update documentation

- get_description moved to struct and updated
computational-metabolomics · Jan 31, 2024 · 0938837 · 0938837
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -35,8 +35,8 @@ name: R-CMD-check-bioc
 ## "/nocache" in the commit message.
 env:
   has_testthat: 'true'
-  run_covr: 'true'
-  run_pkgdown: 'false'
+  run_covr: 'false'
+  run_pkgdown: 'true'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
   run_docker: 'false'
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.17'}
-          - { os: windows-latest, r: 'devel', bioc: '3.17'}
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.17'}
+          - { os: windows-latest, r: '4.3', bioc: '3.17'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -105,23 +105,23 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
-      - 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 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'
@@ -169,35 +169,19 @@ jobs:
           ## 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.
-          gha_repos <- if(
-              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
-          ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.17/bioc",
-              BiocManager::repositories()
-              ) else BiocManager::repositories()
-
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
+          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
 
           ## Pass #1 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)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), 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}
@@ -210,15 +194,15 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_github("r-lib/pkgdown")
+          remotes::install_cran("pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -266,17 +250,17 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
       - name: Build pkgdown site
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
@@ -285,12 +269,12 @@ jobs:
         ## makes the git history recognizable by pkgdown.
 
       - name: Install deploy dependencies
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           apt-get update && apt-get -y install rsync
 
       - name: Deploy pkgdown site to GitHub pages 🚀
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         uses: JamesIves/github-pages-deploy-action@releases/v4
         with:
           clean: false
@@ -301,21 +285,54 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-devel-r-devel-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
           path: check
 
-        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
-        ## account, not your actual dockerhub account password.
-        ## This comes from
-        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
-        ## Check https://github.com/docker/build-push-action/tree/releases/v1
-        ## for more details.
-      - uses: docker/build-push-action@v1
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
+
+  ## Code adapted from
+  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
+  docker-build-and-push:
+    runs-on: ubuntu-latest
+    needs: build-check
+    steps:
+      - name: Checkout Repository
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: actions/checkout@v3
+
+      - name: Register repo name
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        id: reg_repo_name
+        run: |
+          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
+
+      - name: Set up QEMU
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to Docker Hub
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
+      ## account, not your actual dockerhub account password. You can get it
+      ## from https://hub.docker.com/settings/security.
+      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
+      ## for more details.
+      ## Alternatively, try checking
+      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
+
+      - name: Build and Push Docker
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
+        uses: docker/build-push-action@v4
         with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: computational-metabolomics/structtoolbox
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: latest
+          context: .
+          push: true
+          tags: >
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: structToolbox
 Type: Package
 Title: Data processing & analysis tools for Metabolomics and other omics
-Version: 1.13.5
+Version: 1.13.6
 Authors@R: c(
     person(
         c("Gavin","Rhys"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -126,6 +126,6 @@ import(methods)
 import(scales)
 import(stats)
 import(struct)
+import(utils)
 importFrom(scales,squish)
 importFrom(sp,point.in.polygon)
-importFrom(utils,capture.output)
diff --git a/R/PCA_class.R b/R/PCA_class.R
@@ -1,8 +1,6 @@
-#' @eval get_description('PCA')
+#' @eval struct::get_description('PCA')
 #' @import struct
 #' @export PCA
-#' @examples
-#' M = PCA()
 PCA = function(number_components=2,...) {
     out=struct::new_struct('PCA',
         number_components=number_components,

diff --git a/R/forward_selection_by_rank_class.R b/R/forward_selection_by_rank_class.R
@@ -21,7 +21,13 @@
 #' M = run(M,D,balanced_accuracy())
 #'
 #' @export forward_selection_by_rank
-forward_selection_by_rank = function(min_no_vars=1,max_no_vars=100,step_size=1,factor_name,variable_rank,...) {
+forward_selection_by_rank = function(
+        min_no_vars=1,
+        max_no_vars=100,
+        step_size=1,
+        factor_name,
+        variable_rank,
+        ...) {
     out=struct::new_struct('forward_selection_by_rank',
         min_no_vars=min_no_vars,
         max_no_vars=max_no_vars,
@@ -49,21 +55,21 @@ forward_selection_by_rank = function(min_no_vars=1,max_no_vars=100,step_size=1,f
         smoothed='entity',
         searchlist='entity'
     ),
-    prototype = list(variable_rank=c(1,2,3),
+    prototype = list(
         name = 'Forward selection by rank',
         description = paste0('A model is trained and performance metric ',
             'computed by including increasing numbers of features in the model. ',
             'The features to be included in each step are defined by their rank, ',
             'which is computed from another variable e.g. VIP score. An "optimal"', 
             'subset of features is suggested by minimising the input performance metric.'),
         result='results',
-        .params=c('min_no_vars','max_no_vars','step_size','factor_name'),
+        .params=c('min_no_vars','max_no_vars','step_size','factor_name','variable_rank'),
         .outputs=c('metric','results','chosen_vars','smoothed','searchlist'),
         variable_rank=entity(
             name = 'Variable rank',
             description = 'The values used to rank the features.',
             type=c('numeric','integer'),
-            value=numeric(0)
+            value=1
         ),
         min_no_vars = entity(
             name = 'Minimum number of variables',

diff --git a/R/structToolbox.R b/R/structToolbox.R
@@ -7,5 +7,6 @@
 #' @import struct
 #' @import methods
 #' @import stats
+#' @import utils
 NULL
 ## NULL