start pipeline config from thevalidatoR

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Roche
+
+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.

action.yml

@@ -0,0 +1,123 @@
+name: R Package Validation Report
+author: Roche
+description: A Github Action that generates a validation report for an R package.
+
+inputs:
+  report_pkg_dir:
+    description: Path to package's root.
+    required: false
+    default: "."
+  report_template_path:
+    description: |
+      File path of the R markdown template to use for the report.
+      The default template is available [here.](./template.Rmd)
+    required: false
+    default: "./template.Rmd"
+  report_rmarkdown_format:
+    description: |
+      The file format of the validation report. See `rmarkdown::render`'s
+      `output_format` parameter for accepted values.
+    required: false
+    default: "all"
+  report_output_prefix:
+    description: >
+      The output filename prefix for the validation report. If left blank,
+      it defaults to the following convention:
+      `<package name>-<package version>-validation-report`.
+    required: false
+    default: ""
+  additional_tlmgr_packages:
+    description: |
+      Additional tex packages to install with tlmgr.
+    required: false
+    default: "courier ec"
+  no_cache:
+    description: "Disable github action R dependency caching"
+    required: false
+    default: "false"
+  cache_version:
+    description: "Version of the cache. To clean cache bump this version."
+    required: false
+    default: "v1"
+  disable_install_dev_deps:
+    description: |
+      Disable installation of dev dependencies while
+      building the report.
+    required: false
+    default: "false"
+outputs:
+  report_output_filename:
+    description: Filename of the generated report.
+    value: ${{ steps.report-generator.outputs.output-filename }}
+branding: # https://feathericons.com/
+  icon: "award"
+  color: "blue"
+
+runs:
+  using: "composite"
+
+  steps:
+    - name: Get R version
+      id: r_version
+      run: echo "R_VERSION=$(R --version | head -1 | awk '{print $3}')" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Set R Library home on Linux
+      run: |
+        mkdir -p ${RUNNER_TEMP}/Library
+        echo ".libPaths(c('${RUNNER_TEMP}/Library', .libPaths()))" > ~/.Rprofile
+        cat ~/.Rprofile
+      shell: bash
+
+    - name: Set tlmgr cache folder
+      if: "contains(inputs.no_cache, 'false')"
+      id: texlive_version
+      run: |
+        echo "TEX_LIVE_VERSION=$(tlmgr --version |tail -1 |awk '{print $NF}')" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Cache R packages
+      if: "contains(inputs.no_cache, 'false')"
+      uses: actions/cache@v2
+      with:
+        path: /home/runner/work/_temp/Library
+        key: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.r_version.outputs.R_VERSION }}-${{ hashFiles('DESCRIPTION') }}
+        restore-keys: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.r_version.outputs.R_VERSION }}
+
+    - name: Cache Tex packages
+      if: "contains(inputs.no_cache, 'false')"
+      uses: actions/cache@v2
+      with:
+        path: /home/runner/work/_temp/TinyTeX
+        key: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.texlive_version.outputs.TEX_LIVE_VERSION }}-${{ hashFiles(inputs.report_template_path) }}
+        restore-keys: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.texlive_version.outputs.TEX_LIVE_VERSION }}
+
+    - name: Install dependencies
+      run: |
+        ${GITHUB_ACTION_PATH}/dependencies.R
+        export PATH=${RUNNER_TEMP}/TinyTeX/bin/x86_64-linux:${PATH}
+        echo "PATH=${PATH}" >> $GITHUB_ENV
+        tlmgr path add
+        tlmgr update --self
+        [ ! -f "./template.Rmd" ] && cp ${GITHUB_ACTION_PATH}/template.Rmd . || echo "./template.Rmd Already exists"
+      shell: bash
+
+    - name: Install additional tex packages
+      run: tlmgr install ${{ inputs.additional_tlmgr_packages }}
+      shell: bash
+
+    - name: Run report generator
+      id: report-generator
+      run: |
+        ${GITHUB_ACTION_PATH}/report-generator.R
+        filename=$(basename $(cat /tmp/report_file_path.txt))
+        echo "output-filename=${filename}" >> $GITHUB_OUTPUT
+      shell: bash
+      env:
+        # Composite action doesn't set inputs as env vars.
+        # We need to do this manually...
+        INPUT_REPORT_PKG_DIR: ${{ inputs.report_pkg_dir }}
+        INPUT_REPORT_TEMPLATE_PATH: ${{ inputs.report_template_path }}
+        INPUT_REPORT_RMARKDOWN_FORMAT: ${{ inputs.report_rmarkdown_format }}
+        INPUT_REPORT_OUTPUT_PREFIX: ${{ inputs.report_output_prefix }}
+        DISABLE_INSTALL_DEV_DEPS: ${{ inputs.disable_install_dev_deps }}

