ENH: Add windows support

.github/actions/build-iqtree/action.yml

@@ -19,19 +19,68 @@ runs:
         IQ_TREE_2_SHA=$(git rev-parse HEAD)
         echo "iqtree2-sha=${IQ_TREE_2_SHA}" >> "$GITHUB_OUTPUT"
 
-    - uses: actions/cache@v4
-      id: cache
+    - name: Cache IQ-TREE 2 (Windows)
+      if: runner.os == 'Windows'
+      uses: actions/cache@v4
+      id: cache-windows
+      with:
+        key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        path: |
+          src/piqtree/_libiqtree/iqtree2.lib
+          src/piqtree/_libiqtree/iqtree2.dll
+        lookup-only: true
+
+    - name: Cache IQ-TREE 2 (Linux/macOS)
+      if: runner.os != 'Windows'
+      uses: actions/cache@v4
+      id: cache-unix
       with:
         key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
-        path: src/piqtree/_libiqtree/libiqtree2.a
+        path: |
+          src/piqtree/_libiqtree/libiqtree2.a
         lookup-only: true
 
+    - name: Combine Cache Hits
+      id: cache
+      shell: bash
+      run: |
+        if [[ "${{ steps.cache-windows.outputs.cache-hit }}" == 'true' || "${{ steps.cache-unix.outputs.cache-hit }}" == 'true' ]]; then
+          echo "cache-hit=true" >> "$GITHUB_OUTPUT"
+        else
+          echo "cache-hit=false" >> "$GITHUB_OUTPUT"
+        fi
+
+    - name: Install Boost
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      uses: MarkusJx/[email protected]
+      id: install-boost
+      with:
+        boost_version: 1.84.0
+        platform_version: 2022
+        toolset: mingw
+
+    - name: Set Boost Environment Variables
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: |
+        echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
+        echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+
+    - name: Setup MSVC Developer Command Prompt
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      uses: ilammy/msvc-dev-cmd@v1
+
     - name: Build IQ-TREE
       shell: bash
       if: steps.cache.outputs.cache-hit != 'true'
       run: |
-        if [[ "${{ inputs.os }}" == "ubuntu-latest" ]]; then
-        sudo ./build_tools/before_all_linux.sh
+        if [[ "${{ runner.os }}" == "Linux" ]]; then
+          sudo ./build_tools/before_all_linux.sh
+        elif [[ "${{ runner.os }}" == "macOS" ]]; then
+          ./build_tools/before_all_mac.sh
+        elif [[ "${{ runner.os }}" == "Windows" ]]; then
+          ./build_tools/before_all_windows.sh
         else
-        ./build_tools/before_all_mac.sh
-        fi
+          echo "Unrecognized OS: '${{ inputs.os }}'."
+          exit 1
+        fi

.github/actions/setup-piqtree/action.yml

@@ -13,9 +13,24 @@ runs:
     - uses: "actions/setup-python@v5"
       with:
         python-version: ${{ inputs.python-version }}
-
-    - uses: actions/cache/restore@v4
+
+    - name: Cache IQ-TREE 2 (Windows)
+      if: runner.os == 'Windows'
+      uses: actions/cache/restore@v4
+      id: cache-windows
       with:
         key: ${{ inputs.cache-key }}
-        path: src/piqtree/_libiqtree/libiqtree2.a
-        fail-on-cache-miss: true
+        path: |
+          src/piqtree/_libiqtree/iqtree2.lib
+          src/piqtree/_libiqtree/iqtree2.dll
+        fail-on-cache-miss: true
+
+    - name: Cache IQ-TREE 2 (Linux/macOS)
+      if: runner.os != 'Windows'
+      uses: actions/cache/restore@v4
+      id: cache-unix
+      with:
+        key: ${{ inputs.cache-key }}
+        path: |
+          src/piqtree/_libiqtree/libiqtree2.a
+        fail-on-cache-miss: true

