Merge branch 'bschilder_dev'

.Rbuildignore

@@ -1,4 +1,16 @@
-^.*\.Rproj$
+.*\.Rproj$
 ^\.Rproj\.user$
-README.Rmd
-magma.log
+^README.Rmd
+^\.github$
+^doc$
+^Meta$
+^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+
+magma.log
+Dockerfile
+^LICENSE\.md$
+inst/hex/
+MAGMA.Celltyping/inst/hex

.github/workflows/check-bioc-docker.yml

@@ -0,0 +1,336 @@
+## Read more about GitHub actions the features of this GitHub Actions workflow
+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
+##
+## For more details, check the biocthis developer notes vignette at
+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
+##
+## You can add this workflow to other packages using:
+## > biocthis::use_bioc_github_action()
+##
+## Using GitHub Actions exposes you to many details about how R packages are
+## compiled and installed in several operating system.s
+### If you need help, please follow the steps listed at
+## https://github.com/r-lib/actions#where-to-find-help
+##
+## If you found an issue specific to biocthis's GHA workflow, please report it
+## with the information that will make it easier for others to help you.
+## Thank you!
+
+## Acronyms:
+## * GHA: GitHub Action
+## * OS: operating system
+
+on:
+  push:
+  pull_request:
+
+name: R-CMD-check-bioc
+
+## These environment variables control whether to run GHA code later on that is
+## specific to testthat, covr, and pkgdown.
+##
+## If you need to clear the cache of packages, update the number inside
+## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
+## Note that you can always run a GHA test without the cache by using the word
+## "/nocache" in the commit message.
+env:
+  run_bioccheck: 'false'
+  has_testthat: 'true'
+  run_covr: 'true'
+  run_pkgdown: 'true'
+  has_RUnit: 'false'
+  cache-version: 'cache-v1'
+  run_docker: 'false'
+
+jobs:
+  build-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    ## Environment variables unique to this job.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: 'latest', bioc: 'release', cont: "bioconductor/bioconductor_docker:latest", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/release"}
+          - { os: macOS-latest, r: 'latest', bioc: 'release'}
+          - { os: windows-latest, r: 'latest', bioc: 'release'}
+          ## Check https://github.com/r-lib/actions/tree/master/examples
+          ## for examples using the http-user-agent
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      NOT_CRAN: true
+      TZ: UTC
+      GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+      GITHUB_PAT: ${{ secrets.PAT_GITHUB }}
+      RGL_USE_NULL: TRUE
+
+    steps:
+
+      ## Set the R library to the directory matching the
+      ## R packages cache step further below when running on Docker (Linux).
+      - name: Set R Library home on Linux
+        if: runner.os == 'Linux'
+        run: |
+          mkdir /__w/_temp/Library
+          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
+
+      ## Most of these steps are the same as the ones in  
+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
+      ## If they update their steps, we will also need to update ours.
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      # R is already included in the Bioconductor docker image, 
+      # which is only available with Linux as the OS.
+      - name: Setup R from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}  
+
+      ## pandoc is already included in the Bioconductor docker images
+      - name: Setup pandoc from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-pandoc@master 
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-
+
+      - name: Cache R packages on Linux
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
+        uses: actions/cache@v2
+        with:
+          path: /home/runner/work/_temp/Library
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+          echo $sysreqs
+          sudo -s eval "$sysreqs"
+
+      - name: Install macOS system dependencies
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          ## Enable installing XML from source if needed
+          brew install libxml2
+          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+          ## For textshaping, required by ragg, and required by pkgdown
+          brew install harfbuzz fribidi
+
+          ## For installing usethis's dependency gert
+          brew install libgit2
+
+          ## Required for tcltk
+          brew install xquartz --cask
+          
+          ## Required for some ggplot2 functions
+          # brew tap homebrew/cask
+          # brew tap homebrew/cask-fonts
+          # brew install svn
+          # brew install --cask font-roboto
+          brew install libxfont
+
+      - name: Install Windows system dependencies
+        if: runner.os == 'Windows'
+        run: |
+          ## Edit below if you have any Windows system dependencies
+        shell: Rscript {0}
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager", upgrade = "never")
+        shell: Rscript {0}
+
+      # Linux Bioconductor docker comes with bioconductor installed
+      - name: Set BiocVersion
+        if: runner.os != 'Linux'
+        run: |
+          #### BiocManager::install doesn't understand "latest" #####