dependencies.R

@@ -0,0 +1,42 @@
+#!/usr/bin/env Rscript
+
+# Install latest ackages from Github
+# Requires dev version of covr (>= 3.5.1.9003)
+# Also install other package dependencies (for tests)
+github_packages <- c(
+    "r-lib/covr",
+    "pharmaR/riskmetric",
+    "Genentech/covtracer"
+)
+lapply(github_packages, remotes::install_github)
+
+# CRAN
+options(repos = c("https://cloud.r-project.org/"))
+ncores <- parallel::detectCores(all.tests = FALSE, logical = TRUE)
+if (!require("git2r")) install.packages("git2r", upgrade = "never", Ncpus = ncores)
+if (!require("kableExtra")) install.packages("kableExtra", upgrade = "never", Ncpus = ncores)
+if (!require("tinytex")) install.packages("tinytex", upgrade = "never", Ncpus = ncores)
+
+# Conditionally install TinyTex
+if(!dir.exists(paste(Sys.getenv("RUNNER_TEMP"), "TinyTeX", sep="/"))) {
+# nolint start
+  tinytex_installer <- '
+export TINYTEX_DIR=${RUNNER_TEMP}/TinyTeX
+wget -qO- "https://raw.githubusercontent.com/yihui/tinytex/master/tools/install-unx.sh" | sh -s - --admin --no-path
+mkdir -p ${RUNNER_TEMP}/TinyTeX
+cp -r ~/.TinyTeX/. ${RUNNER_TEMP}/TinyTeX
+rm -rf ~/.TinyTeX
+${RUNNER_TEMP}/TinyTeX/bin/*/tlmgr path add
+tlmgr update --self
+tlmgr install latex-bin luatex xetex ae bibtex context inconsolata listings makeindex metafont mfware parskip pdfcrop tex tools url xkeyval
+'
+  # nolint end
+  system(tinytex_installer)
+  tinytex::r_texmf()
+  permission_update <- '
+chown -R root:staff ${RUNNER_TEMP}/TinyTeX
+chmod -R g+w ${RUNNER_TEMP}/TinyTeX
+chmod -R g+wx ${RUNNER_TEMP}/TinyTeX/bin
+'
+  system(permission_update)
+}

report-generator.R

@@ -0,0 +1,66 @@
+#!/usr/bin/env Rscript
+
+# Location
+cat(sprintf("Current dir is: '%s'", getwd()))
+
+# CVE-2022-24765 exception
+git_safe_dir <- system(
+  sprintf("git config --global --add safe.directory '%s'", getwd())
+)
+
+# Get the action inputs from preset env vars
+pkg_dir <- normalizePath(Sys.getenv("INPUT_REPORT_PKG_DIR", "."))
+template_path <- Sys.getenv("INPUT_REPORT_TEMPLATE_PATH", "/template.Rmd")
+report_format <- Sys.getenv("INPUT_REPORT_RMARKDOWN_FORMAT", "all")
+report_output_prefix <- Sys.getenv("INPUT_REPORT_OUTPUT_PREFIX", "")
+disable_install_dev_deps <- tolower(
+  Sys.getenv("DISABLE_INSTALL_DEV_DEPS")
+) %in% c("yes", "y", "t", "true")
+
+# fail with meaningful message if REPORT_PKG_DIR does not appear to be a package
+desc_file <- file.path(pkg_dir, "DESCRIPTION")
+if (!file.exists(desc_file)) {
+  stop(sprintf(
+    paste(sep = "\n",
+      "Could not find package at '%s'",
+      "    ",
+      "    Specify a directory by definining environment variable:",
+      "        INPUT_REPORT_PKG_DIR=<repository subdirectory>",
+      "    "
+    ),
+    pkg_dir
+  ))
+}
+
+# Install package dependencies
+if (!disable_install_dev_deps) {
+    options("remotes.git_credentials" = git2r::cred_user_pass(
+        username = "token",
+        password = remotes:::github_pat()
+    ))
+    devtools::install_dev_deps(pkg_dir, upgrade = "never")
+}
+
+# Set the output file name
+if (report_output_prefix == "") {
+  desc <- read.dcf(desc_file)
+  pkg_name <- toString(desc[, "Package"])
+  pkg_version <- toString(desc[, "Version"])
+  report_output_prefix <- paste0(
+    pkg_name, "-", pkg_version, "-validation-report"
+  )
+}
+
+# allow rmarkdown to choose appropriate file extension for output format
+report_file_path <- rmarkdown::render(
+  template_path,
+  output_dir = getwd(),  # create report wherever R script was called
+  output_file = report_output_prefix,
+  output_format = report_format,
+  params = list(pkg_dir = pkg_dir)
+)
+
+# Create a tmp file which contains the final report filename
+writeLines(report_file_path, "/tmp/report_file_path.txt")
+
+cat(sprintf("Created report at: '%s'\n\n", report_file_path))

