From 27ccc513d5e4487e33873cc0e8342af87f46bbb5 Mon Sep 17 00:00:00 2001
From: Integer Limit <103940576+IntegerLimit@users.noreply.github.com>
Date: Tue, 30 Apr 2024 22:06:56 +1000
Subject: [PATCH 1/4] Expand CI System to Build for Mac x86-64 and Windows
 x86-64

---
 .github/workflows/build.yaml | 167 +++++++++++++++++++++++++++++++++++
 .github/workflows/ci.yaml    |  90 -------------------
 2 files changed, 167 insertions(+), 90 deletions(-)
 create mode 100644 .github/workflows/build.yaml
 delete mode 100644 .github/workflows/ci.yaml

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
new file mode 100644
index 000000000..d552cada1
--- /dev/null
+++ b/.github/workflows/build.yaml
@@ -0,0 +1,167 @@
+name: Build
+
+on:
+  push: 
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+
+# If a Second Commit is Pushed After, and Build is Not Complete, Cancel
+# Extremely Important with the High Computation Time and Power Required of Arm Linux Builds
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-linux-x86-64:
+    name: Linux x86-64
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        gcc-version: [10, 12]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        submodules: "recursive"
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update -q -y
+        sudo apt-get install -q -y gcc-${{ matrix.gcc-version }} g++-${{ matrix.gcc-version}} cmake libeigen3-dev libboost-dev
+
+    - name: Build
+      run: |
+        mkdir build
+        cd build
+        export CXXFLAGS="-std=c++14" # this is important to be able to build with g++ newer than v10
+        cmake .. -DCMAKE_C_COMPILER=$(which gcc-${{ matrix.gcc-version }}) -DCMAKE_CXX_COMPILER=$(which g++-${{ matrix.gcc-version }})
+        make -j
+        file iqtree2 | grep x86-64
+
+  build-linux-aarch64:
+    name: Linux aarch64
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: "recursive"
+
+      - name: Build on Linux ARM64
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: aarch64
+          distro: ubuntu20.04
+          githubToken: ${{ github.token }}
+          dockerRunArgs: |
+            --volume "${PWD}:/iqtree2"
+          install: |
+            apt-get update -q -y
+            apt-get install -q -y cmake gcc g++ file libeigen3-dev libboost-dev
+          run: |
+            cd /iqtree2
+            mkdir build
+            cd build
+            cmake ..
+            make -j
+            file iqtree2 | grep aarch64
+
+  build-macos-x86_64:
+    name: Mac OS x86-64
+    runs-on: macos-13 # Mac OS 14 Does Not Support x86-64
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: "recursive"
+  
+      - name: Install dependencies
+        run: brew install make eigen boost libomp
+  
+      - name: Build
+        run: |
+          set -x
+          mkdir build
+          cd build
+          export LDFLAGS="-L/usr/local/opt/libomp/lib"
+          export CPPFLAGS="-I/usr/local/opt/libomp/include"
+          export CXXFLAGS="-I/usr/local/opt/libomp/include"
+          cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
+          gmake -j
+          file iqtree2 | grep x86_64
+
+  build-macos-arm:
+    name: Mac OS ARM64
+    runs-on: macos-14
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: "recursive"
+  
+      - name: Install dependencies
+        run: brew install make eigen boost libomp
+
+      - name: Build
+        run: |
+          set -x
+          mkdir build
+          cd build
+          export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
+          export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
+          export CXXFLAGS="-I/opt/homebrew/opt/libomp/include"
+          cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
+          gmake -j
+          file iqtree2 | grep arm64
+
+  build-windows-x86-64:
+    name: Windows x86-64
+    runs-on: windows-2022
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: "recursive"
+
+      - name: Install LLVM v14
+        shell: cmd
+        run: choco install llvm --version=14.0.6 --allow-downgrade
+              
+      - name: Install Boost
+        uses: MarkusJx/install-boost@v2.4.5
+        id: install-boost
+        with:
+            boost_version: 1.84.0
+            platform_version: 2022
+            toolset: mingw
+
+      - name: Install Eigen3
+        shell: cmd
+        run: choco install eigen
+
+      - name: Compile
+        shell: cmd
+        run: |
+          if exist build rd /s /q build
+          mkdir build
+          cd build
+          -DBoost_INCLUDE_DIR=${{steps.install-boost.outputs.BOOST_ROOT}}/include\
+          -DBoost_LIBRARY_DIRS=${{steps.install-boost.outputs.BOOST_ROOT}}/lib
+          cmake -G "MinGW Makefiles" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_FLAGS=--target=x86_64-pc-windows-gnu -DCMAKE_CXX_FLAGS=--target=x86_64-pc-windows-gnu -DCMAKE_MAKE_PROGRAM=mingw32-make ..
+          make -j
+        env:
+          BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }}
+
+      - name: Check File Arch
+        shell: bash
+        run: |
+          cd build
+          file iqtree2.exe | grep x86-64
+
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
deleted file mode 100644
index 46c3f97f0..000000000
--- a/.github/workflows/ci.yaml
+++ /dev/null
@@ -1,90 +0,0 @@
-name: Linux x86_64
-
-on:
-  push: 
-    branches: ["master"]
-  pull_request:
-    branches: ["master"]
-
-jobs:
-  build:
-    name: Linux x86_64
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        gcc-version: [10, 12]
-
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-      with:
-        submodules: "recursive"
-
-    - name: Install dependencies
-      run: |
-        sudo apt-get update -q -y
-        sudo apt-get install -q -y gcc-${{ matrix.gcc-version }} g++-${{ matrix.gcc-version}} cmake libeigen3-dev libboost-dev
-
-    - name: Build
-      run: |
-        mkdir build
-        cd build
-        export CXXFLAGS="-std=c++14" # this is important to be able to build with g++ newer than v10
-        cmake .. -DCMAKE_C_COMPILER=$(which gcc-${{ matrix.gcc-version }}) -DCMAKE_CXX_COMPILER=$(which g++-${{ matrix.gcc-version }})
-        make -j
-        file iqtree2 | grep x86-64
-
-  build-aarch64:
-    name: Linux aarch64
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          submodules: "recursive"
-
-      - name: Build on Linux ARM64
-        uses: uraimo/run-on-arch-action@v2
-        with:
-          arch: aarch64
-          distro: ubuntu20.04
-          githubToken: ${{ github.token }}
-          dockerRunArgs: |
-            --volume "${PWD}:/iqtree2"
-          install: |
-            apt-get update -q -y
-            apt-get install -q -y cmake gcc g++ file libeigen3-dev libboost-dev
-          run: |
-            cd /iqtree2
-            mkdir build
-            cd build
-            cmake ..
-            make -j
-            file iqtree2 | grep aarch64
-
-  build-macos-m:
-    name: Mac OS ARM64
-    runs-on: macos-14
-
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-      with:
-        submodules: "recursive"
-
-    - name: Install dependencies
-      run: brew install make eigen boost libomp
-
-    - name: Build
-      run: |
-        set -x
-        mkdir build
-        cd build
-        export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
-        export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
-        export CXXFLAGS="-I/opt/homebrew/opt/libomp/include"
-        cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
-        gmake -j
-        file iqtree2 | grep arm64

