From 34e65fad1338ab05b6f9ddd145ef2bb3e45c267b Mon Sep 17 00:00:00 2001
From: Anthony Gitter <gitter@biostat.wisc.edu>
Date: Fri, 26 Apr 2024 11:18:27 -0500
Subject: [PATCH] Switch to setup-matlab for macOS testing

---
 .github/workflows/install-test.yml | 44 ++++++++++++++++--------------
 1 file changed, 24 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/install-test.yml b/.github/workflows/install-test.yml
index 443b581..935bde8 100644
--- a/.github/workflows/install-test.yml
+++ b/.github/workflows/install-test.yml
@@ -68,26 +68,30 @@ jobs:
         environment-file: tests/environment.yml
         auto-activate-base: false
         miniconda-version: 'latest'
-    - name: Cache MATLAB runtime installer
-      id: cache-installer
-      uses: actions/cache@v1
+#    - name: Cache MATLAB runtime installer
+#      id: cache-installer
+#      uses: actions/cache@v1
+#      with:
+#        path: installer
+#        key: ${{ runner.os }}-matlab-R2020a-installer
+#    - name: Download MATLAB runtime installer
+#      if: steps.cache-installer.outputs.cache-hit != 'true'
+#      run: wget --quiet --directory-prefix=installer http://ssd.mathworks.com/supportfiles/downloads/R2020a/Release/2/deployment_files/installer/complete/maci64/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip
+#    - name: Install MATLAB runtime
+#      run: |
+#        unzip -d . -q installer/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip
+#        hdiutil mount MATLAB_Runtime_R2020a_Update_2_maci64.dmg
+#        cp -R /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64 .
+#        hdiutil unmount /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64
+#        sudo ./MATLAB_Runtime_R2020a_Update_2_maci64/InstallForMacOSX.app/Contents/MacOS/InstallForMacOSX -mode silent -agreeToLicense yes
+#        MATLAB_RUNTIME_PATH=/Applications/MATLAB/MATLAB_Runtime/v98
+#        echo "MATLAB_RUNTIME_PATH=$MATLAB_RUNTIME_PATH" >> $GITHUB_ENV
+#        echo "DYLD_LIBRARY_PATH=$MATLAB_RUNTIME_PATH/runtime/maci64:$MATLAB_RUNTIME_PATH/sys/os/maci64:$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_ENV
+#        echo "$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_PATH
+    - name: Set up MATLAB
+      uses: matlab-actions/setup-matlab@v2
       with:
-        path: installer
-        key: ${{ runner.os }}-matlab-R2020a-installer
-    - name: Download MATLAB runtime installer
-      if: steps.cache-installer.outputs.cache-hit != 'true'
-      run: wget --quiet --directory-prefix=installer http://ssd.mathworks.com/supportfiles/downloads/R2020a/Release/2/deployment_files/installer/complete/maci64/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip
-    - name: Install MATLAB runtime
-      run: |
-        unzip -d . -q installer/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip
-        hdiutil mount MATLAB_Runtime_R2020a_Update_2_maci64.dmg
-        cp -R /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64 .
-        hdiutil unmount /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64
-        sudo ./MATLAB_Runtime_R2020a_Update_2_maci64/InstallForMacOSX.app/Contents/MacOS/InstallForMacOSX -mode silent -agreeToLicense yes
-        MATLAB_RUNTIME_PATH=/Applications/MATLAB/MATLAB_Runtime/v98
-        echo "MATLAB_RUNTIME_PATH=$MATLAB_RUNTIME_PATH" >> $GITHUB_ENV
-        echo "DYLD_LIBRARY_PATH=$MATLAB_RUNTIME_PATH/runtime/maci64:$MATLAB_RUNTIME_PATH/sys/os/maci64:$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_ENV
-        echo "$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_PATH
+        release: R2020a # must match the release used to compile the code       
     - name: Download SINGE
       run: |
         wget --quiet https://github.com/gitter-lab/SINGE/releases/download/$SINGE_VERSION/SINGE_mac.tgz
@@ -95,6 +99,6 @@ jobs:
     - name: Run and test SINGE
       shell: bash -l {0}
       run: |
-        bash SINGE.sh $MATLAB_RUNTIME_PATH standalone data1/X_SCODE_data.mat data1/gene_list.mat Output tests/example_hyperparameters.txt
+        bash SINGE.sh ${{ steps.setup-matlab.outputs.matlabroot }} standalone data1/X_SCODE_data.mat data1/gene_list.mat Output tests/example_hyperparameters.txt
         ls -l Output
         bash tests/compare_example_output.sh Output tests/reference/latest 1e-02 1e-02