Add files from internal repo

Add pkgdown to gh actions

Add pre-commit, roxygenize and R CMD CHECK actions

Pin pre-commit version

Create LICENSE

Fix pre-commit

Cleanup

.Rbuildignore

@@ -0,0 +1,2 @@
+^doc$
+^Meta$

.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = false
+insert_final_newline = false
+
+[*.{yml,yaml,R,r,Rmd,rmd,qmd}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

.github/workflows/pkgdown.yml

@@ -0,0 +1,49 @@
+# The purpose of this action is to generate the website using pkgdown.
+# On a commit to the main branch, the website will be deployed on github pages.
+# In pull requests, a zip file with the website will be generated which can be downloaded
+# in order to preview the website.
+#
+# 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]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
+        uses: JamesIves/github-pages-deploy-action@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pre-commit.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main, master]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/action@v3.0.0

.github/workflows/roxygenize.yml

@@ -0,0 +1,43 @@
+# The purpose of this action is to run `document()` of the roxygen2 package on each commit.
+# If new documentation was generated, it will automatically add a commit to the current branch.
+# This has the same effect as running `document()` locally, but
+#  * ensures it cannot be forgotten
+#  * saves setting up the development environment locally, which is especially useful for new contributors.
+#
+# 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:
+  pull_request:
+    paths: ["R/**", ".github/workflows"]
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - 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
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: Roxygenize

.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

.gitignore

@@ -1,11 +1,20 @@
+## custom
+/exploratory/
+/doc/
+
+## editors
+.vscode
+
+## R
 .Rproj.user
 .Rhistory
 .Rdata
 .httr-oauth
 .DS_Store
-.vscode
 inst/doc
-/doc/
 /Meta/
+<<<<<<< HEAD
 
-/exploratory/
+/exploratory/
+=======
+>>>>>>> 9a40da3 (Add files from internal repo)

.lintr

@@ -0,0 +1,6 @@
+linters: linters_with_defaults(
+    object_length_linter = NULL,
+    object_usage_linter = NULL,
+    line_length_linter(120),
+    commented_code_linter = NULL
+  )

.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+# 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: v0.3.2.9007
+    hooks:
+      - id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style, --scope=tokens]
+        exclude: "exploratory.*$"
+      - id: readme-rmd-rendered
+        exclude: "exploratory.*$"
+      - id: parsable-R
+      - id: no-browser-statement
+        exclude: "exploratory.*$"
+      - id: no-debug-statement
+        exclude: "exploratory.*$"
+      - id: deps-in-desc
+        args: [--allow_private_imports]
+        exclude: "exploratory.*$"
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer
+        exclude: '\.Rd'
+  - repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+    rev: v1.5.1
+    hooks:
+      # Only reuiqred when https://pre-commit.ci is used for config validation
+      - id: check-pre-commit-ci-config
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        exclude: "(inst/extdata|data)/.*"
+        # `exclude: <regex>` to allow committing specific files
+  - 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

DESCRIPTION

@@ -0,0 +1,29 @@
+Package: MAEio
+Title: Read Various Data Sources into MultiAssayExperiment objects 
+Version: 0.0.0.9000
+Authors@R: 
+    person("Gregor", "Sturm", , "gregor.sturm@boehringer-ingelheim.com", role = c("aut", "cre"))
+Description: Read Various Data Sources into MultiAssayExperiment objects
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Suggests: 
+    knitr,
+    rmarkdown,
+    purrr,
+    conflicted,
+    testthat (>= 3.0.0)
+Depends:
+    SummarizedExperiment,
+    readxl,
+    MultiAssayExperiment,
+    tibble,
+    pbapply,
+    tidyr,
+    purrr,
+    dplyr,
+    BumpyMatrix,
+    rvest
+Config/testthat/edition: 3
+biocViews:
+VignetteBuilder: knitr

Jenkinsfile

@@ -0,0 +1,10 @@
+pipeline {
+    agent any
+    stages {
+        stage('hello') {
+            steps {
+                sh 'echo Hello Jenkins!'
+            }
+        }
+    }
+}