initial commit

.Rbuildignore

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+^renv$
+^renv\.lock$
+^LICENSE\.md$
+.github
+Dockerfile
+_pkgdown.yml
+^.*\.Rproj$
+^\.Rproj\.user$

.github/workflows/basic_checks.yaml

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+name: Check, build, and push image
+
+on: [push, pull_request]
+
+env:
+  cache-version: v1
+
+jobs:
+  r-build-and-check:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Query dependencies and update old packages
+        run: |
+          BiocManager::install(ask=FALSE)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v4
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-
+
+      - name: Install dependencies
+        run: |
+          BiocManager::repositories()
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Build pkgdown
+        run: |
+           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
+
+      # deploy needs rsync? Seems so.
+      - name: Install deploy dependencies
+        run: |
+          apt-get update
+          apt-get -y install rsync
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: docs # The folder the action should deploy.
+
+  docker-build-and-push:
+    #needs: r-build-and-check
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set Environment Variables
+        run: |
+          REPO_LOWER="$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')"
+          REGISTRY=ghcr.io
+          echo "BUILD_DATE=$(date +'%Y-%m-%d %H:%M:%S')" >> $GITHUB_ENV
+          echo "GIT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV
+          echo "REGISTRY=${REGISTRY}" >> $GITHUB_ENV
+          echo "IMAGE=${REGISTRY}/${REPO_LOWER}" >> $GITHUB_ENV
+
+      - name: Show environment
+        run: |
+          env
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3
+
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@v3
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: |
+            ${{ env.IMAGE }}:latest
+            ${{ env.IMAGE }}:${{ env.GIT_SHA }}

.gitignore

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+inst/doc
+*~
+.Rproj.user
+*Rproj
+renv/
+renv.lock
+.Rprofile
+docs/
+.DS_Store

DESCRIPTION

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+Package: iSEEtheTeam
+Title: Package demo for EuroBioC2024
+Version: 1.0.0
+Authors@R: 
+    c(person(given = "Kevin",
+             family = "Rue-Albrecht",
+             role = "aut",
+             email = "kevinrue67@gmail.com",
+             comment = c(ORCID = "0000-0003-3899-3872")),
+     person(given = "Federico",
+             family = "Marini",
+             role = c("aut", "cre"),
+             email = "marinif@uni-mainz.de",
+             comment = c(ORCID = "0000-0003-3252-7758")),
+      person(given = "Charlotte",
+             family = "Soneson",
+             role = "aut",
+             email = "charlottesoneson@gmail.com",
+             comment = c(ORCID = "0000-0003-3833-2169"))
+      )
+Description: This package provides the environment and materials for the
+    package demo at the European Bioconductor Meeting 2024.
+    The environment includes the iSEE package and all its extensions
+    developed under the iSEE organisation.
+    The materials provide a brief overview of the core package functionality,
+    and a walkthrough of the development of an example extension package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Depends: 
+    Biobase
+Imports:
+    iSEE,
+    iSEEde,
+    iSEEhex,
+    iSEEhub,
+    iSEEindex,
+    iSEEpathways,
+    iSEEu,
+    shiny,
+    shinyWidgets
+Suggests:
+    airway,
+    BiocStyle,
+    DESeq2,
+    fgsea,
+    knitr,
+    org.Hs.eg.db,
+    pkgdown,
+    rmarkdown,
+    scRNAseq,
+    scater,
+    scuttle,
+    sessioninfo
+URL: https://isee.github.io/iSEEDemoEuroBioC2024/
+BugReports: https://github.com/iSEE/iSEEDemoEuroBioC2024/issues/new/choose
+VignetteBuilder: knitr
+DockerImage: ghcr.io/isee/iseedemoeurobioc2024:latest

Dockerfile

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+FROM bioconductor/bioconductor_docker:devel
+
+WORKDIR /home/rstudio
+
+COPY --chown=rstudio:rstudio . /home/rstudio/
+
+RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)"
+
+RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())"

