Merge pull request #18 from loriab/pylibefp_buildsys

Add pylibefp python bindings to upstream libefp
libefp2 · Apr 1, 2024 · 96fd560 · 96fd560
2 parents cdc28e6 + 81f4827
commit 96fd560
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Showing 21 changed files with 4,811 additions and 1,092 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,6 +20,7 @@ jobs:
             cmargs: >
               -D BUILD_SHARED_LIBS=ON
               -D LIBEFP_ENABLE_OPENMP=ON
+            pytest-marker-expr: "test"  # i.e., all
 
           - label: L-Gnu
             runs-on: ubuntu-latest
@@ -29,49 +30,57 @@ jobs:
             cmargs: >
               -D BUILD_SHARED_LIBS=ON
               -D LIBEFP_ENABLE_OPENMP=ON
+            pytest-marker-expr: "test"
+
+          - label: L-Intel
+            runs-on: ubuntu-latest
+            python-version: "3.10"
+            blas: MKL
+            build_type: Release
+            cmargs: >
+              -D CMAKE_C_COMPILER=icx
+              -D CMAKE_CXX_COMPILER=icpx
+              -D CMAKE_C_FLAGS="--gcc-toolchain=${CONDA_PREFIX} --sysroot=${CONDA_PREFIX}/${HOST}/sysroot -target ${HOST}"
+              -D CMAKE_CXX_FLAGS="--gcc-toolchain=${CONDA_PREFIX} --sysroot=${CONDA_PREFIX}/${HOST}/sysroot -target ${HOST}"
+              -D BUILD_SHARED_LIBS=ON
+              -D LIBEFP_ENABLE_OPENMP=OFF
+            pytest-marker-expr: "not dict_5"  # the forced fail fails?
 
           - label: M-Clang
-            # test nans on macos-latest (macos-12)
+            # NaNs in tests on macos-latest (macos-12)
             runs-on: macos-13
             python-version: "3.10"
             blas: OBL
             build_type: Release
             cmargs: >
               -D BUILD_SHARED_LIBS=ON
               -D LIBEFP_ENABLE_OPENMP=ON
+            pytest-marker-expr: "test"
 
           - label: M-Clang
-            # test nans on macos-latest (macos-12)
+            # NaNs in tests on macos-latest (macos-12)
             runs-on: macos-13
             python-version: "3.10"
             blas: ACC
             build_type: Release
             cmargs: >
               -D BUILD_SHARED_LIBS=ON
               -D LIBEFP_ENABLE_OPENMP=ON
+            pytest-marker-expr: "test"
 
-          - label: W-ClangCL
+          - label: W-MinGW
             runs-on: windows-latest
             python-version: "3.10"
             blas: MKL
             build_type: Release
             cmargs: >
               -D CMAKE_C_COMPILER="gcc.exe"
+              -D CMAKE_CXX_COMPILER="g++.exe"
               -D CMAKE_Fortran_COMPILER="gfortran.exe"
               -D BUILD_SHARED_LIBS=OFF
               -D LIBEFP_ENABLE_OPENMP=ON
               # using gnu, not clang-cl, for consistent compiler stack incl. Fortran
-
-          - label: L-Intel
-            runs-on: ubuntu-latest
-            python-version: "3.10"
-            blas: MKL
-            build_type: Release
-            cmargs: >
-              -D CMAKE_C_COMPILER=icx
-              -D CMAKE_C_FLAGS="--gcc-toolchain=${CONDA_PREFIX} --sysroot=${CONDA_PREFIX}/${HOST}/sysroot -target ${HOST}"
-              -D BUILD_SHARED_LIBS=ON
-              -D LIBEFP_ENABLE_OPENMP=OFF
+            pytest-marker-expr: "test"
 
     name: "Build • 🐍 ${{ matrix.cfg.python-version }} • ${{ matrix.cfg.label }} • ${{ matrix.cfg.blas }}"
     runs-on: ${{ matrix.cfg.runs-on }}
@@ -97,6 +106,12 @@ jobs:
             #ACC- libblas=*=*accelerate
             #OBL- libblas=*=*openblas
             #OBL- openblas=*=*openmp*
+            # pylibefp
+            - cxx-compiler
+            - pybind11
+            - qcelemental
+            #- libpython
+            - pytest
           EOF
           if [[ "${{ runner.os }}" == "Linux" ]]; then
             :
@@ -114,6 +129,7 @@ jobs:
             sed -i "s;fortran-compiler;m2w64-gcc-fortran;g" export.yaml
             sed -i "s;#${{ matrix.cfg.blas }};;g" export.yaml
             sed -i "s;openmp;pthreads;g" export.yaml  # W openblas is pthreads
+            sed -i "s;#- libpython;- libpython;g" export.yaml
           fi
           # model sed for L/W
           #   sed -i "s;;;g" export.yaml
@@ -202,7 +218,36 @@ jobs:
               return 0;
           }
           EOF
-          cmake -S . -B build -G Ninja --log-level verbose -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="${CONDA_PREFIX};${{github.workspace}}/installed"
+          cmake -S . -B build -G Ninja --log-level verbose -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="${CONDA_PREFIX};${{ github.workspace }}/installed"
           cmake --build build
           ./build/hello
 
