Merge pull request #13 from NICHD-BSPC/tests

- Added testthat tests
- Addressed comments from Bioconductor review

Author: mitraak

.Rbuildignore

@@ -10,3 +10,7 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^run-tests\.R$
+^application-map\.md$
+^carnation_application_note\.md$
+^testing*.md$

.github/workflows/bioccheck.yaml

@@ -0,0 +1,73 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+#
+# See https://github.com/r-lib/actions/tree/master/examples#readme for
+# additional example workflows available for the R community.
+
+name: bioccheck
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: git setup
+        # Set up git and export env vars to be used in later steps.
+        #   Note the unconventional mechanism for exporting envs by appending to
+        #   $GITHUB_ENV.
+        id: git-setup
+        run: |
+          git config --global user.email "action@github.com"
+          git config --global user.name "GitHub Action"
+          echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
+          echo "WORKDIR=$(pwd)" >> $GITHUB_ENV
+          echo "VERSION=$( cat DESCRIPTION | grep Version | awk '{print $2}')" >> $GITHUB_ENV
+
+      - name: install miniforge
+        run: |
+          wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+          bash Miniforge3.sh -b -p "${HOME}/conda"
+          rm Miniforge3.sh
+
+      - name: Run BiocCheck
+        run: |
+          source "${HOME}/conda/etc/profile.d/conda.sh"
+          conda config --add channels conda-forge
+          conda config --set channel_priority strict
+
+          # make the env one above WORKDIR
+          echo "  - bioconductor-bioccheck" >> requirements.yaml
+          conda env create -p ../env-bioccheck --file requirements.yaml
+          conda activate ../env-bioccheck
+
+          # create tmp dir for build and check
+          cd .. && mkdir bioccheck && cd bioccheck
+
+          Rscript -e "library(BiocCheck); BiocCheck('../carnation')"
+          tar cvzf bioccheck.tar.gz ../carnation.BiocCheck/
+          mv bioccheck.tar.gz ${WORKDIR}/bioccheck.tar.gz
+
+      - name: bioccheck log
+        uses: actions/upload-artifact@v4
+        with:
+          name: bioccheck-log
+          path: bioccheck.tar.gz
+
+
+

.github/workflows/conda.yml

@@ -10,7 +10,7 @@ name: conda
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "main", "devel" ]
   pull_request:
     types:
       - opened
@@ -45,15 +45,6 @@ jobs:
           bash Miniforge3.sh -b -p "${HOME}/conda"
           echo "^Miniforge3\.sh$" >> .Rbuildignore
 
-      - name: conda env pinned
-        run: |
-          source "${HOME}/conda/etc/profile.d/conda.sh"
-          conda config --add channels conda-forge
-          conda config --set channel_priority strict
-
-          # make env one above WORKDIR
-          conda env create -p ../env --file requirements-pinned.yaml
-
       - name: conda env unpinned
         run: |
           source "${HOME}/conda/etc/profile.d/conda.sh"
@@ -76,23 +67,40 @@ jobs:
       - name: Check, install & load library
         run: |
           source "${HOME}/conda/etc/profile.d/conda.sh"
-          conda activate ../env
+          conda activate ../env-unpinned
 
           # create tmp dir for build and check
           cd .. && mkdir tmp && cd tmp
 
           # build, check
-          R CMD build --no-build-vignettes --no-manual ../carnation
-          R CMD check --as-cran --no-manual --no-vignettes carnation_${VERSION}.tar.gz
+          time R CMD build --no-manual ../carnation
+          time R CMD check --no-manual --no-vignettes --timings --as-cran carnation_${VERSION}.tar.gz
 
           mv carnation_${VERSION}.tar.gz ${WORKDIR}/carnation.tar.gz
+          tar cvf rcmdcheck.tar.gz carnation.Rcheck
+          mv rcmdcheck.tar.gz ${WORKDIR}/rcmdcheck.tar.gz
 
       - name: env tarball
         uses: actions/upload-artifact@v4
         with:
           name: carnation-bundle
           path: carnation.tar.gz
 
+      - name: R CMD check log
+        uses: actions/upload-artifact@v4
+        with:
+          name: carnation-rcmdcheck
+          path: rcmdcheck.tar.gz
+
+      - name: conda env pinned
+        run: |
+          source "${HOME}/conda/etc/profile.d/conda.sh"
+          conda config --add channels conda-forge
+          conda config --set channel_priority strict
+
+          # make env one above WORKDIR
+          conda env create -p ../env --file requirements-pinned.yaml
+
       - name: remotes install
         run: |
           source "${HOME}/conda/etc/profile.d/conda.sh"
@@ -103,3 +111,5 @@ jobs:
 
 
 
+
+

.gitignore

@@ -1,2 +1,9 @@
+.DS_Store
 inst/doc
 docs
+debug*
+run_*.R
+test_*.R
+application*.md
+carnation_application_note.md
+testing*.md

