Stabilize CI and workflow build paths

lmorency · lmorency · commit f76ff750f5f4 · 2026-03-08T01:06:44.000-05:00
diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
@@ -1,23 +1,10 @@
-name: C/C++ CI
+name: Legacy C/C++ workflow (manual only)
 
 on:
-  push:
-    branches: [ "claude/write-implementation-MglRZ" ]
-  pull_request:
-    branches: [ "claude/write-implementation-MglRZ" ]
+  workflow_dispatch:
 
 jobs:
-  build:
-
+  deprecated:
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v4
-    - name: configure
-      run: ./configure
-    - name: make
-      run: make
-    - name: make check
-      run: make check
-    - name: make distcheck
-      run: make distcheck
+      - run: echo 'Deprecated workflow. Use .github/workflows/ci.yml instead.'
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,62 +1,102 @@
-name: FlexAIDdS CI (C++20)
+name: FlexAID CI
 
 on:
   push:
-    branches: ["claude/implement-todo-item-AJIMS", "main", "master"]
   pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  build:
+  pure_python_results:
+    name: Pure Python results tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest
+      - name: Run read-only loader tests
+        run: |
+          PYTHONPATH=python pytest -q \
+            python/tests/test_results_io.py \
+            python/tests/test_results_loader_models.py
+
+  cxx_core_build:
+    name: C++ core build (${{ matrix.name }})
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            compiler: g++
+          - name: linux-gcc
+            os: ubuntu-latest
             cc: gcc
-          - os: ubuntu-latest
-            compiler: clang++
+            cxx: g++
+          - name: linux-clang
+            os: ubuntu-latest
             cc: clang
-          - os: macos-latest
-            compiler: clang++
+            cxx: clang++
+          - name: macos-clang
+            os: macos-latest
             cc: clang
-
-    runs-on: ${{ matrix.os }}
-
+            cxx: clang++
     steps:
       - uses: actions/checkout@v4
-
-      - name: Install dependencies (Linux)
+      - name: Install Linux dependencies
         if: runner.os == 'Linux'
         run: |
-          sudo apt-get update -qq
-          sudo apt-get install -y cmake build-essential libomp-dev
-
-      - name: Install dependencies (macOS)
+          sudo apt-get update
+          sudo apt-get install -y cmake ninja-build libeigen3-dev libomp-dev
+      - name: Install macOS dependencies
         if: runner.os == 'macOS'
-        run: brew install cmake libomp
-
-      - name: Verify C++20 compiler support
-        run: |
-          ${{ matrix.compiler }} --version
-          echo '#include <span>
-          #include <concepts>
-          template<std::integral T> T id(T x){return x;}
-          int main(){std::span<int> s; return id(0);}' > /tmp/cxx20_check.cpp
-          ${{ matrix.compiler }} -std=c++20 /tmp/cxx20_check.cpp -o /tmp/cxx20_check
-          echo "C++20 support confirmed."
-
+        run: |
+          brew install cmake ninja libomp eigen
       - name: Configure
-        env:
-          CXX: ${{ matrix.compiler }}
-          CC:  ${{ matrix.cc }}
-        run: |
-          cmake -B build \
-                -DCMAKE_BUILD_TYPE=Release \
-                -DCMAKE_CXX_STANDARD=20 \
-                -DCMAKE_CXX_STANDARD_REQUIRED=ON \
-                -DCMAKE_CXX_EXTENSIONS=OFF \
-                -DFLEXAIDS_USE_OPENMP=ON
-
+        shell: bash
+        run: |
+          export CC=${{ matrix.cc }}
+          export CXX=${{ matrix.cxx }}
+          cmake -S . -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DFLEXAIDS_USE_CUDA=OFF \
+            -DFLEXAIDS_USE_METAL=OFF \
+            -DBUILD_PYTHON_BINDINGS=OFF
       - name: Build
-        run: cmake --build build --verbose --parallel $(nproc 2>/dev/null || sysctl -n hw.ncpu)
+        run: cmake --build build --parallel
+
+  python_bindings_smoke:
+    name: Python bindings smoke test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake ninja-build
+          python -m pip install --upgrade pip
+          python -m pip install 'pybind11[global]' pytest
+      - name: Configure Python bindings
+        run: |
+          cmake -S . -B build-python -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DBUILD_PYTHON_BINDINGS=ON \
+            -DFLEXAIDS_USE_OPENMP=OFF \
+            -DFLEXAIDS_USE_EIGEN=OFF \
+            -DFLEXAIDS_USE_CUDA=OFF \
+            -DFLEXAIDS_USE_METAL=OFF \
+            -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=${{ github.workspace }}/python/flexaidds
+      - name: Build Python extension
+        run: cmake --build build-python --parallel --target _core
+      - name: Run statmech smoke test
+        run: |
+          PYTHONPATH=python pytest -q python/tests/test_statmech_smoke.py
diff --git a/.github/workflows/cmake-multi-platform.yml b/.github/workflows/cmake-multi-platform.yml
@@ -1,75 +1,10 @@
-# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
-# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
-name: CMake on multiple platforms
+name: Legacy multi-platform workflow (manual only)
 
