Add accessor functions, multi-h5 modeling

.circleci/config.yml

@@ -1,65 +1,112 @@
 version: 2
 
-steps: &steps
-  steps:
-    - checkout
-    - run:
-        name: Install libraries
-        command: |
-          apt update \
-          && apt install -y --no-install-recommends \
-            curl \
-            r-cran-devtools \
-            r-bioc-rhdf5 \
-            r-bioc-delayedarray \
-            pandoc \
-            texlive-latex-recommended \
-            texlive-fonts-recommended \
-            texlive-fonts-extra
-    - run:
-        name: Install package dependencies
-        command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
-    - run:
-        name: Check code style
-        command: |
-          R -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes"); if (!requireNamespace("styler", quietly = TRUE) || as.character(utils::packageVersion("styler")) != "1.11.0") remotes::install_version("styler", version = "1.11.0", upgrade = "never")'
-          R -e 'result <- styler::style_pkg(dry = "on", style = styler::tidyverse_style, strict = FALSE); if (!all(result[["changed"]] == FALSE)) { message("Code style check found files that would be reformatted. Run styler::style_pkg(style = styler::tidyverse_style) locally."); print(result[result[["changed"]], "file", drop = FALSE]) }'
-    - run:
-        name: Build package
-        command: R CMD build .
-    - run:
-        name: Check package
-        command: R CMD check *tar.gz
-    - run:
-        name: Calculate and upload code coverage
-        command: |
-          R -e 'if (!requireNamespace("covr", quietly = TRUE)) install.packages("covr")'
-          R -e 'cov <- covr::package_coverage(type = "tests"); covr::to_cobertura(cov, filename = "coverage.xml"); print(cov); cat(sprintf("Total coverage: %.2f%%\n", covr::percent_coverage(cov)))'
-          if command -v curl >/dev/null 2>&1; then
-            curl -Os https://uploader.codecov.io/latest/linux/codecov || echo "Codecov uploader download failed; continuing."
-          else
-            echo "curl not found; skipping Codecov upload."
-          fi
-          if [ -f codecov ]; then
-            chmod +x codecov
-            ./codecov -f coverage.xml -n "circleci-r-tests" || echo "Codecov upload failed; continuing."
-          else
-            echo "Codecov uploader not available; skipping upload."
-          fi
-
+setup_steps: &setup_steps
+  - checkout
+  - run:
+      name: Install libraries
+      command: |
+        apt update \
+        && apt install -y --no-install-recommends \
+          curl \
+          r-cran-devtools \
+          r-bioc-rhdf5 \
+          r-bioc-delayedarray \
+          pandoc \
+          texlive-latex-recommended \
+          texlive-fonts-recommended \
+          texlive-fonts-extra
+  - run:
+      name: Install package dependencies
+      command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
+  - run:
+      name: Check code style
+      command: |
+        R -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes"); if (!requireNamespace("styler", quietly = TRUE) || as.character(utils::packageVersion("styler")) != "1.11.0") remotes::install_version("styler", version = "1.11.0", upgrade = "never")'
+        R -e 'result <- styler::style_pkg(dry = "on", style = styler::tidyverse_style, strict = FALSE); if (!all(result[["changed"]] == FALSE)) { message("Code style check found files that would be reformatted. Run styler::style_pkg(style = styler::tidyverse_style) locally."); print(result[result[["changed"]], "file", drop = FALSE]) }'
+  - run:
+      name: Build package
+      command: R CMD build .
+  - persist_to_workspace:
+      root: .
+      paths:
+        - "*.tar.gz"
 
 jobs:
-  releaseJammy:
+  setup_and_build:
+    docker:
+      - image: rocker/r2u:jammy
+    steps: *setup_steps
+
+  check_package:
+    docker:
+      - image: rocker/r2u:jammy
+    steps:
+      - checkout
+      - run:
+          name: Install libraries
+          command: |
+            apt update \
+            && apt install -y --no-install-recommends \
+              curl \
+              r-cran-devtools \
+              r-bioc-rhdf5 \
+              r-bioc-delayedarray \
+              pandoc \
+              texlive-latex-recommended \
+              texlive-fonts-recommended \
+              texlive-fonts-extra
+      - run:
+          name: Install package dependencies
+          command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
+      - attach_workspace:
+          at: .
+      - run:
+          name: Check package
+          command: R CMD check *tar.gz
+
+  calculate_coverage:
     docker:
       - image: rocker/r2u:jammy
-    <<: *steps
+    steps:
+      - checkout
+      - run:
+          name: Install libraries
+          command: |
+            apt update \
+            && apt install -y --no-install-recommends \
+              curl \
+              r-cran-devtools \
+              r-bioc-rhdf5 \
+              r-bioc-delayedarray \
+              pandoc \
+              texlive-latex-recommended \
+              texlive-fonts-recommended \
+              texlive-fonts-extra
+      - run:
+          name: Install package dependencies
+          command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
+      - run:
+          name: Calculate and upload code coverage
+          command: |
+            R -e 'if (!requireNamespace("covr", quietly = TRUE)) install.packages("covr")'
+            R -e 'cov <- covr::package_coverage(type = "tests"); covr::to_cobertura(cov, filename = "coverage.xml"); print(cov); cat(sprintf("Total coverage: %.2f%%\\n", covr::percent_coverage(cov)))'
+            if command -v curl >/dev/null 2>&1; then
+              curl -Os https://uploader.codecov.io/latest/linux/codecov || echo "Codecov uploader download failed; continuing."
+            else
+              echo "curl not found; skipping Codecov upload."
+            fi
+            if [ -f codecov ]; then
+              chmod +x codecov
+              ./codecov -f coverage.xml -n "circleci-r-tests" || echo "Codecov upload failed; continuing."
+            else
+              echo "Codecov uploader not available; skipping upload."
+            fi
 
   build_and_deploy:
     environment:
       TZ: "/usr/share/zoneinfo/America/New_York"
     docker:
       - image: cimg/base:2020.09
-    # working_directory: tmp/src/modelarray_build    # the code will be check-ed out to here
     steps:
       - checkout
       - setup_remote_docker:
@@ -96,7 +143,7 @@ workflows:
   version: 2
   build_test_deploy:
     jobs:
-      - releaseJammy:
+      - setup_and_build:
           filters:
             branches:
               ignore:
@@ -105,16 +152,37 @@ workflows:
             tags:
               only: /.*/
 
-      - build_and_deploy:
+      - check_package:
           requires:
-            - releaseJammy
+            - setup_and_build
           filters:
             branches:
-              only: main
               ignore:
                 - gh-pages
                 - /^gh-pages.*/
-            tags:   # make sure any `git tag` triggers the run
+            tags:
               only: /.*/
 
+      - calculate_coverage:
+          requires:
+            - setup_and_build
+          filters:
+            branches:
+              ignore:
+                - gh-pages
+                - /^gh-pages.*/
+            tags:
+              only: /.*/
 
+      - build_and_deploy:
+          requires:
+            - check_package
+            - calculate_coverage
+          filters:
+            branches:
+              only: main
+              ignore:
+                - gh-pages
+                - /^gh-pages.*/
+            tags:
+              only: /.*/

DESCRIPTION

@@ -40,7 +40,7 @@ Imports:
     rlang,
     tibble,
     tidyr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests:
     rmarkdown,
     knitr,

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,h5summary)
 export("%>%")
 export(ModelArray)
 export(ModelArray.gam)
@@ -8,13 +9,28 @@ export(ModelArray.wrap)
 export(analyseOneElement.gam)
 export(analyseOneElement.lm)
 export(analyseOneElement.wrap)
+export(analysisNames)
+export(elementMetadata)
 export(exampleElementData)
 export(gen_gamFormula_contIx)
 export(gen_gamFormula_fxSmooth)
+export(h5summary)
+export(mergeModelArrays)
+export(nElements)
+export(nInputFiles)
 export(numElementsTotal)
+export(results)
+export(scalarNames)
+export(scalars)
+export(sources)
 export(writeResults)
+exportMethods(analysisNames)
+exportMethods(elementMetadata)
 exportMethods(exampleElementData)
+exportMethods(nElements)
+exportMethods(nInputFiles)
 exportMethods(results)
+exportMethods(scalarNames)
 exportMethods(scalars)
 exportMethods(show)
 exportMethods(sources)
@@ -26,6 +42,7 @@ import(mgcv)
 import(tibble)
 importClassesFrom(DelayedArray,DelayedArray)
 importFrom(DelayedArray,DelayedArray)
+importFrom(DelayedArray,acbind)
 importFrom(DelayedArray,realize)
 importFrom(HDF5Array,HDF5ArraySeed)
 importFrom(crayon,black)
@@ -51,3 +68,4 @@ importFrom(stats,lm)
 importFrom(stats,p.adjust)
 importFrom(stats,p.adjust.methods)
 importFrom(stats,terms)
+importFrom(utils,head)