.github/workflows/build_wheels.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        # manylinux (x86)
+        # manylinux x86_64
         - os: ubuntu-latest
           platform_id: manylinux_x86_64
 
@@ -22,6 +22,10 @@ jobs:
         - os: macos-14
           platform_id: macosx_arm64
 
+        # Windows x86_64
+        - os: windows-latest
+          platform_id: win_amd64
+
     steps:
       - uses: "actions/checkout@v4"
         with:
@@ -35,21 +39,37 @@ jobs:
           platforms: arm64
 
       - name: Set macOS Deployment Target
-        if: ${{startsWith(matrix.os, 'macos')}}
+        if: runner.os == 'macOS'
         run: |
           if [[ "${{ matrix.os }}" == "macos-13" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=13.0" >> $GITHUB_ENV
           elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
           fi
 
+      - name: Install Boost
+        if: runner.os == 'Windows'
+        uses: MarkusJx/[email protected]
+        id: install-boost
+        with:
+          boost_version: 1.84.0
+          platform_version: 2022
+          toolset: mingw
+
+      - name: Setup MSVC Developer Command Prompt
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].3
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
+          CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
+          CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
           CIBW_BUILD: "*${{matrix.platform_id}}"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: pytest {package}/tests

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14] # Intel linux, Intel Mac, ARM Mac
+        os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
 
     steps:
       - uses: "actions/checkout@v4"
@@ -35,7 +35,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14] # Intel linux, Intel Mac, ARM Mac
+        os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
         python-version: ["3.11", "3.12", "3.13"] 
     steps:
       - uses: "actions/checkout@v4"
@@ -48,10 +48,15 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
-      - name: Install llvm
-        if: matrix.os != 'ubuntu-latest'
+      - name: Install llvm (macOS)
+        if: runner.os == 'macOS'
         run: |
           brew install llvm
+
+      - name: Install llvm (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          choco install -y llvm --version=14.0.6 --allow-downgrade
 
       - name: Run Nox Testing
         run: |

.github/workflows/release.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        # manylinux (x86)
+        # manylinux x86_64
         - os: ubuntu-latest
           platform_id: manylinux_x86_64
 
@@ -22,6 +22,10 @@ jobs:
         - os: macos-14
           platform_id: macosx_arm64
 
+        # Windows x86_64
+        - os: windows-latest
+          platform_id: win_amd64
+
     steps:
       - uses: "actions/checkout@v4"
         with:
@@ -35,23 +39,41 @@ jobs:
           platforms: arm64
 
       - name: Set macOS Deployment Target
-        if: ${{startsWith(matrix.os, 'macos')}}
+        if: runner.os == 'macOS'
         run: |
           if [[ "${{ matrix.os }}" == "macos-13" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=13.0" >> $GITHUB_ENV
           elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
           fi
-
+
+      - name: Install Boost
+        if: runner.os == 'Windows'
+        uses: MarkusJx/[email protected]
+        id: install-boost
+        with:
+          boost_version: 1.84.0
+          platform_version: 2022
+          toolset: mingw
+
+      - name: Setup MSVC Developer Command Prompt
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].3
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
+          CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
+          CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
+          CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
           CIBW_BUILD: "*${{matrix.platform_id}}"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: pytest {package}/tests
+          CIBW_TEST_SKIP: "*-macosx_universal2:x86_64" # skip x86 on m1 mac
           CIBW_SKIP: pp* # Disable building PyPy wheels on all platforms
 
       - name: Upload wheels

.gitignore

@@ -12,6 +12,9 @@
 
 # piqtree specific ignores
 src/piqtree/_libiqtree/**/*.a
+src/piqtree/_libiqtree/**/*.dll
+src/piqtree/_libiqtree/**/*.lib
+src/*.dll
 
