Github build and pip actions, clang bug, change to py3.8

.github/workflows/cmake.yml

@@ -0,0 +1,80 @@
+# This provided workflow file is focused on testing a Python project using pip, the package installer for Python. 
+# There's also a specialized job for building and testing the package in a Mingw64 environment on Windows.
+name: CMake build
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+
+      # Set up a matrix to run the following 3 configurations:
+      # 1. <Windows, Release, latest MSVC compiler toolchain on the default runner image, default generator>
+      # 2. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
+      # 3. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
+      #
+      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        build_type: [Release]
+        c_compiler: [gcc, clang, cl]
+        include:
+          - os: windows-latest
+            c_compiler: cl
+            cpp_compiler: cl
+          - os: ubuntu-latest
+            c_compiler: gcc
+            cpp_compiler: g++
+          - os: ubuntu-latest
+            c_compiler: clang
+            cpp_compiler: clang++
+        exclude:
+          - os: windows-latest
+            c_compiler: gcc
+          - os: windows-latest
+            c_compiler: clang
+          - os: ubuntu-latest
+            c_compiler: cl
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set reusable strings
+      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
+        -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
+        -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        -S ${{ github.workspace }}
+
+    - name: Build
+      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config ${{ matrix.build_type }}
+
+    - name: Test
+      working-directory: ${{ steps.strings.outputs.build-output-dir }}
+      # Execute tests defined by the CMake configuration. Note that --build-config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest --build-config ${{ matrix.build_type }}

.github/workflows/pip.yml

@@ -0,0 +1,69 @@
+# This provided workflow file is focused on testing a Python project using pip, the package installer for Python. 
+# There's also a specialized job for building and testing the package in a Mingw64 environment on Windows.
+name: Pip install
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        python-version: ["3.8", "3.11"]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Add requirements
+      run: python -m pip install --upgrade wheel setuptools
+
+    - name: Build and install
+      run: pip install --verbose .
+
+  build-mingw64:
+    runs-on: windows-latest
+    defaults:
+      run:
+        shell: msys2 {0}
+    steps:
+    - uses: msys2/setup-msys2@v2
+      with:
+        update: true
+        install: >-
+          mingw-w64-x86_64-gcc
+          mingw-w64-x86_64-python-pip
+          mingw-w64-x86_64-python-wheel
+          mingw-w64-x86_64-python-pandas
+          mingw-w64-x86_64-meson
+          mingw-w64-x86_64-python-scikit-learn
+
+    - uses: actions/checkout@v3
+
+    - name: Add requirements
+      # This is required because --no-build-isolation disable dependences
+      # installation
+      run: python -m pip install pybind11 meson-python
+
+    - name: Build and install
+      # --no-build-isolation is required because the vanilla setuptool does not
+      # support Mingw64.See patches here:
+      # https://github.com/msys2/MINGW-packages/tree/master/mingw-w64-python-setuptools
+      # Without those patches build_ext fails with:
+      # error: --plat-name must be one of ('win32', 'win-amd64', 'win-arm32', 'win-arm64')
+      run: pip install --no-build-isolation .

README.md

@@ -1,3 +1,6 @@
+[![CMake build](https://github.com/algtudelft/pystreed/actions/workflows/cmake.yml/badge.svg)](https://github.com/algtudelft/pystreed/actions/workflows/cmake.yml)
+[![Pip install](https://github.com/algtudelft/pystreed/actions/workflows/pip.yml/badge.svg)](https://github.com/algtudelft/pystreed/actions/workflows/pip.yml)
+
 # STreeD: Separable Trees with Dynamic programming
 By: Jacobus G. M. van der Linden
 

pyproject.toml

@@ -4,7 +4,7 @@ requires = [
     "pybind11>=2.10.0"
 ]
 build-backend = "setuptools.build_meta"
-target-version = "py37"
+target-version = "py38"
 
 [project]
 name = "pystreed"
@@ -22,7 +22,7 @@ maintainers = [
 dependencies =[
     "pandas>=1.0.0",
     "numpy>=1.18.0",
-    "scikit-learn >=1.2.0,<1.3"
+    "scikit-learn >=1.2.0"
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

src/bindings.cpp

@@ -42,8 +42,8 @@ void NumpyToSTreeDData(const py::array_t<int, py::array::c_style>& _X,
                         AData& data, ADataView& data_view) {
     const bool regression = std::is_same<LT, double>::value;
     std::vector<const AInstance*> instances;
-    auto X = _X.unchecked<2>();
-    auto y = _y.unchecked<1>();
+    auto X = _X.template unchecked<2>(); // Template keyword because of a bug in the clang compiler
+    auto y = _y.template unchecked<1>(); // Template keyword because of a bug in the clang compiler
     const int num_instances = int(X.shape(0));
     const int num_features = int(X.shape(1));
 
@@ -74,7 +74,7 @@ void NumpyToSTreeDData(const py::array_t<int, py::array::c_style>& _X,
 }
 
 std::vector<bool> NumpyRowToBoolVector(const py::array_t<int, py::array::c_style>& _X) {
-    auto X = _X.unchecked<1>();
+    auto X = _X.template unchecked<1>(); // Template keyword because of a bug in the clang compiler
     std::vector<bool> v(X.shape(0));
     for (py::size_t j = 0; j < X.shape(0); j++) {
         v[j] = X(j);

test/correct_solution_test.cpp

@@ -180,7 +180,7 @@ void EnumerateSolverSetupOptions(std::vector<SolverSetup>& solver_setups) {
 
 void GetF1ScoreTests(std::vector<F1ScoreTestSetup>& f1_score_tests) {
 	f1_score_tests.push_back({
-		"data/f1score/yeast.csv", 2, 3, { /*										  
+		"data/classification/yeast.csv", 2, 3, { /*										  
 			{0, 823}, {1, 784}, {2, 756}, {6, 753}, {9, 733}, {11, 701}, {18, 692}, {21, 679}, {22, 663}, {26, 628}, 
 		{33, 605}, {35, 573}, {42, 564}, {45, 551}, {54, 548}, {59, 532}, {64, 521}, {67, 501}, {73, 491}, {77, 463},
 		{96, 460}, {97, 456}, {104, 420}, {113, 377}, {139, 372}, {140, 367}, {147, 364}, {154, 358}, {156, 321}, {167, 301},