DESCRIPTION

@@ -1,9 +1,13 @@
 Package: carnation
 Title: Shiny App to Explore RNA-Seq Analysis
-Version: 0.99.0
-Authors@R: 
-    person("Apratim", "Mitra", , "apratim.mitra@nih.gov", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3279-0054"))
+Version: 0.99.7
+Authors@R:
+    c(
+        person("Apratim", "Mitra", , "apratim.mitra@nih.gov",
+               role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3279-0054")),
+        person("Ryan", "Dale", , "ryan.dale@nih.gov",
+               role = c("fnd"), comment = c(ORCID = "0000-0003-2664-3744"))
+    )
 Description: Interactive Shiny dashboard app that can be used to
     explore RNA-Seq analysis results including differential expression (DE),
     functional enrichment and pattern analysis. Several visualizations
@@ -17,9 +21,9 @@ Description: Interactive Shiny dashboard app that can be used to
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
-    R (>= 4.3.0)
+    R (>= 4.6.0)
 Imports:
     BiocParallel,
     colorspace,
@@ -56,11 +60,17 @@ Imports:
     visNetwork,
     yaml
 Suggests:
+    airway,
+    BiocStyle,
     knitr,
-    rmarkdown
+    org.Hs.eg.db,
+    DEGreport,
+    rmarkdown,
+    testthat
 VignetteBuilder: knitr
 URL: https://nichd-bspc.github.io/carnation/
+BugReports: https://github.com/NICHD-BSPC/carnation/issues
 biocViews:
     GUI, GeneExpression, Software, ShinyApps, GO, Transcription,
     Transcriptomics, Visualization, DifferentialExpression,
-    Pathways
+    Pathways, GeneSetEnrichment

NAMESPACE

@@ -26,19 +26,18 @@ export(fuzzyPlotUI)
 export(genePlotServer)
 export(genePlotUI)
 export(get_access_path)
-export(get_common_path_from_list)
 export(get_config)
 export(get_degplot)
 export(get_gene_counts)
 export(get_project_name_from_path)
+export(get_upset_table)
 export(get_y_init)
 export(getcountplot)
 export(gs_radar)
 export(heatmapServer)
 export(heatmapUI)
 export(helpButtonServer)
 export(helpButtonUI)
-export(helpModal)
 export(horizonServer)
 export(horizonUI)
 export(in_admin_group)
@@ -49,6 +48,7 @@ export(loadDataUI)
 export(maPlotServer)
 export(maPlotUI)
 export(makeEnrichResult)
+export(make_example_carnation_object)
 export(make_final_object)
 export(metadataServer)
 export(metadataUI)
@@ -88,12 +88,15 @@ importFrom(ComplexUpset,intersection_size)
 importFrom(ComplexUpset,upset)
 importFrom(ComplexUpset,upset_modify_themes)
 importFrom(ComplexUpset,upset_query)
+importFrom(DESeq2,DESeq)
 importFrom(DESeq2,DESeqDataSetFromMatrix)
 importFrom(DESeq2,counts)
 importFrom(DESeq2,design)
 importFrom(DESeq2,estimateSizeFactors)
+importFrom(DESeq2,makeExampleDESeqDataSet)
 importFrom(DESeq2,normalizationFactors)
 importFrom(DESeq2,plotPCA)
+importFrom(DESeq2,results)
 importFrom(DESeq2,sizeFactors)
 importFrom(DESeq2,varianceStabilizingTransformation)
 importFrom(DT,DTOutput)

NEWS.md

@@ -0,0 +1,25 @@
+# carnation
+
+## v0.99.7
+
+- Add unit tests
+- Address Bioconductor review comments
+
+## v0.99.6
+
+- Made `R CMD check` more efficient by switching multiple module server
+  examples to `examplesIf interactive()`.
+
+## v0.99.3
+
+- removed `clusterProfiler` & `DEGreport` from Suggests
+- added examples to exported functions
+
+## v0.99.1
+
+- Updated vignette with carnation app screenshots
+- Added vignette dependencies to Suggests
+
+## v0.99.0
+
+- carnation submitted to bioconductor for review

R/access-functions.R

@@ -6,21 +6,24 @@
 #'
 #' @return path to access yaml
 #'
+#' @examples
+#' p <- get_access_path()
+#'
 #' @export
 get_access_path <- function(){
   if(Sys.getenv('CARNATION_ACCESS_YAML') != ''){
     path <- Sys.getenv('CARNATION_ACCESS_YAML')
     if(!dir.exists(path)){
       stop(
-        paste('Environment variable "CARNATION_ACCESS_YAML" exists',
-              'but specified location does not exist on disk:', path)
+        'Environment variable "CARNATION_ACCESS_YAML" exists',
+        'but specified location does not exist on disk:', path
       )
     }
   } else {
     path <- path.expand('~')
     message(
-      paste('Environment variable "CARNATION_ACCESS_YAML" not found.',
-            'Using default location to save access yaml:', path)
+      'Environment variable "CARNATION_ACCESS_YAML" not found.',
+      'Using default location to save access yaml:', path
     )
   }
   file.path(path, '.carnation-access.yaml')
@@ -38,6 +41,25 @@ get_access_path <- function(){
 #' @param u user name
 #' @param admin Admin user group
 #'
+#' @return list of user groups and data areas
+#'
+#' @examples
+#' # save access details to file
+#' home <- Sys.getenv('HOME')
+#'
+#' # create carnation data area if it doesn't exist
+#' carnation_home <- file.path(home, 'carnation/data')
+#' if(!dir.exists(carnation_home)) dir.create(carnation_home)
+#'
+#' create_access_yaml(user = 'admin',
+#'                    user_group = 'admin',
+#'                    data_area = carnation_home)
+#'
+#' # get current user access details
+#' al <- read_access_yaml()
+#'
+#' lst <- check_user_access(al, u='admin')
+#'
 #' @export
 check_user_access <- function(al, u, admin='admin'){