+          if("${{ matrix.config.bioc }}" %in% c("latest","release")){
+            BiocManager::install(update = TRUE, ask = FALSE)
+          } else {
+            BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          }
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 1
+        run: |
+          ## Try installing the package dependencies in steps. First the local
+          ## dependencies, then any remaining dependencies to avoid the
+          ## issues described at
+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+          ## https://github.com/r-lib/remotes/issues/296
+          ## Ideally, all dependencies should get installed in the first pass.
+
+          ## Set the repos source depending on the OS
+          ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
+          ## though based on https://bit.ly/bioc2021-package-binaries
+          ## the Azure link will be the main one going forward. 
+          
+          bioc_ver <- BiocManager::version()
+          gha_repos <- if(
+              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
+          ) c(
+              "AnVIL" = file.path("https://bioconductordocker.blob.core.windows.net/packages",bioc_ver,"bioc"),
+              BiocManager::repositories()
+              ) else BiocManager::repositories()
+
+          ## For running the checks
+          ### hrbrthemes necessary to avoid ggplot2 errors on MacOS: https://stackoverflow.com/a/66423481/13214824
+          
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          install.packages(c("rcmdcheck", "BiocCheck", "rmarkdown"), repos = gha_repos)
+
+          ## 1st pass at installing dependencies
+          ## This pass uses AnVIL-powered fast binaries
+          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
+          ## The speed gains only apply to the docker builds. 
+          
+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
+        continue-on-error: true
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 2
+        run: |
+          ## Pass #2 at installing dependencies
+          ## This pass does not use AnVIL and will thus update any packages
+          ## that have seen been updated in Bioconductor
+          
+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+        shell: Rscript {0}
+
+      - name: Install BiocGenerics
+        if:  env.has_RUnit == 'true'
+        run: |
+          ## Install BiocGenerics
+          BiocManager::install("BiocGenerics")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Install pkgdown
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_github("r-lib/pkgdown")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          if(!require("sessioninfo")) install.packages("sessioninfo")
+          tryCatch({
+            sessioninfo::session_info(pkgs, include_base = TRUE)
+          }, error = function(x){utils::sessionInfo()})
+        shell: Rscript {0}
+
+      - name: Run CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          DISPLAY: 99.0
+        run: |
+          options(crayon.enabled = TRUE)
+          if(!require("sessioninfo")) install.packages("rcmdcheck")
+          rcmdcheck::rcmdcheck(
+              args = c("--no-manual", "--timings"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+              error_on = "warning",
+              check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      ## Might need an to add this to the if:  && runner.os == 'Linux'
+      - name: Reveal testthat details
+        if:  env.has_testthat == 'true'
+        run: find . -name testthat.Rout -exec cat '{}' ';'
+
+      - name: Run RUnit tests
+        if:  env.has_RUnit == 'true'
+        run: |
+          BiocGenerics:::testPackage()
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        if: env.run_bioccheck == 'true'
+        env:
+          DISPLAY: 99.0
+        run: |
+          if(!require("BiocManager")) install.packages("BiocManager") 
+          if(!require("BiocCheck")) BiocManager::install("BiocCheck")
+          BiocCheck::BiocCheck(
+              dir('check', 'tar.gz$', full.names = TRUE),
+              `quit-with-status` = TRUE,
+              `no-check-R-ver` = TRUE,
+              `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}
+
+      - name: Test coverage
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Install package
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: R CMD INSTALL .
+
+      - name: Render README
+        env:
+          DISPLAY: 99.0
+        run: |
+          if(file.exists("README.Rmd")){
+            if(!require("rmarkdown")) install.packages("rmarkdown");
+            rmarkdown::render("README.Rmd", output_format = rmarkdown::github_document(html_preview = FALSE));
+          }
+        shell: Rscript {0}
+
+      - name: Build and deploy pkgdown site
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
+        shell: bash {0}
+        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
+        ## at least one locally before this will work. This creates the gh-pages
+        ## branch (erasing anything you haven't version controlled!) and
+        ## makes the git history recognizable by pkgdown.
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-results
+          path: check 
+