Enable CI for dso-r (#10)

* Add github actions for test and release * enable pre-commit * Remove python deps * fix syntax * Roxygenize with pre-commit * Update pre-commit hook * Add missing params documentation * Set workflow permissions * autofixes * pre-commit autofixes * disable autoformatting in certain unit tests * pre-commit autofixes * pre-commit autofixes * Fix missing params docs * pre-commit autofixes * trigger CI * updated to remove warnings * updated dsoParams class to remove warnings; * pre-commit autofixes * trigger CI * updated .Rbuildignore * updated * updated dsoparams class * bumped version * pre-commit autofixes * trigger CI --------- Co-authored-by: grst <[email protected]> Co-authored-by: zxBIB Schreyer,Daniel (TMCP Data Sc) EXTERNAL <[email protected]> Co-authored-by: DSchreyer <[email protected]>
Boehringer-Ingelheim · Oct 18, 2024 · 1b7a290 · 1b7a290
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,5 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.pre-commit-config\.yaml$
+^\.github$
+^CHANGELOG\.md$
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,41 @@
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: pre-commit
+
+jobs:
+  pre-commit:
+    permissions:
+      # Give the default GITHUB_TOKEN write permission to commit and push the
+      # added or changed files to the repository.
+      contents: write
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref }}
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - uses: pre-commit/[email protected]
+
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        if: '!cancelled()'
+        with:
+          commit_message: pre-commit autofixes
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,43 @@
+name: Build and Attach R Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          http-user-agent: release
+          use-public-rspm: true
+
+      - name: Build package
+        run: |
+          R CMD build .
+          FILENAME=$(ls dso_*.tar.gz)
+          echo "FILENAME=${FILENAME}" >> $GITHUB_ENV
+
+      - name: Check version
+        run: |
+          VERSION=$(echo $FILENAME | sed 's/.*_\(.*\).tar.gz/\1/')
+          if [ "v${VERSION}" != "${GITHUB_REF#refs/tags/}" ]; then
+            echo "Version mismatch. Tag version and package version should be the same."
+            exit 1
+          fi
+
+      - name: Attach tarball to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ github.event.release.upload_url }}
+          asset_path: ./${{ env.FILENAME }}
+          asset_name: ${{ env.FILENAME }}
+          asset_content_type: application/gzip
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,50 @@
+# The purpose of this workflow is to execute `R CMD check` on different R and OS version.
+#
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, 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: macOS-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,49 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3
+    hooks:
+      - id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style, --scope=tokens]
+      - id: parsable-R
+      - id: no-browser-statement
+      - id: no-debug-statement
+      - id: deps-in-desc
+        args: [--allow_private_imports]
+      - id: roxygenize
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: end-of-file-fixer
+        exclude: '\.Rd'
+      - id: detect-private-key
+      - id: check-ast
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+    rev: v1.5.1
+    hooks:
+      # Only reuiqred when https://pre-commit.ci is used for config validation
+      - id: check-pre-commit-ci-config
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        exclude: "(inst/extdata|data)/.*"
+  # - repo: https://github.com/pre-commit/mirrors-prettier
+  #   rev: v3.0.0-alpha.6
+  #   hooks:
+  #     - id: prettier
+  #       language_version: "17.9.1"
+
+ci:
+  autoupdate_schedule: monthly
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,16 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.4.3
+
+### Improvements
+
+-   updated .Rbuildignore ignoring package redundant files
+-   added precommit configs
+-   included methods show
+-   set class of dsoParams object
+-   fixed R CMD check warnings
+
 ## v0.4.2
 
 ### Improvements

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,22 +1,25 @@
 Package: dso
 Type: Package
-Title: dso R companion package 
-Version: 0.4.2
+Title: dso R companion package
+Version: 0.4.3
 Author: Daniel Schreyer<[email protected]>,
-    Gregor Sturm<[email protected]>, 
+    Gregor Sturm<[email protected]>,
     Thomas Schwarzl<[email protected]>
 Maintainer: Daniel Schreyer<[email protected]>,
-    Gregor Sturm<[email protected]>, 
+    Gregor Sturm<[email protected]>,
     Thomas Schwarzl<[email protected]>
-Description: Collection of functions used with the DevOps dso application. 
+Description: Collection of functions used with the DevOps dso application.
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
     yaml,
     glue,
-    here
-RoxygenNote: 7.3.1
-Suggests: 
+    here,
+    stringr,
+    methods,
+    rlang
+RoxygenNote: 7.3.2
+Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -11,11 +11,13 @@ export(read_params)
 export(safe_get)
 export(set_stage)
 export(stage_here)
+exportClasses(dsoParams)
 exportMethods(as.list)
 exportMethods(show)
 importFrom(glue,glue)
 importFrom(here,here)
 importFrom(here,i_am)
+importFrom(methods,show)
 importFrom(rlang,caller_env)
 importFrom(stringr,coll)
 importFrom(stringr,str_match_all)

