Merge pull request #41 from pepkit/dev

v0.4.0

.github/workflows/new-build-R.yml

@@ -0,0 +1,85 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_cran("covr")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Report test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.3.2
-Date: 2020-06-03
+Version: 0.4.0
+Date: 2020-10-15
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
     role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre")))
 Maintainer: Michal Stolarczyk <michal@virginia.edu>

NEWS.md

@@ -1,3 +1,13 @@
+# pepr 0.4.0 - 2020-10-14
+
+## Changed
+
+* added multiple subsample_table support
+
+## Fixed
+
+* issues with config file determination
+
 # pepr 0.3.2 - 2020-06-03
 
 ## Changed

R/config.R

@@ -60,6 +60,8 @@ setMethod(
 .expandList <- function(x) {
   if(is.list(x))
     return(lapply(x, .expandList))
+  if(length(x) > 1)
+    return(unname(sapply(x, .expandList)))
   return(suppressWarnings(.expandPath(x)))
 }
 
@@ -129,12 +131,12 @@ setMethod("[[", "Config", function(x, i) {
 
 
 .DollarNames.Config <- function(x, pattern = "")
-  grep(pattern, grep(names(x), value=TRUE))
+  grep(paste0("^", pattern), grep(names(x), value=TRUE))
 
 #' @rdname select-config
 #' @export
 setMethod("$", "Config", function(x, name){
-  matches = grep(name, names(x))
+  matches = grep(paste0("^", name), names(x))
   if(length(matches) == 0)
     return(NULL)
   hits = x[[matches]]

R/project.R

@@ -25,7 +25,7 @@ setMethod("initialize", "Project", function(.Object, ...) {
         # check if file path provided
         .Object@file = .makeAbsPath(ellipsis$file, parent = path.expand(getwd()))
         # instantiate config object and stick it in the config slot
-        .Object@config = Config(ellipsis$file, ellipsis$amendments)
+        .Object@config = Config(.Object@file, ellipsis$amendments)
         .Object = .loadSampleAnnotation(.Object)
         .Object = .modifySamples(.Object)
     }
@@ -479,40 +479,37 @@ setMethod(
 }
 
 
-#' Merge samples defined in sample table with ones in subsample table
+#' Load single subsample annotation
 #'
 #' @param .Object an object of \code{"\linkS4class{Project}"}
+#' @param path string, a path to the subsample table to read and incorporate
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
-.mergeAttrs = function(.Object){
-    cfg = config(.Object)
-    if (!CFG_SUBSAMPLE_TABLE_KEY %in% names(cfg)) return(.Object)
-    sampleSubannotationPath = cfg[[CFG_SUBSAMPLE_TABLE_KEY]]
-    samples = sampleTable(.Object)
-    samples = .listifyDF(samples)
-    if (.safeFileExists(sampleSubannotationPath)) {
-        samplesSubannotation = data.table::fread(sampleSubannotationPath)
+.loadSubsampleAnnotation = function(.Object, path) {
+    if (.safeFileExists(path)) {
+        samplesSubannotation = data.table::fread(path)
     } else{
         samplesSubannotation = data.table::data.table()
     }
     subNames = unique(samplesSubannotation$sample_name)
+    samples = sampleTable(.Object)
+    samples = .listifyDF(samples)
     rowNum = nrow(samples)
     # Creating a list to be populated in the loop and inserted
     # into the samples data.table as a column. This way the "cells"
     # in the samples table can consist of multiple elements
-    colList = vector("list", rowNum)
     for (iName in subNames) {
         whichNames = which(samplesSubannotation$sample_name == iName)
         subTable = samplesSubannotation[whichNames,]
         dropCol = which(names(samplesSubannotation[whichNames,]) == "sample_name")
         subTable = subset(subTable, select = -dropCol)
+        colList = vector("list", rowNum)
         for (iColumn in seq_len(ncol(subTable))) {
             colName = names(subset(subTable, select = iColumn))
             if (!any(names(samples) == colName)) {
                 # The column doesn't exist, creating
                 samples[, colName] = NULL
             } else{
-                # colList=as.list(unname(samples[, ..colName]))[[1]]
                 colList = samples[[colName]]
             }
             # The column exists
@@ -532,3 +529,20 @@ setMethod(
     .Object@samples = samples
     return(.Object)
 }
+
+
+
+#' Merge samples defined in sample table with ones in subsample table(s)
+#'
+#' @param .Object an object of \code{"\linkS4class{Project}"}
+#'
+#' @return an object of \code{"\linkS4class{Project}"}
+.mergeAttrs = function(.Object){
+    cfg = config(.Object)
+    if (!CFG_SUBSAMPLE_TABLE_KEY %in% names(cfg)) return(.Object)
+    sampleSubannotationPath = cfg[[CFG_SUBSAMPLE_TABLE_KEY]]
+    for(p in sampleSubannotationPath){
+        .Object = .loadSubsampleAnnotation(.Object, p)    
+    }
+    return(.Object)
+}

