Fix(45)-fix_ci_yaml

.github/workflows/ci.yml

@@ -0,0 +1,48 @@
+name: R CI
+on:
+  push:
+    branches: [main, fix/45-fix_ci_yaml]
+  pull_request:
+    branches: [main, fix/45-fix_ci_yaml]
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up pdflatex
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y texlive-latex-base
+          sudo apt-get install texlive-fonts-extra 
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      # - name: Install covr package
+      #   run: Rscript -e 'install.packages("covr")'
+
+      - name: Install Dependencies
+        run: |
+          R -e 'install.packages(c("devtools", "covr", "ggplot2", "WriteXLS", "gridExtra", "Cairo"))'
+
+      - name: Build and test
+        run: |
+          R CMD build .  
+          R CMD check .
+        # R CMD check --as-cran *tar.gz 
+
+      - name: Run Tests and Generate Coverage
+        run: |
+          Rscript -e 'library(devtools); devtools::test()'
+          Rscript -e 'library(covr); covr::codecov()'
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.travis.yml

@@ -1,8 +1,37 @@
 language: r
+sudo: false
 cache: packages
 
-r_github_packages:
-     - r-lib/covr
+branches:
+  only:
+    - main
+    - master
+    - CI/CD
+    - test
+    - fix/45-fix_ci_yaml
+
+before_install:
+  - sudo apt-get update
+  - sudo apt-get install -y texlive-latex-base
+  - sudo apt-get install texlive-fonts-extra
+
+install:
+  - Rscript -e 'install.packages("covr")'
+  - R -e 'install.packages(c("devtools", "ggplot2", "WriteXLS", "gridExtra", "Cairo"))'
+
+script:
+  - R CMD build .
+  - R CMD check --as-cran *tar.gz
+  - Rscript -e 'library(devtools); devtools::test()'
+  - Rscript -e 'library(covr); covr::codecov()'
 
 after_success:
-     - Rscript -e 'covr::coveralls()'
+  - Rscript -e 'covr::codecov()'
+
+addons:
+  apt:
+    packages:
+      - libxml2-dev
+
+notifications:
+  email: false

DESCRIPTION

@@ -2,21 +2,22 @@ Package: samplyzer
 Title: What the Package Does (one line, title case)
 Version: 0.0.0.9000
 Authors@R: person("Xiao", "Li", email = "xiaoli@broadinstitute.org", role = c("aut", "cre"))
+Author: Xiao Li
+Maintainer: Xiao Li <xiaoli@broadinstitute.org>
 Description: What the package does (one paragraph).
 Depends: R (>= 3.3.2)
 License: What license is it under?
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1.9000
+RoxygenNote: 7.2.3
 Suggests: knitr,
     rmarkdown,
     Cairo,
     testthat,
-    covr
-Remotes: r-lib/covr
 VignetteBuilder: knitr
 Imports: class (>= 7.3-14),
     ggplot2 (>= 2.2.1),
     WriteXLS (>= 4.0.0),
     grid (>= 3.3.2),
-    gridExtra (>= 2.2.1)
+    gridExtra (>= 2.2.1),
+    covr

NAMESPACE

@@ -16,10 +16,15 @@ S3method(sort,sampleDataset)
 export(PCplots)
 export(calZscore)
 export(flagSamples)
+export(geom_split_violin)
 export(getAttr)
 export(hasAttr)
 export(inferAncestry)
+export(multiplotWithSharedLegend)
+export(outlierPlots)
+export(runQcExplorer)
 export(sampleDataset)
 export(sampleQcPlot)
 export(save)
+export(scatter)
 export(setAttr)

R/plot.R

@@ -90,14 +90,25 @@ sampleQcPlot.sampleDataset <- function(
 
 
 #' Produce outlier plot
+#' @param sds sample dataset sds
+#' @param ... other arguments
 #'
+#' @export
+
 outlierPlots <- function(...) UseMethod('outlierPlots')
 
-#' @param tab input table with
+#' Produce outlier plot
+#'
+#' @param tab input table with sample information and metrics
 #' @param qcMetrics which metrics to plot
 #' @param strat by which factor to stratify the dots
-#' @param main title of the
-#' @return
+#' @param main title of the plot
+#' @param outliers vector of sample IDs to highlight as outliers
+#' @param primaryID the primary ID for labeling
+#' @param type type of plot, either 'violin' or 'density'
+#' @return a list of outlier plots
+#'
+#'
 
 outlierPlots.default <- function(tab, qcMetrics, strat, main, outliers,
                          primaryID=NULL, type='violin'){
@@ -192,7 +203,7 @@ PCplots <- function (sds, showPlot=T, cor=F, outliers=NULL) {
 #' generate multi panel plots
 #'
 #' @param plotlist a list of plot
-#' @param file
+#' @param file file
 #' @param ncols number of columns in the plot
 #'
 

README.md

@@ -1,8 +1,7 @@
 # samplyzer
-[![Build Status](https://travis-ci.com/xiaoli0/samplyzer.svg?branch=master)](https://travis-ci.org/xiaoli0/samplyzer)
-[![AppVeyor Build  Status](https://ci.appveyor.com/api/projects/status/github/xiaoli0/samplyzer?branch=master&svg=true)](https://ci.appveyor.com/project/xiaoli0/samplyzer)  
-[![Coverage Status](https://coveralls.io/repos/github/xiaolicbs/samplyzer/badge.svg?branch=master)](https://coveralls.io/github/xiaolicbs/samplyzer?branch=master)  
-samplyzer is an R package and Web Application that enables efficient exploration of sample level QC statistics.
+[![R CI](https://github.com/x-lab/samplyzer/actions/workflows/ci.yml/badge.svg)](https://github.com/x-lab/samplyzer/actions/workflows/ci.yml)
+[![AppVeyor Build  Status](https://ci.appveyor.com/api/projects/status/u8scd9ecoe67k9cw?svg=true)](https://ci.appveyor.com/project/1677953017/samplyzer)
+[![codecov](https://codecov.io/gh/x-lab/samplyzer/graph/badge.svg?token=eNYYjuMXIw)](https://codecov.io/gh/x-lab/samplyzer)
 
 ## Requirements
 * R >= 3.3.2

appveyor.yml

@@ -0,0 +1,42 @@
+init:
+  ps: |
+    $ErrorActionPreference = "Stop"
+    Invoke-WebRequest http://raw.githubusercontent.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+    Import-Module '..\appveyor-tool.ps1'
+
+install:
+  ps: Bootstrap
+
+# Adapt as necessary starting from here
+build_script:
+  - R -e "install.packages(c('devtools', 'covr', 'ggplot2', 'WriteXLS', 'gridExtra', 'Cairo'), repos='https://cloud.r-project.org/')"
+# - travis-tool.sh install_deps
+
+test_script:
+  - travis-tool.sh run_tests
+
+on_failure:
+  - travis-tool.sh dump_logs
+
+environment:
+  my_variable:
+    secure: dfWwR38iwmYAo9ub0Rg/24EXPUVttaLwhuinDYH3oyIjkt7ozFoyE43t6W9G/w2l  #GitHub Access Token
+
+artifacts:
+  - path: '*.Rcheck\**\*.log'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.out'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.fail'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.Rout'
+    name: Logs
+
+  - path: '\*_*.tar.gz'
+    name: Bits
+
+  - path: '\*_*.zip'
+    name: Bits