tests/README.md

@@ -0,0 +1,3 @@
+# Tests
+
+Directory for artifacts used in testing Github Actions workflows.

tests/packages/README.md

@@ -0,0 +1,3 @@
+# Packages for testing 
+
+Example R packages that can be used for testing Github Actions within this repository.

tests/packages/aragog/DESCRIPTION

@@ -0,0 +1,12 @@
+Package: aragog
+Version: 0.1.0
+Title: Hagrid's giant spider
+Description: Aragog was an Acromantula owned by Rubeus Hagrid.
+    Aragog was able to communicate with humans with speech.
+Author: JK Rowling <[email protected]>
+Maintainer: Insights Engineering <[email protected]>
+License: file LICENSE
+Type: Package
+Encoding: UTF-8
+RoxygenNote: 7.0.2
+Suggests: testthat

tests/packages/aragog/LICENSE

@@ -0,0 +1 @@
+Wizarding World

tests/packages/aragog/NAMESPACE

@@ -0,0 +1,3 @@
+# Generated by roxygen2: do not edit by hand
+
+export(aragog)

tests/packages/aragog/R/main.R

@@ -0,0 +1,10 @@
+#' aragog
+#'
+#' Get Hagrid's spider's name
+#' @author Insights Engineering <[email protected]>
+#' @title Get the spider's name
+#' @return string. The spider's name
+#' @export
+aragog <- function() {
+  return("Aragog")
+}

tests/packages/aragog/README.md

@@ -0,0 +1,3 @@
+# aragog
+
+An R package about [Aragog](https://harrypotter.fandom.com/wiki/Aragog).

tests/packages/aragog/tests/test_main.R

@@ -0,0 +1,10 @@
+library(aragog)
+library(testthat)
+
+check_spider <- function() {
+  stopifnot(identical(aragog(), "Aragog"))
+}
+
+test_that("The spider's name is Aragog", {
+  check_spider()
+})

tests/packages/buckbeak/DESCRIPTION

@@ -0,0 +1,14 @@
+Package: buckbeak
+Version: 0.1.0
+Title: Hagrid's hippogriff
+Description: Buckbeak, later renamed Witherwings, was a male hippogriff.
+    He lived with Rubeus Hagrid during Harry Potter's third year at Hogwarts,
+    along with a few other hippogriffs.
+Author: JK Rowling <[email protected]>
+Maintainer: Insights Engineering <[email protected]>
+License: GPL-3
+Type: Package
+Encoding: UTF-8
+Depends: aragog, dplyr
+Suggests: testthat
+RoxygenNote: 7.0.2

tests/packages/buckbeak/NAMESPACE

@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+export(buckbeak)
+export(hagrids_pets)

tests/packages/buckbeak/R/main.R

@@ -0,0 +1,23 @@
+library(aragog)
+
+#' buckbeak
+#'
+#' Hagrid's hippogriff name
+#' @author Insights Engineering <[email protected]>
+#' @title Get the hippogriff's name
+#' @return string. The hippogriff's name
+#' @export
+buckbeak <- function() {
+  return("Buckbeak")
+}
+
+#' hagrids_pets
+#'
+#' Hagrid's pets' names
+#' @author Insights Engineering <[email protected]>
+#' @title Get Hagrid's pets' names
+#' @return string. The spider and the hippogriff's name
+#' @export
+hagrids_pets <- function() {
+  return(paste(c("Buckbeak", "and", aragog()), collapse = " "))
+}

tests/packages/buckbeak/README.md

@@ -0,0 +1,3 @@
+# buckbeak
+
+An R package about [Buckbeak](https://harrypotter.fandom.com/wiki/Buckbeak).