Put back ADMIXTOOLS into the CI pipeline

bodkan · Oct 7, 2024 · b968a4f · b968a4f
1 parent 1c51c2c
commit b968a4f
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -48,56 +48,56 @@ jobs:
         if: runner.os == 'macOS'
         run: brew install gdal
 
-      # - name: Install ADMIXTOOLS dependencies (Linux)
-      #   if: runner.os == 'Linux'
-      #   run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev
+      - name: Install ADMIXTOOLS dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev
 
-      # - name: Install ADMIXTOOLS dependencies (macOS)
-      #   if: runner.os == 'macOS'
-      #   run: brew install openblas gsl lapack bedtools
+      - name: Install ADMIXTOOLS dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: brew install openblas gsl lapack bedtools
 
-      # - name: Compile and install ADMIXTOOLS (Linux) # + macOS)
-      #   # if: runner.os != 'Windows'
-      #   if: runner.os == 'Linux'
-      #   run: |
-      #     # create a single directory for all external software
-      #     mkdir -p ~/deps
-      #     cd ~/deps
-      #
-      #     # download and unpack the ADMIXTOOLS source code
-      #     curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz
-      #     tar xf v7.0.2.tar.gz
-      #     cd AdmixTools-7.0.2
-      #
-      #     # set compiler flags (compilation on macOS was failing unable to find
-      #     # openblas library files)
-      #     export LDFLAGS="-L/usr/local/opt/openblas/lib"
-      #     export CPPFLAGS="-I/usr/local/opt/openblas/include"
-      #
-      #     # compile ADMIXTOOLS and move binaries under bin/
-      #     cd src
-      #     make clobber
-      #     make LDLIBS="-llapack" all
-      #     make install
-      #
-      #     # download testing data for unit tests
-      #     cd ../
-      #     curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
-      #     tar xf AdmixTools_Example_Data.tar_.gz
-      #
-      #     # run the Perl script with tests for the compiled binaries
-      #     cd examples
-      #     # fix unportable Perl shebang
-      #     if [[ "$OSTYPE" == "darwin"* ]]; then
-      #       sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog
-      #     else
-      #       sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog
-      #     fi
-      #     ./mklog
-      #     cd ../
-      #
-      #     # we need to do this in bash because of $OSTYPE above
-      #   shell: bash
+      - name: Compile and install ADMIXTOOLS (Linux) # + macOS)
+        # if: runner.os != 'Windows'
+        if: runner.os == 'Linux'
+        run: |
+          # create a single directory for all external software
+          mkdir -p ~/deps
+          cd ~/deps
+
+          # download and unpack the ADMIXTOOLS source code
+          curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz
+          tar xf v7.0.2.tar.gz
+          cd AdmixTools-7.0.2
+
+          # set compiler flags (compilation on macOS was failing unable to find
+          # openblas library files)
+          export LDFLAGS="-L/usr/local/opt/openblas/lib"
+          export CPPFLAGS="-I/usr/local/opt/openblas/include"
+
+          # compile ADMIXTOOLS and move binaries under bin/
+          cd src
+          make clobber
+          make LDLIBS="-llapack" all
+          make install
+
+          # download testing data for unit tests
+          cd ../
+          curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
+          tar xf AdmixTools_Example_Data.tar_.gz
+
+          # run the Perl script with tests for the compiled binaries
+          cd examples
+          # fix unportable Perl shebang
+          if [[ "$OSTYPE" == "darwin"* ]]; then
+            sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog
+          else
+            sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog
+          fi
+          ./mklog
+          cd ../
+
+          # we need to do this in bash because of $OSTYPE above
+        shell: bash
 
       - name: Compile and install SLiM on Unix
         if: runner.os != 'Windows'

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -25,49 +25,49 @@ jobs:
         if: runner.os == 'macOS'
         run: brew install gdal
 
-      # - name: Install ADMIXTOOLS dependencies
-      #   run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev
-
-      # - name: Compile and install ADMIXTOOLS
-      #   run: |
-      #     # create a single directory for all external software
-      #     mkdir -p ~/deps
-      #     cd ~/deps
-      #
-      #     # download and unpack the ADMIXTOOLS source code
-      #     curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz
-      #     tar xf v7.0.2.tar.gz
-      #     cd AdmixTools-7.0.2
-      #
-      #     # set compiler flags (compilation on macOS was failing unable to find
-      #     # openblas library files)
-      #     export LDFLAGS="-L/usr/local/opt/openblas/lib"
-      #     export CPPFLAGS="-I/usr/local/opt/openblas/include"
-      #
-      #     # compile ADMIXTOOLS and move binaries under bin/
-      #     cd src
-      #     make clobber
-      #     make LDLIBS="-llapack" all
-      #     make install
-      #
-      #     # download testing data for unit tests
-      #     cd ../
-      #     curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
-      #     tar xf AdmixTools_Example_Data.tar_.gz
-      #
-      #     # run the Perl script with tests for the compiled binaries
-      #     cd examples
-      #     # fix unportable Perl shebang
-      #     if [[ "$OSTYPE" == "darwin"* ]]; then
-      #       sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog
-      #     else
-      #       sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog
-      #     fi
-      #     ./mklog
-      #     cd ../
-      #
-      #     # we need to do this in bash because of $OSTYPE above
-      #   shell: bash
+      - name: Install ADMIXTOOLS dependencies
+        run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev
+
+      - name: Compile and install ADMIXTOOLS
+        run: |
+          # create a single directory for all external software
+          mkdir -p ~/deps
+          cd ~/deps
+
+          # download and unpack the ADMIXTOOLS source code
+          curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz
+          tar xf v7.0.2.tar.gz
+          cd AdmixTools-7.0.2
+
+          # set compiler flags (compilation on macOS was failing unable to find
+          # openblas library files)
+          export LDFLAGS="-L/usr/local/opt/openblas/lib"
+          export CPPFLAGS="-I/usr/local/opt/openblas/include"
+
+          # compile ADMIXTOOLS and move binaries under bin/
+          cd src
+          make clobber
+          make LDLIBS="-llapack" all
+          make install
+
+          # download testing data for unit tests
+          cd ../
+          curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
+          tar xf AdmixTools_Example_Data.tar_.gz
+
+          # run the Perl script with tests for the compiled binaries
+          cd examples
+          # fix unportable Perl shebang
+          if [[ "$OSTYPE" == "darwin"* ]]; then
+            sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog
+          else
+            sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog
+          fi
+          ./mklog
+          cd ../
+
+          # we need to do this in bash because of $OSTYPE above
+        shell: bash
 
       - name: Compile and install SLiM
         run: |