R/utils.R

@@ -126,17 +126,21 @@
 #' @export 
 #' @return Target itself if already absolute, else target nested within parent.
 .makeAbsPath = function(perhapsRelative, parent) {
-  if (!.isDefined(perhapsRelative)) return(perhapsRelative)
-  perhapsRelative = .expandPath(perhapsRelative)
-  if (.isAbsolute(perhapsRelative)) {
-    abspath = perhapsRelative
-  } else {
-    abspath = file.path(path.expand(parent), perhapsRelative)
+  res = c()
+  for(pR in perhapsRelative){
+    if (!.isDefined(pR)) return(pR)
+    pR = .expandPath(pR)
+    if (.isAbsolute(pR)) {
+      abspath = pR
+    } else {
+      abspath = file.path(path.expand(parent), pR)
+    }
+    if (!.isAbsolute(abspath)) 
+      stop("Relative path ", pR, " and parent ", parent ,
+           " failed to create absolute path: ", abspath)
+    res = append(res, abspath)
   }
-  if (!.isAbsolute(abspath)) 
-    stop("Relative path ", perhapsRelative, " and parent ", parent ,
-         " failed to create absolute path: ", abspath)
-  return(abspath)
+  return(res)
 }
 
 # Must test for is.null first, since is.na(NULL) returns a logical(0) which is

README.md

@@ -1,7 +1,7 @@
 [![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/pepr)](http://cranlogs.r-pkg.org/badges/grand-total/pepr)
 [![CRAN](http://www.r-pkg.org/badges/version-last-release/pepr)](http://www.r-pkg.org/badges/version-last-release/pepr)
-[![Build Status](https://travis-ci.org/pepkit/pepr.svg?branch=master)](https://travis-ci.org/pepkit/pepr)
-[![Coverage Status](https://coveralls.io/repos/github/pepkit/pepr/badge.svg?branch=dev)](https://coveralls.io/github/pepkit/pepr?branch=dev&service=github)
+![R-CMD-check](https://github.com/pepkit/pepr/workflows/R-CMD-check/badge.svg)
+[![codecov](https://codecov.io/gh/pepkit/pepr/branch/master/graph/badge.svg)](https://codecov.io/gh/pepkit/pepr)
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
 # The `pepr` package: Portable Encapsulated Projects in R
@@ -25,7 +25,7 @@ Load a project and explore metadata like this:
 library("pepr")
 cfgPath = system.file(
     "extdata",
-    paste0("example_peps-master"),
+    "example_peps-master",
     "example_basic",
     "project_config.yaml",
     package = "pepr"

inst/extdata/example_peps-master/example_subtable1/project_config.yaml

@@ -1,4 +1,5 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
 subsample_table: subsample_table.csv
-output_dir: $HOME/example_results
+looper:
+  output_dir: $HOME/example_results

inst/extdata/example_peps-master/example_subtable2/project_config.yaml

@@ -1,8 +1,9 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
 subsample_table: subsample_table.csv
-output_dir: $HOME/hello_looper_results
-pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
+looper:
+  output_dir: $HOME/hello_looper_results
+  pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
 
 sample_modifiers:
   derive:

inst/extdata/example_peps-master/example_subtable3/project_config.yaml

@@ -1,8 +1,9 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
 subsample_table: subsample_table.csv
-output_dir: $HOME/hello_looper_results
-pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
+looper:
+  output_dir: $HOME/hello_looper_results
+  pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
 
 sample_modifiers:
   derive:

inst/extdata/example_peps-master/example_subtable4/project_config.yaml

@@ -1,6 +1,7 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
 subsample_table: subsample_table.csv
-output_dir: $HOME/hello_looper_results
-pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
+looper:
+  output_dir: $HOME/hello_looper_results
+  pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
 

inst/extdata/example_peps-master/example_subtable5/project_config.yaml

@@ -1,8 +1,9 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
 subsample_table: subsample_table.csv
-output_dir: $HOME/hello_looper_results
-pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
+looper:
+  output_dir: $HOME/hello_looper_results
+  pipeline_interfaces: [../pipeline/pipeline_interface.yaml]
 
 sample_modifiers:
   derive: