Feature: Select a prefix for the validation report (#55)

* tlmgr fails if it is not updated on runtime

* Some more enhancements

* Couple 'o bugfixes

* Composite actions are silly

* Remove docker references

* Get basename of output file

.github/workflows/test.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     name: ${{ matrix.package.name }}
     container:
-      image: rocker/verse:4.1.1
+      image: rocker/verse:4.1.2
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
@@ -35,10 +35,12 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Generate validation report for ${{ matrix.package.name }}
+        id: validation
         uses: ./
         with:
           report_pkg_dir: ${{ matrix.package.report_pkg_dir }}
           report_template_path: ${{ matrix.package.report_template_path }}
+          report_output_prefix: validation_report
           report_rmarkdown_format: ${{ matrix.package.report_rmarkdown_format }}
           additional_tlmgr_packages: ${{ matrix.package.additional_tlmgr_packages }}
 
@@ -47,5 +49,5 @@ jobs:
         if: success()
         with:
           name: ${{ matrix.package.name }} validation report
-          path: validation_report.*
+          path: ${{ steps.validation.outputs.report_output_filename }}
           if-no-files-found: error

.github/workflows/test_no_cache.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     name: ${{ matrix.package.name }}
     container:
-      image: rocker/verse:4.1.1
+      image: rocker/verse:4.1.2
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
@@ -30,9 +30,11 @@ jobs:
 
       - name: Generate validation report for ${{ matrix.package.name }}
         uses: ./
+        id: validation
         with:
           report_pkg_dir: ${{ matrix.package.report_pkg_dir }}
           report_template_path: ${{ matrix.package.report_template_path }}
+          report_output_prefix: validation_report
           report_rmarkdown_format: ${{ matrix.package.report_rmarkdown_format }}
           no_cache: true
 
@@ -41,5 +43,5 @@ jobs:
         if: success()
         with:
           name: ${{ matrix.package.name }} validation report
-          path: validation_report.*
+          path: ${{ steps.validation.outputs.report_output_filename }}
           if-no-files-found: error

README.md

@@ -1,6 +1,6 @@
 # thevalidatoR
- <img src='https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/thevalidatoR.png' align="right" height="131.5" />
 
+ <img src='https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/thevalidatoR.png' align="right" height="131.5" />
 
 [<img src="http://pharmaverse.org/shields/thevalidatoR.png">](https://pharmaverse.org) 
 [![SuperLinter](https://github.com/insightsengineering/thevalidatoR/actions/workflows/lint.yaml/badge.svg)](https://github.com/insightsengineering/thevalidatoR/actions/workflows/lint.yaml)
@@ -33,62 +33,72 @@ A Github Action that generates a validation report for an R package. The four ma
 - Attach report as object to release
 
 ### Action Type
+
 Composite
 
 ### Author
+
 Roche
 
 ### Inputs
 
-* `report_pkg_dir`:
+- `report_pkg_dir`:
 
   _Description_: Path to package's root
 
   _Required_: `false`
 
   _Default_: `.`
 
-* `report_template_path`:
+- `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`:
+- `report_rmarkdown_format`:
 
   _Description_: The output format to use when rendering the report. Value is used by `rmarkdown::render`'s `output_format` parameter.
 
   _Required_: `false`
 
   _Default_: `pdf_document`
 
-* `additional_tlmgr_packages`:
+- `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`:
+- `no_cache`:
 
   _Description_: Disable github action R dependency caching.
 
   _Required_: `false`
 
   _Default_: `false`
 
-* `cache_version`:
+- `cache_version`:
 
   _Description_: Version of the cache. To clean cache bump this version.
 
   _Required_: `false`
 
   _Default_: `v1`
 
-* `disable_install_dev_deps`:
+- `disable_install_dev_deps`:
 
   _Description_: Disable installation of dev dependencies while building the report.
 
@@ -97,16 +107,19 @@ Roche
   _Default_: `false`
 
 ### Outputs
-None
+
+- `report_output_filename`:
+
+  _Description_: Filename of the generated report.
 
 <!-- END_ACTION_DOC -->
 
 ## How to use
 
 To use this GitHub Action you will need to complete the following:
 
-* Create a new file in your repository called `.github/workflows/r-pkg-validation.yml`
-* Copy the template over (and edit if you wish to modify it)
+- Create a new file in your repository called `.github/workflows/r-pkg-validation.yml`
+- Copy the template over (and edit if you wish to modify it)
 
 ### Quickstart
 
@@ -138,6 +151,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Build report 🏗
+        id: validation
         uses: insightsengineering/thevalidatoR@main
         # see parameters above for custom templates and other formats
 
@@ -146,14 +160,14 @@ jobs:
         if: success()
         uses: svenstaro/upload-release-action@v2
         with:
-          file: ./validation_report.pdf
-          asset_name: validation-report.pdf
+          file: ${{ steps.validation.outputs.report_output_filename }}
+          asset_name: ${{ steps.validation.outputs.report_output_filename }}
           repo_token: ${{ secrets.GITHUB_TOKEN }}
           tag: ${{ github.ref }}
           overwrite: false
 ```
 
-### V1.0 Examples 
+### V1.0 Examples
 
 #### rbmi
 

action.yml

@@ -19,6 +19,13 @@ inputs:
       `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.
@@ -38,6 +45,10 @@ inputs:
       building the report.
     required: false
     default: "false"
+outputs:
+  report_output_filename:
+    description: Filename of the generated report.
+    value: ${{ steps.report-generator.outputs.output-filename }}
 branding: # https://feathericons.com/
   icon: "award"
   color: "blue"
@@ -86,6 +97,7 @@ runs:
         export PATH=${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
 
@@ -94,12 +106,17 @@ runs:
       shell: bash
 
     - name: Run report generator
-      run: ${GITHUB_ACTION_PATH}/report-generator.R
+      id: report-generator
+      run: |
+        ${GITHUB_ACTION_PATH}/report-generator.R
+        filename=$(basename $(cat /tmp/report_file_path.txt))
+        echo "::set-output name=output-filename::${filename}"
       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 }}

report-generator.R

@@ -7,10 +7,14 @@ cat(sprintf("Current dir is: '%s'", getwd()))
 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")
-disable_install_dev_deps <- tolower(Sys.getenv("DISABLE_INSTALL_DEV_DEPS")) %in% c('yes', 'y', 't', 'true')
+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
-if (!file.exists(file.path(pkg_dir, "DESCRIPTION"))) {
+desc_file <- file.path(pkg_dir, "DESCRIPTION")
+if (!file.exists(desc_file)) {
   stop(sprintf(
     paste(sep = "\n",
       "Could not find package at '%s'",
@@ -24,21 +28,34 @@ if (!file.exists(file.path(pkg_dir, "DESCRIPTION"))) {
 }
 
 # Install package dependencies
-if (!disable_install_dev_deps){
+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 = "validation_report",
+  output_file = report_output_prefix,
   output_format = report_format,
   params = list(pkg_dir = pkg_dir)
 )
 
-cat(sprintf("Created report at: '%s'", report_file_path))
+# 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))

template.Rmd

@@ -66,7 +66,7 @@ documentation of the installation of this package on an open source R environmen
 - Traceability matrix of specifications (documented behaviours) and testing
 - Risk assessment benchmarks
 
-This report is fully automated, so is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful. Validation is system dependent, so specific to the validation environment environment used by this gh-action (see `https://github.com/insightsengineering/thevalidatoR/blob/main/Dockerfile` for the base dockerfile, and details in this document for the session info).
+This report is fully automated, so is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful. Validation aims to be system independent as the underlying workflow is based on the ["composite"](https://docs.github.com/en/actions/creating-actions/creating-a-composite-action) type of Github Action.
 
 # Installation environment and package