From d289dcb56a47c082f472bd0c2816969deae5fcd8 Mon Sep 17 00:00:00 2001
From: Integer Limit <103940576+IntegerLimit@users.noreply.github.com>
Date: Thu, 2 May 2024 21:32:12 +1000
Subject: [PATCH 2/4] Rename `build.yaml` Back To `ci.yaml`

---
 .github/workflows/{build.yaml => ci.yaml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{build.yaml => ci.yaml} (100%)

diff --git a/.github/workflows/build.yaml b/.github/workflows/ci.yaml
similarity index 100%
rename from .github/workflows/build.yaml
rename to .github/workflows/ci.yaml

From df6ac7e2b59f468b0008cf0fd24eac2e69d54796 Mon Sep 17 00:00:00 2001
From: Integer Limit <103940576+IntegerLimit@users.noreply.github.com>
Date: Thu, 2 May 2024 21:56:56 +1000
Subject: [PATCH 3/4] Use Major Version Specification for Boost Install Step

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index d552cada1..3a33f33dd 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -135,7 +135,7 @@ jobs:
         run: choco install llvm --version=14.0.6 --allow-downgrade
               
       - name: Install Boost
-        uses: MarkusJx/install-boost@v2.4.5
+        uses: MarkusJx/install-boost@v2
         id: install-boost
         with:
             boost_version: 1.84.0

From f359701aebb41886cb4efba3423b26dcbd8f4547 Mon Sep 17 00:00:00 2001
From: Integer Limit <103940576+IntegerLimit@users.noreply.github.com>
Date: Fri, 3 May 2024 12:43:02 +1000
Subject: [PATCH 4/4] Use Specific Version Specifier for Boost Install Step

Action does not include proper tags to be able to use major version specification.
---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 3a33f33dd..d552cada1 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -135,7 +135,7 @@ jobs:
         run: choco install llvm --version=14.0.6 --allow-downgrade
               
       - name: Install Boost
-        uses: MarkusJx/install-boost@v2
+        uses: MarkusJx/install-boost@v2.4.5
         id: install-boost
         with:
             boost_version: 1.84.0