LICENSE

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+YEAR: 2020
+COPYRIGHT HOLDER: Sean Davis

LICENSE.md

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+# MIT License
+
+Copyright (c) 2020 Sean Davis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(AaronLun)
+export(CharlotteSoneson)
+export(FedericoMarini)
+export(KevinRue)
+exportClasses(AaronLun)
+exportClasses(CharlotteSoneson)
+exportClasses(FedericoMarini)
+exportClasses(KevinRue)
+exportMethods(.defineOutput)
+exportMethods(.fullName)
+exportMethods(.panelColor)
+exportMethods(.refineParameters)
+exportMethods(.renderOutput)
+exportMethods(initialize)
+import(iSEE)
+import(methods)
+importClassesFrom(iSEE,Panel)
+importFrom(methods,callNextMethod)
+importFrom(shiny,imageOutput)
+importFrom(shiny,renderImage)
+importFrom(shiny,tagList)
+importFrom(shinyWidgets,addSpinner)

R/AaronLun.R

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+.photoFile <- "PhotoFile"
+
+collated <- character(0)
+collated[.photoFile] <- "character"
+
+#' @importClassesFrom iSEE Panel
+#' @export
+setClass("AaronLun", contains="Panel", slots=collated)
+
+#' Aaron Lun
+#' 
+#' @name AaronLun-class
+#' 
+#' @aliases 
+#' initialize,AaronLun-method
+#' .refineParameters,AaronLun-method
+#' .panelColor,AaronLun-method
+#' .fullName,AaronLun-method
+#' .defineOutput,AaronLun-method
+#' .renderOutput,AaronLun-method
+NULL
+
+#' Aaron Lun
+#' 
+#' @export
+#' @examples
+#' library(SummarizedExperiment)
+#' library(iSEE)
+#' 
+#' se <- SummarizedExperiment()
+#' 
+#' iSEE(se, initial = list(AaronLun()))
+AaronLun <- function(...) {
+    new("AaronLun", ...)
+}
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod("initialize", "AaronLun", function(.Object, ...) {
+    args <- list(...)
+
+    args <- .emptyDefault(args, .photoFile, system.file(package = "iSEEtheTeam", "images", "aaron-lun.png"))
+
+    do.call(callNextMethod, c(list(.Object), args))
+})
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod(".refineParameters", "AaronLun", function(x, se) {
+    x <- callNextMethod()
+
+    if (is.null(x)) {
+        return(NULL)
+    }
+
+    x
+})
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod(".panelColor", "AaronLun", function(x) {
+    "#dc3545"
+})
+
+#' @export
+setMethod(".fullName", "AaronLun", function(x) "Aaron Lun")
+
+#' @importFrom shiny imageOutput
+#' @importFrom shinyWidgets addSpinner
+#' @export
+setMethod(".defineOutput", "AaronLun", function(x) {
+    plot_name <- .getEncodedName(x)
+    addSpinner(
+        imageOutput(plot_name, height=paste0(slot(x, .organizationHeight), "px")),
+        color=.panelColor(x)
+    )
+})
+
+#' @export
+#' @importFrom shiny renderImage tagList
+setMethod(".renderOutput", "AaronLun", function(x, se, output, pObjects, rObjects) {
+    plot_name <- .getEncodedName(x)
+    force(se) # defensive programming to avoid difficult bugs due to delayed evaluation.
+
+    # width  <- session$clientData[[paste0("output_", plot_name, "_width")]]
+    # height <- session$clientData[[paste0("output_", plot_name, "_height")]]
+
+    # nocov start
+    output[[plot_name]] <- renderImage({
+        list(src = x[[.photoFile]],
+            width = "100%",
+            # height = "100%",
+            alt = "Aaron Lun")
+    }, deleteFile = FALSE)
+    # nocov end
+
+    callNextMethod()
+})