diff --git a/R/class-dsoParams.R b/R/class-dsoParams.R
@@ -1,7 +1,18 @@
+#' dsoParams class
+#'
+#' @slot params A list of lists containing parameters
+#' @export
+setClass("dsoParams",
+  slots = list(
+    params = "list"
+  )
+)
+
 #' A "dsoParams" and its constructor:
 #'
 #' @title dsoParams: list with safe access
 #' @param x empty, or a recursive list of lists which is converted to dsoParams
+#'
 #' @examples
 #' # initiating empty
 #' params <- dsoParams()
@@ -15,25 +26,26 @@
 #' params <- dsoParams(params)
 #'
 #' @export
-dsoParams <- function( x = list()) {
-  if(! is.list(x))
+dsoParams <- function(x = list()) {
+  if (!is.list(x)) {
     stop("x needs to be a list or a list of lists.")
-
+  }
   # recursively
   x <- lapply(x, function(y) {
-      if(is.list(y)) {
-        dsoParams(y)
-      } else {
-        y
-      }
+    if (is.list(y)) {
+      dsoParams(y)
+    } else {
+      y
+    }
   })
   class(x) <- c("dsoParams", "list")
   return(x)
 }
 
-
 #' overriding the the $ operator to add secure list calling so that
 #' it cannot return NULL when call does not exist
+#' @param x dsoParams object
+#' @param name field name
 #' @export
 `$.dsoParams` <- function(x, name) {
   if (!name %in% names(x)) {
@@ -45,44 +57,55 @@ dsoParams <- function( x = list()) {
 
 #' And the [[ operator:  to add secure list calling so that
 #' it cannot return NULL when call does not exist
+#' @param x dsoParams object
+#' @param i index for `[[` operator
+#' @param ... additional arguments passed to the `[[` operator
 #' @export
 `[[.dsoParams` <- function(x, i, ...) {
   if (is.character(i) && !i %in% names(x)) {
     stop(paste("Element '", i, "' does not exist in dsoParams", sep = ""))
   } else if (is.numeric(i) && (i < 1 || i > length(x))) {
     stop(paste("Index '", i, "' is out of bounds in dsoParams", sep = ""))
   }
+
+
   NextMethod()
 }
 
 #' Custom print method for dsoParams class
+#' @param x dsoParams object
+#' @param ... additional parameters are ignored
 #' @export
-print.dsoParams <- function(object, ...) {
-  cat(yaml::as.yaml(object))
+print.dsoParams <- function(x, ...) {
+  cat(yaml::as.yaml(x))
 }
 
 #' Custom show method for dsoParams class
+#' @importFrom methods show
+#' @param object dsoParams object
 #' @export
-setMethod(f = "show",
-          signature = "dsoParams",
-          definition = function(object) {
-            cat(yaml::as.yaml(object))
-          })
+setMethod(
+  f = "show",
+  signature = "dsoParams",
+  definition = function(object) {
+    cat(yaml::as.yaml(object))
+  }
+)
 
-# Custom as.list method for dsoParams class
+#' Custom as.list method for dsoParams class
+#' @param x dsoParams object
+#' @return A list
 #' @export
 setMethod(
-  f = "as.list",  
+  f = "as.list",
   signature = "dsoParams",
   definition = function(x) {
     lapply(x, function(y) {
-      if("dsoParams" %in% class(y)) {
+      if ("dsoParams" %in% class(y)) {
         as.list(unclass(y))
       } else {
-        x
+        y
       }
     })
   }
 )
-
-
diff --git a/R/compile_config.R b/R/compile_config.R
@@ -6,6 +6,8 @@
 #'
 #' @keywords dso dvc yaml compile config
 #'
+#' @param dir directory (including subdirectories and relevant parent files) to compile. By default compiles the current working directory.
+#'
 #' @export
 #'
 #' @examples