+      # Step is unnecessary; remove for debugging.
+      - name: Confound Environment - test fetched pybind11
+        if: ${{ matrix.cfg.blas == 'OBL' }}
+        run: mamba remove pybind11
+
+      - name: Build & Install Python bindings
+        run: |
+            cd python
+            cmake \
+              -S . \
+              -B build \
+              -G Ninja \
+              -D CMAKE_PREFIX_PATH="${CONDA_PREFIX};${{ github.workspace }}/installed" \
+              -D CMAKE_INSTALL_PREFIX="${{ github.workspace }}/installed" \
+              ${{ matrix.cfg.cmargs }}
+            cmake --build build --target install
+
+      # psi4 with MKL avail for qmefp test
+      - name: Install Psi4 for QM/EFP testing
+        if: ${{ matrix.cfg.blas == 'MKL' }}
+        run: conda install psi4 -c conda-forge
+
+      - name: Test (pytest) -- unit tests Python bindings
+        run: |
+            PYTHONPATH="${{ github.workspace }}/installed/lib" \
+            pytest --cache-clear -v -rws --color=yes \
+              --durations=50 --durations-min=1 --strict-markers \
+              -k "${{ matrix.cfg.pytest-marker-expr }}" \
+              "${{ github.workspace }}/installed/"
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,10 +1,18 @@
 cmake_minimum_required(VERSION 3.16)
+if (POLICY CMP0135)
+	cmake_policy(SET CMP0135 NEW)
+endif ()
+
+# extract project version from source
+file(STRINGS "src/efp.h" _src_efp_h REGEX "LIBEFP_VERSION_STRING")
+if (${_src_efp_h} MATCHES "^#define LIBEFP_VERSION_STRING \"(.*)\"$")
+    set(_libefp_VERSION ${CMAKE_MATCH_1})
+endif()
 
 project(
   libefp
-  # sync VERSION here with src/efp.h LIBEFP_VERSION_STRING
   # someday when Makefile dropped, configure efp.h.in from cmake
-  VERSION 1.8.0
+  VERSION ${_libefp_VERSION}
   LANGUAGES C
   )
 set(libefp_AUTHORS "Ilya A. Kaliman, Lori A. Burns, Dmitry Morozov, Carlos H. Borca, Yen (Terri) Bui, Yongbin Kim, Lyudmila V. Slipchenko")
@@ -32,6 +40,12 @@ if (${efp}_IS_TOP_LEVEL)
     if (DEFINED ENABLE_OPENMP)
         message(FATAL_ERROR "Use LIBEFP_ENABLE_OPENMP instead of ENABLE_OPENMP.")
     endif()
+    if (DEFINED FRAGLIB_UNDERSCORE_L)
+        message(WARNING "Using FRAGLIB_UNDERSCORE_L=OFF is deprecated and may be removed as soon as v1.10. Please adapt your fragment search to handle name and name_L.")
+    endif()
+    if (DEFINED FRAGLIB_DEEP)
+        message(WARNING "Using FRAGLIB_DEEP=OFF is deprecated and may be removed as soon as v1.10. Please adapt your fraglib library usage to handle a list of paths.")
+    endif()
 endif()
 
 option_with_default(CMAKE_BUILD_TYPE "Build type" Release)
@@ -43,12 +57,15 @@ endif()
 option_with_print(LIBEFP_ENABLE_OPENMP "Enable OpenMP parallelization. Psi4 wants OFF" OFF)
 option_with_print(ENABLE_GENERIC "Enable mostly static linking in shared library" OFF)
 include(xhost)  # defines: option(ENABLE_XHOST "Enable processor-specific optimization" ON)
-option_with_print(FRAGLIB_UNDERSCORE_L "Installed fragment library has names ending in _L. Psi4 wants OFF" ON)
-option_with_print(FRAGLIB_DEEP "Installed fragment libary has hierarchical, not flat, filestructure. Psi4 wants OFF" ON)
+option_with_print(FRAGLIB_UNDERSCORE_L "DEPRECATED: Installed fragment library has names ending in _L. Psi4 wants OFF" ON)
+option_with_print(FRAGLIB_DEEP "DEPRECATED: Installed fragment libary has hierarchical, not flat, filestructure. Psi4 wants OFF" ON)
 option_with_print(INSTALL_DEVEL_HEADERS "Install additional namespaced devel headers beyond convenience efp.h" OFF)
 option_with_default(LIBEFP_CMAKECONFIG_INSTALL_DIR "Directory within CMAKE_INSTALL_PREFIX to which CMake configuration files installed" "share/cmake/libefp")
 option_with_print(LIBEFP_ENABLE_EFPMD "Build standalone efpmd executable (requires Fortran). This also enables testing" ON)
 
+option_with_default(PYMOD_INSTALL_LIBDIR "If LIBEFP_ENABLE_PYTHON, location within CMAKE_INSTALL_LIBDIR to which python modules are installed" /)
+option_with_print(LIBEFP_ENABLE_PYTHON "Build Python bindings (requires CXX, Python, and Pybind11)" OFF)
+
 ######################### Process & Validate Options ###########################
 include(autocmake_safeguards)
 include(custom_static_library)
@@ -163,6 +180,12 @@ target_link_libraries(
     $<$<TARGET_EXISTS:OpenMP::OpenMP_C>:OpenMP::OpenMP_C>
   )
 
+# pylibefp bindings
+if (LIBEFP_ENABLE_PYTHON)
+    enable_language(CXX)
+    add_subdirectory(python)
+endif()
+
 # efpmd executable
 if (LIBEFP_ENABLE_EFPMD)
     # needed to link the Fortran routines in libff into the efpmd executable