-dplyr \
+            r-cran-glue \
+            r-cran-gratia \
+            r-cran-hdf5r \
+            r-cran-hdf5r.extra \
+            r-cran-magrittr \
+            r-cran-mgcv \
+            r-cran-pbapply \
+            r-cran-pbmcapply \
+            r-bioc-rhdf5 \
+            r-cran-tibble \
+            r-cran-tidyr \
+            r-cran-tidyverse \
+            git \
+            python3-venv \
+        && apt-get clean \
+        && rm -rf /var/lib/apt/lists/*
+
+## Install optional TileDB backend dependencies for ModelArray
+RUN R -e 'install.packages(c("jsonlite", "tiledb", "BiocManager"))' \
+        && R -e 'BiocManager::install("TileDBArray", ask = FALSE, update = FALSE)'
+
+## Install ModelArrayIO (Python package and modelarrayio CLI)
+RUN python3 -m venv /opt/modelarrayio \
+        && /opt/modelarrayio/bin/pip install --no-cache-dir git+https://github.com/PennLINC/ModelArrayIO.git
+
+ENV PATH="/opt/modelarrayio/bin:${PATH}"
 
 
 ## Install ModelArray (R package)
 COPY . /ModelArray
 WORKDIR /ModelArray
 RUN R -e 'devtools::install()'
 
+## Verify the R and Python TileDB paths are available
+RUN R -e 'library(ModelArray); stopifnot(requireNamespace("tiledb", quietly = TRUE)); stopifnot(requireNamespace("TileDBArray", quietly = TRUE))' \
+        && /opt/modelarrayio/bin/modelarrayio --version
+
 ## Add metadata:
 ARG BUILD_DATE
 ARG VCS_REF
@@ -30,4 +65,4 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
         # but someone says it is "git branch name"?? ref: https://guide.opencord.org/cord-5.0/build_images.html
       org.label-schema.schema-version="1.0"
 # ^^these information can be viewed by:
-    # docker inspect pennlinc/modelarray_confixel:<docker_tag>
+    # docker inspect pennlinc/modelarray_confixel:<docker_tag>

NAMESPACE

@@ -1,8 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,ModelArraySummary)
 S3method(print,h5summary)
 export("%>%")
 export(ModelArray)
+export(ModelArraySummary)
 export(ModelArray.gam)
 export(ModelArray.lm)
 export(ModelArray.wrap)

R/ModelArray-package.R

@@ -3,12 +3,13 @@
 #' @description
 #' The ModelArray package provides an S4 class and associated methods for
 #' performing massively univariate statistical analyses on element-wise
-#' (fixel, voxel, or vertex) neuroimaging data stored in HDF5 files.
+#' (fixel, voxel, or vertex) neuroimaging data stored in HDF5 files or
+#' TileDB stores.
 #'
 #' @details
 #' The core workflow is:
 #' \enumerate{
-#'   \item Inspect an HDF5 file with \code{\link{h5summary}()}
+#'   \item Inspect storage with \code{\link{ModelArraySummary}()}
 #'   \item Load data with \code{\link{ModelArray}()}
 #'   \item Fit models with \code{\link{ModelArray.lm}},
 #'     \code{\link{ModelArray.gam}}, or \code{\link{ModelArray.wrap}}
@@ -28,7 +29,7 @@
 #' \linkS4class{ModelArray}, \code{\link{ModelArray}},
 #' \code{\link{ModelArray.lm}}, \code{\link{ModelArray.gam}},
 #' \code{\link{ModelArray.wrap}}, \code{\link{mergeModelArrays}},
-#' \code{\link{h5summary}}
+#' \code{\link{ModelArraySummary}}
 #'
 #' @section Centralized imports:
 #' The following imports are consolidated here because they cannot be