Merge pull request #33 from statisticalbiotechnology/fix/gh-actions-macos

Fix/gh actions macos

Author: MatthewThe

.github/workflows/build_and_release.yml

@@ -81,17 +81,19 @@ jobs:
 
   build-osx:
     runs-on: macos-latest
+    env:
+      JAVA_HOME: ""
     steps:
     - uses: actions/checkout@v2
     - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
+      run: mkdir -p my_rel my_build
     - name: configure_and_make
-      run: admin/builders/osx64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build -g
+      run: admin/builders/osx64_build.sh -s `pwd`/.. -r `pwd`/my_rel -b `pwd`/my_build -g
     - name: Upload packages
       uses: actions/upload-artifact@v4
       with:
         name: osx-packages
-        path: ../my_rel
+        path: my_rel
 
   build-win64:
     runs-on: windows-latest

CMakeLists.txt

@@ -1,7 +1,7 @@
 #############################################################################
 # NAME AND VERSION
 ###############################################################################
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.5)
 
 if(APPLE)
   # https://gitlab.kitware.com/cmake/cmake/issues/19067

admin/builders/install_proteowizard.sh

@@ -19,13 +19,7 @@ fi
 cd proteowizard
 
 # undo position independent code fix introduced here: https://github.com/ProteoWizard/pwiz/pull/1980
-sed -i 's/ -no-pie -fno-pie//g' Jamroot.jam
-
-
-toolset=""
-if [[ "$OSTYPE" == "darwin"* ]]; then
-  toolset="toolset=clang"
-fi
+sed -i.bak 's/ -no-pie -fno-pie//g' Jamroot.jam
 
 echo "Building ProteoWizard and Boost, this may take some time.."
 
@@ -60,14 +54,18 @@ echo "Building ProteoWizard and Boost, this may take some time.."
 
 status=$?
 if [ $status -ne 0 ]; then
-    echo "❌ Build failed. Showing log:"
+    echo "❌ Build failed with status $status. Showing log:"
     cat ../pwiz_installation.log
     exit $status
+else
+    echo "✅ Build succeeded."
 fi
 
+echo "Updating Proteowizard and Boost libraries and include files."
+
 # manually copy some libraries and headers used by maracluster but not by proteowizard
-find build-*-x86_64/ -type f | grep -i libboost_regex-.*\.a$ | xargs -I{} cp {} ../lib
-find build-*-x86_64/ -type f | grep -i libboost_program_options-.*\.a$ | xargs -I{} cp {} ../lib
+find build-*/ -type f | grep -i libboost_regex-.*\.a$ | xargs -I{} cp {} ../lib
+find build-*/ -type f | grep -i libboost_program_options-.*\.a$ | xargs -I{} cp {} ../lib
 
 rsync -ap --include "*/" --include "*.h" --include "*.hpp" --exclude "*"  libraries/zlib-1.2.3/ ../include
 rsync -ap --include "*/" --include "*.h" --include "*.hpp" --exclude "*" libraries/boost_aux/boost/ ../include/boost
@@ -90,4 +88,5 @@ wget --no-verbose --no-check-certificate https://github.com/boostorg/unordered/a
 tar -xzf boost_unordered.tar.gz
 rsync -ap --include "*/" --include "*.hpp" --include '*.ipp' --exclude '*' unordered-boost-1.86.0/include/boost/ include/boost
 
-touch pwiz_successful.txt
+touch pwiz_successful.txt
+echo "✅ Update libraries and include files succeeded."

admin/builders/osx64_build.sh

@@ -25,25 +25,29 @@ if [[ ! -d /Applications/XCode.app ]]
     exit 1
 fi
 
-package_manager_installed=true
-if [[ -d /opt/local/var/macports ]]
-  then
-    echo "[ Package manager ] : MacPorts "
+package_manager_installed=false
+if [[ -d /opt/local/var/macports ]]; then
+    echo "[ Package manager ] : MacPorts"
     package_manager="sudo port"
     other_packages="gnutar wget coreutils libomp cmake"
-elif [[ -f ${HOME}/bin/brew ]]
-  then
-    echo "[ Package manager ] : Homebrew "
-    package_manager=$HOME/bin/brew
-    other_packages="gnu-tar wget coreutils libomp cmake"
-elif [[ -f /usr/local/bin/brew ]]
-  then
-    echo "[ Package manager ] : Homebrew "
-    package_manager="brew"
-    ${package_manager} update || true # brew.rb raises an error on the vagrant box, just ignore it
-    other_packages="gnu-tar wget coreutils libomp cmake"
+    package_manager_installed=true
 else
-    package_manager_installed=false
+    brew_paths=(
+        "$HOME/bin/brew"
+        "/opt/homebrew/bin/brew"
+        "/usr/local/bin/brew"
+    )
+
+    for path in "${brew_paths[@]}"; do
+        if [[ -x "$path" ]]; then
+            echo "[ Package manager ] : Homebrew"
+            package_manager="$path"
+            other_packages="gnu-tar wget coreutils libomp cmake"
+            "$package_manager" update || true
+            package_manager_installed=true
+            break
+        fi
+    done
 fi
 
 if [ "$package_manager_installed" == false ]