 # docs
 data

build_tools/before_all_windows.sh

@@ -0,0 +1,13 @@
+# Install dependencies using choco
+
+export Boost_INCLUDE_DIR=$(echo $Boost_INCLUDE_DIR | sed 's|\\|/|g')
+export Boost_LIBRARY_DIRS=$(echo $Boost_LIBRARY_DIRS | sed 's|\\|/|g')
+
+echo "Boost_INCLUDE_DIR: $Boost_INCLUDE_DIR"
+echo "Boost_LIBRARY_DIRS: $Boost_LIBRARY_DIRS"
+
+choco install -y llvm --version=14.0.6 --allow-downgrade
+choco install -y eigen 
+
+# Build IQ-TREE
+bash build_tools/build_iqtree.sh

build_tools/build_iqtree.sh

@@ -9,11 +9,37 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
     echo $CXXFLAGS    
     cmake -DBUILD_LIB=ON -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
     gmake -j
+elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
+    echo "Building for Windows."
+
+    if [[ -n "$BOOST_ROOT" ]]; then
+        export Boost_INCLUDE_DIR="${BOOST_ROOT}"
+        export Boost_LIBRARY_DIRS="${BOOST_ROOT}"
+    fi
+
+    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=make \
+        -DBoost_INCLUDE_DIR=$Boost_INCLUDE_DIR \
+        -DBoost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS \
+        -DIQTREE_FLAGS="cpp14" \
+        -DBUILD_LIB=ON \
+        ..
+    make -j
 else
     echo "Building for linux."
-    cmake -DBUILD_LIB=ON ..
+    cmake -DBUILD_LIB=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j
 fi
 
 cd ../..
-mv iqtree2/build/libiqtree2.a src/piqtree/_libiqtree/
+
+if [[ "$OSTYPE" == "darwin"* || "$OSTYPE" == "linux"* ]]; then
+    mv iqtree2/build/libiqtree2.a src/piqtree/_libiqtree/
+elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
+    mv iqtree2/build/iqtree2.lib src/piqtree/_libiqtree/
+    mv iqtree2/build/iqtree2.dll src/piqtree/_libiqtree/
+fi

changelog.md

@@ -1,4 +1,24 @@
 
+<a id='changelog-0.5.0'></a>
+# Changes in release "0.5.0"
+
+## Contributors
+
+- @GavinHuttley added `nj_tree` as a hook for `cogent3.Alignment.quick_tree`.
+- @YapengLang handled negative branch lengths from the rapidNJ tree.
+- @rmcar17, @thomaskf general maintanence on the piqtree/IQ-TREE sides including work on windows behind the scenes.
+
+## ENH
+
+- Add support for Python 3.13, remove support for 3.10
+- IQ-TREE's rapidNJ implementation can be used as a hook for `quick_tree` on `cogent3` alignment objects. Try `Alignment.quick_tree(use_hook="piqtree")`.
+- `nj_tree` now by default does not allow negative branch lengths. Set `allow_negative=True` if this behaviour is desired.
+- Allow `str` to be used for `model` in `build_tree` and `fit_tree`. The value is automatically coerced into the `Model` class.
+
+## API
+
+- Simplify API for `piqtree_phylo` and `piqtree_fit` apps. Both now take a single parameter for the model, matching the parameter for `model` in `build_tree` and `fit_tree`.
+
 <a id='changelog-0.4.0'></a>
 # Changes in release "0.4.0"
 

docs/developers/release.md

@@ -8,7 +8,7 @@ The documentation is fetched by readthedocs from the "Build Docs" GitHub Action.
 
 - The `piqtree` version has been correctly bumped.
 - The testing, linting and type checking all pass on all supported platforms.
-- The code has been throuroughly tested (check what's been missed in the coverage report).
+- The code has been thoroughly tested (check what's been missed in the coverage report).
 - The documentation builds and appears correct.
 - The documentation has been updated on readthedocs (this must be triggered from readthedocs).
 - The "Release" GitHub Action has correctly uploaded to Test PyPI.