refactor: dockerized wheel build + fast-build script, quick Mordred test, remove in-repo RDKit port

.gitignore

@@ -1,9 +1,10 @@
 .vscode
 __pycache__
-_skbuild
+_src
 dist
 
 MANIFEST.in
 .DS_Store
 *.csv
+!src/test/data/example.csv
 *.egg-info

CMakeLists.txt

@@ -0,0 +1,131 @@
+cmake_minimum_required(VERSION 3.28)
+project(osmordred LANGUAGES CXX)
+
+# Prefer conda prefix for discovery
+if(DEFINED ENV{CONDA_PREFIX})
+  list(PREPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}")
+endif()
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+add_library(_osmordred MODULE osmordred/osmordred.cpp)
+set_target_properties(_osmordred PROPERTIES PREFIX "" SUFFIX ".so" POSITION_INDEPENDENT_CODE ON)
+
+# ---------- Python ----------
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module)
+target_link_libraries(_osmordred PRIVATE Python3::Module)
+if(TARGET Python3::Python)
+  target_link_libraries(_osmordred PRIVATE Python3::Python)
+endif()
+if(DEFINED Python3_INCLUDE_DIRS)
+  target_include_directories(_osmordred PRIVATE ${Python3_INCLUDE_DIRS})
+endif()
+string(REGEX REPLACE "^([0-9]+)\\.([0-9]+).*" "\\1\\2" PYXY "${Python3_VERSION}")
+
+# ---------- Eigen ----------
+find_package(Eigen3 3.3 REQUIRED NO_MODULE)
+target_link_libraries(_osmordred PRIVATE Eigen3::Eigen)
+
+# ---------- Boost (non-Python) ----------
+find_package(Boost 1.86 REQUIRED COMPONENTS headers system iostreams serialization)
+target_link_libraries(_osmordred PRIVATE Boost::system Boost::iostreams Boost::serialization)
+
+# ---------- Boost.Python / NumPy (robust: find actual .so names) ----------
+set(_bpy_candidates "boost_python${PYXY}" "boost_numpy${PYXY}" "boost_python3" "boost_numpy3" "boost_python" "boost_numpy")
+foreach(kind IN ITEMS python numpy)
+  set(_names "")
+  foreach(n IN LISTS _bpy_candidates)
+    if(n MATCHES "boost_${kind}.*")
+      list(APPEND _names "${n}")
+    endif()
+  endforeach()
+  if(DEFINED ENV{CONDA_PREFIX})
+    find_library(BOOST_${kind}_LIB NAMES ${_names} PATHS "$ENV{CONDA_PREFIX}/lib" NO_DEFAULT_PATH)
+  endif()
+  if(NOT BOOST_${kind}_LIB)
+    find_library(BOOST_${kind}_LIB NAMES ${_names})
+  endif()
+  if(NOT BOOST_${kind}_LIB)
+    message(FATAL_ERROR "Could not find libboost_${kind} for Python ${Python3_VERSION}. Try: conda install -c conda-forge boost")
+  endif()
+endforeach()
+target_link_libraries(_osmordred PRIVATE ${BOOST_python_LIB} ${BOOST_numpy_LIB})
+
+# ---------- RDKit: try config/module; else manual headers+libs ----------
+find_package(RDKit QUIET)
+
+if(TARGET RDKit::RDKit)
+  target_link_libraries(_osmordred PRIVATE RDKit::RDKit)
+else()
+  # If module didn’t give variables, try to locate manually
+  if(NOT RDKit_INCLUDE_DIRS)
+    # Look for a directory that contains 'rdkit/GraphMol/ROMol.h'
+    find_path(RDKIT_INCLUDE_BASE
+      NAMES rdkit/GraphMol/ROMol.h
+      PATHS "$ENV{CONDA_PREFIX}/include" "/usr/local/include" "/usr/include"
+    )
+    if(NOT RDKIT_INCLUDE_BASE)
+      message(FATAL_ERROR "RDKit headers not found. Install RDKit in this env, e.g.: conda install -c conda-forge rdkit")
+    endif()
+    set(RDKit_INCLUDE_DIRS "${RDKIT_INCLUDE_BASE}")
+  endif()
+  target_include_directories(_osmordred PRIVATE ${RDKit_INCLUDE_DIRS})
+
+  # Core libs typically needed by descriptor/fingerprint code
+  set(_rdkit_core_libs
+    RDKitGraphMol
+    RDKitRDGeneral
+    RDKitDataStructs
+    RDKitSmilesParse
+    RDKitSubstructMatch
+    RDKitSubgraphs
+    RDKitFingerprints
+    RDKitDescriptors
+    RDKitPartialCharges
+  )
+
+  set(RDKIT_MANUAL_LIBS "")
+  foreach(lib ${_rdkit_core_libs})
+    if(DEFINED ENV{CONDA_PREFIX})
+      find_library(${lib}_PATH NAMES ${lib} PATHS "$ENV{CONDA_PREFIX}/lib" NO_DEFAULT_PATH)
+    endif()
+    if(NOT ${lib}_PATH)
+      find_library(${lib}_PATH NAMES ${lib})
+    endif()
+    if(${lib}_PATH)
+      list(APPEND RDKIT_MANUAL_LIBS ${${lib}_PATH})
+    endif()
+  endforeach()
+
+  # Require at least the absolute minimum set:
+  set(_min_required RDKitGraphMol RDKitRDGeneral RDKitDataStructs RDKitSmilesParse RDKitSubstructMatch)
+  foreach(req IN LISTS _min_required)
+    if(NOT DEFINED ${req}_PATH)
+      message(FATAL_ERROR "Missing required RDKit library: ${req}. Check RDKit installation in this env (conda install -c conda-forge rdkit).")
+    endif()
+  endforeach()
+
+  target_link_libraries(_osmordred PRIVATE ${RDKIT_MANUAL_LIBS})
+endif()
+
+# ---------- LAPACKE / LAPACK (remove if unused) ----------
+find_path(LAPACKE_INCLUDE_DIR lapacke.h PATHS "$ENV{CONDA_PREFIX}/include" NO_DEFAULT_PATH)
+find_library(LAPACKE_LIBRARY lapacke PATHS "$ENV{CONDA_PREFIX}/lib" NO_DEFAULT_PATH)
+if(LAPACKE_INCLUDE_DIR AND LAPACKE_LIBRARY)
+  target_include_directories(_osmordred PRIVATE ${LAPACKE_INCLUDE_DIR})
+  target_link_libraries(_osmordred PRIVATE ${LAPACKE_LIBRARY})
+else()
+  find_package(LAPACK QUIET)
+  if(LAPACK_FOUND)
+    target_link_libraries(_osmordred PRIVATE LAPACK::LAPACK)
+  endif()
+endif()
+
+# ---------- RPATH ----------
+set_target_properties(_osmordred PROPERTIES
+  BUILD_RPATH "$ORIGIN;$ORIGIN/..;$ENV{CONDA_PREFIX}/lib"
+  INSTALL_RPATH "$ORIGIN;$ORIGIN/..;$ENV{CONDA_PREFIX}/lib"
+)
+
+install(TARGETS _osmordred LIBRARY DESTINATION osmordred)