From 6a0dc3c84c610340186177c76a8405d1dd514551 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Fri, 24 May 2024 16:24:37 +0930
Subject: [PATCH] add workflows github action

---
 .github/workflows/rworkflows.yml | 57 ++++++++++++++++++++++++++++++++
 .gitignore                       | 26 +++++++++------
 2 files changed, 73 insertions(+), 10 deletions(-)
 create mode 100644 .github/workflows/rworkflows.yml

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
new file mode 100644
index 0000000..94d43eb
--- /dev/null
+++ b/.github/workflows/rworkflows.yml
@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io
diff --git a/.gitignore b/.gitignore
index 7ed9207..2720722 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,29 +1,35 @@
+# RStudio files
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
 HPCell.Rproj
+
+# macOS files
 .DS_Store
 ._.DS_Store
+
+# Generic files
 file*
-HPCell.Rproj
+
+# Project specific files
 input_file.rds
 input_reference.rds
 reference_azimuth.rds
 temp_computing_resources.rds
 tissue.rds
-README.md
+
+# Exclude pipeline and scripts directories and files
 pipeline_store
 pipeline_store.R
 R_scripts
-.R
-.RDataTmp
-.RDataTmp1
-.github
 Pipeline_benchmarking_script.R
+
+# Data directories
 fibrosis_data
-.R
-.RDataTmp
-.RDataTmp1
-.github
 
+# Temporary R data files
+.RDataTmp*
+
+# Exclude README from being ignored
+!README.md
\ No newline at end of file