ENH: Refactor test.yml3.

Author: ntustison

.github/workflows/test.yml

@@ -23,9 +23,8 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev python3 python3-pip
 
-      # 🧠 Cache R packages
       - name: Cache R packages
         uses: actions/cache@v3
         with:
@@ -34,41 +33,36 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-r-pkgs-
 
-      # ✅ Install key R packages (pin reticulate version!)
-      - name: Install R dependencies
-        run: |
-          Rscript -e 'install.packages(c("remotes", "testthat", "tensorflow", "reticulate"), repos = "https://cloud.r-project.org")'
-          Rscript -e 'remotes::install_version("reticulate", version = "1.34.0", repos = "https://cloud.r-project.org")'
+      - name: Cache reticulate environment
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/share/r-reticulate
+          key: ${{ runner.os }}-reticulate-${{ hashFiles('DESCRIPTION') }}
+          restore-keys: |
+            ${{ runner.os }}-reticulate-
 
-      # ✅ Install and configure Miniconda (clean Python)
-      - name: Install and configure Miniconda
+      - name: Install Python deps
         run: |
-          Rscript -e 'reticulate::install_miniconda(force = TRUE)'
-          Rscript -e 'reticulate::use_miniconda("r-reticulate", required = TRUE)'
-          Rscript -e 'reticulate::py_config()'
+          python3 -m pip install --upgrade pip
+          pip install tensorflow==2.9.1 numpy h5py
 
-      # ✅ Install TensorFlow into that Python environment
-      - name: Install TensorFlow
+      - name: Install R dependencies
         run: |
-          Rscript -e 'tensorflow::install_tensorflow()'
+          Rscript -e 'install.packages(c("remotes", "testthat", "reticulate", "tensorflow"), repos = "https://cloud.r-project.org")'
 
-      # ✅ Configure GitHub PAT (ensure this secret exists!)
-      - name: Configure GitHub PAT
+      - name: Point reticulate to system Python
         run: |
-          echo "GITHUB_PAT=${{ secrets.GH_PAT }}" >> $GITHUB_ENV
-          echo "GITHUB_PAT=${{ secrets.GH_PAT }}" >> ~/.Renviron
+          Rscript -e 'reticulate::use_python("/usr/bin/python3", required = TRUE)'
+          Rscript -e 'reticulate::py_config()'
 
-      # ✅ Install ANTsR from GitHub
       - name: Install ANTsR
         run: |
           Rscript -e 'remotes::install_github("ANTsX/ANTsR", dependencies = TRUE)'
 
-      # ✅ Install ANTsRNet (current repo)
       - name: Install ANTsRNet
         run: |
           Rscript -e 'remotes::install_local(".", dependencies = TRUE)'
 
-      # ✅ Run tests
       - name: Run tests
         run: |
           Rscript -e 'testthat::test_dir("tests/testthat", reporter = testthat::SummaryReporter$new())'