From 57705939987ac9571b449d8748e55554c511dcbb Mon Sep 17 00:00:00 2001
From: Fleming Kretschmer <fleming.kretschmer@uni-jena.de>
Date: Thu, 8 Feb 2024 13:19:37 +0100
Subject: [PATCH] adapted normal preprocessing workflow to work with docker

---
 .github/workflows/preprocess.yaml | 48 ++++++-------------------------
 1 file changed, 9 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/preprocess.yaml b/.github/workflows/preprocess.yaml
index b1a810c..d7aafae 100644
--- a/.github/workflows/preprocess.yaml
+++ b/.github/workflows/preprocess.yaml
@@ -11,10 +11,14 @@ on:
 jobs:
   preprocess:
     name: Preprocess raw data
-    # NOTE: on windows as computing of descriptors has a bug on linux right now
-    runs-on: windows-2019
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} # needed for pulling R packages from github
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/${{ github.actor }}/repo_rt_preprocessing:latest
+      env:
+        RENV_PATHS_LIBRARY: '/renv/library'
+    defaults:
+      run:
+        shell: bash
 
     steps:
     - name: Checkout fork repository
@@ -36,46 +40,11 @@ jobs:
       run: echo "files=$(for f in ${{ steps.files.outputs.all }}; do basename $(dirname $f); done | grep -E '^[0-9]+$' | sort | uniq | tr '\n' ' ')" >> $GITHUB_OUTPUT
 
     - name: List all added files
-      shell: bash {0}
       run: |
         for f in ${{ steps.filesfolders.outputs.files }}; do
           ls -lh raw_data/$f
         done
 
-    - name: Pyton dependencies
-      run: pip install -r scripts/Python/requirements.txt
-
-    - name: Setup java
-      uses: actions/setup-java@v3
-      with:
-        distribution: 'temurin'
-        java-version: '17'
-
-    - name: Set RENV_PATHS_ROOT
-      shell: bash
-      run: |
-        echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV
-
-    - name: Setup R
-      uses: r-lib/actions/setup-r@v2
-      with:
-        use-public-rspm: true
-        r-version: 4.2.2
-
-    - name: Restore Renv package cache
-      uses: actions/cache@v3
-      with:
-        path: ${{ env.RENV_PATHS_ROOT }}
-        key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-        restore-keys: |
-          ${{ runner.os }}-renv-
-
-    - name: Activate renv
-      shell: Rscript {0}
-      run: |
-        options(renv.config.mran.enabled = FALSE)
-        renv::restore()
-
     - name: Standardize compounds
       run: Rscript scripts/R_ci/compounds_standardize.R ${{ steps.filesfolders.outputs.files }}
 
@@ -117,6 +86,7 @@ jobs:
       run: |
         git config --global user.email 'actions@github.com'
         git config --global user.name 'Github Actions'
+        git config --global safe.directory '*'
         # Use LFS storage of main repository: no push access to fork LFS storage
         # TODO: change once repository is moved
         git config lfs.url 'https://github.com/f-kretschmer/pr_test_repo.git/info/lfs'