 on:
-  push:
-    branches: [ "claude/write-implementation-MglRZ" ]
-  pull_request:
-    branches: [ "claude/write-implementation-MglRZ" ]
+  workflow_dispatch:
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
-      fail-fast: false
-
-      # Set up a matrix to run the following 3 configurations:
-      # 1. <Windows, Release, latest MSVC compiler toolchain on the default runner image, default generator>
-      # 2. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
-      # 3. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
-      #
-      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
-      matrix:
-        os: [ubuntu-latest, windows-latest]
-        build_type: [Release]
-        c_compiler: [gcc, clang, cl]
-        include:
-          - os: windows-latest
-            c_compiler: cl
-            cpp_compiler: cl
-          - os: ubuntu-latest
-            c_compiler: gcc
-            cpp_compiler: g++
-          - os: ubuntu-latest
-            c_compiler: clang
-            cpp_compiler: clang++
-        exclude:
-          - os: windows-latest
-            c_compiler: gcc
-          - os: windows-latest
-            c_compiler: clang
-          - os: ubuntu-latest
-            c_compiler: cl
-
+  deprecated:
+    runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set reusable strings
-      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
-      id: strings
-      shell: bash
-      run: |
-        echo "build-output-dir=${{ 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 }}
+      - run: echo 'Deprecated workflow. Use .github/workflows/ci.yml instead.'
diff --git a/.github/workflows/cmake-single-platform.yml b/.github/workflows/cmake-single-platform.yml
@@ -1,39 +1,10 @@
-# This starter workflow is for a CMake project running on a single platform. There is a different starter workflow if you need cross-platform coverage.
-# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-multi-platform.yml
-name: CMake on a single platform
+name: Legacy single-platform workflow (manual only)
 
 on:
-  push:
-    branches: [ "claude/write-implementation-MglRZ" ]
-  pull_request:
-    branches: [ "claude/write-implementation-MglRZ" ]
-
-env:
-  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
-  BUILD_TYPE: Release
+  workflow_dispatch:
 
 jobs:
-  build:
-    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
-    # You can convert this to a matrix build if you need cross-platform coverage.
-    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+  deprecated:
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v4
-
-    - 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 ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
-
-    - name: Build
-      # Build your program with the given configuration
-      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
-
-    - name: Test
-      working-directory: ${{github.workspace}}/build
-      # Execute tests defined by the CMake configuration.
-      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: ctest -C ${{env.BUILD_TYPE}}
-
+      - run: echo 'Deprecated workflow. Use .github/workflows/ci.yml instead.'
diff --git a/python/flexaidds/__init__.py b/python/flexaidds/__init__.py
@@ -1,15 +1,25 @@
 """flexaidds: Python bindings and read-only analysis helpers for FlexAID∆S."""
 
-from ._core import StatMechEngine, Thermodynamics
 from .models import BindingModeResult, DockingResult, PoseResult
 from .results import load_results
 
+try:
+    from ._core import StatMechEngine, Thermodynamics
+    HAS_CORE_BINDINGS = True
+except ImportError:
+    StatMechEngine = None
+    Thermodynamics = None
+    HAS_CORE_BINDINGS = False
+
 __all__ = [
-    "StatMechEngine",
-    "Thermodynamics",
+    "HAS_CORE_BINDINGS",
     "PoseResult",
     "BindingModeResult",
     "DockingResult",
     "load_results",
 ]
+
+if HAS_CORE_BINDINGS:
+    __all__.extend(["StatMechEngine", "Thermodynamics"])
+
 __version__ = "0.1.0"
diff --git a/python/tests/test_statmech_smoke.py b/python/tests/test_statmech_smoke.py
@@ -1,14 +1,26 @@
+import math
+
+import pytest
+
 import flexaidds as fd
 
+pytestmark = pytest.mark.skipif(
+    not fd.HAS_CORE_BINDINGS or fd.StatMechEngine is None,
+    reason="pybind11 core extension not built",
+)
 
-def test_statmech_smoke():
-    engine = fd.StatMechEngine(300.0)
-    engine.add_sample(-7.0)
+
+def test_statmech_engine_smoke() -> None:
+    engine = fd.StatMechEngine(temperature=300.0)
+    engine.add_sample(-7.5)
     engine.add_sample(-6.0)
+    engine.add_sample(-5.5, multiplicity=2.0)
+
     thermo = engine.compute()
 
-    assert hasattr(thermo, "free_energy")
-    assert hasattr(thermo, "mean_energy")
-    assert hasattr(thermo, "entropy")
-    assert hasattr(thermo, "heat_capacity")
-    assert hasattr(thermo, "std_energy")
+    assert math.isfinite(thermo.free_energy)
+    assert math.isfinite(thermo.mean_energy)
+    assert math.isfinite(thermo.entropy)
+    assert math.isfinite(thermo.heat_capacity)
+    assert math.isfinite(thermo.std_energy)
+    assert thermo.free_energy <= thermo.mean_energy
