changing build system used by pip (setuptools -> scikit-build-core)

.gitignore

@@ -12,6 +12,7 @@ tags
 /docs/_build
 /.eggs/
 .gdb_history
+.*.swp
 
 # files generated by cmake
 /CMakeFiles/

CMakeLists.txt

@@ -9,13 +9,19 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1"
 project(gemmi LANGUAGES C CXX VERSION ${gemmi_version_str})
 message(STATUS "Gemmi version ${PROJECT_VERSION}")
 
-include(GNUInstallDirs)  # for CMAKE_INSTALL_LIBDIR
+include(GNUInstallDirs)  # for CMAKE_INSTALL_LIBDIR, etc
+
+if (DEFINED SKBUILD)  # building with scikit-build-core (pip install)
+  # we set wheel.install-dir="/data" in pyproject.toml,
+  # so here we need to only set paths to /platlib and /scripts
+  set(PYTHON_INSTALL_DIR "${SKBUILD_PLATLIB_DIR}")
+  #set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}")
+endif()
 
 option(BUILD_SHARED_LIBS "Build using shared library" OFF)
 option(BUILD_GEMMI_PROGRAM "Build gemmi command-line program" ON)
 option(USE_FORTRAN "Build Fortran bindings" OFF)
 option(USE_PYTHON "Build Python bindings" OFF)
-option(INSTALL_EGG_INFO "Install .egg-info via setup.py" ON)
 option(EXTRA_WARNINGS "Set extra warning flags" OFF)
 option(USE_WMAIN "(Windows only) take Unicode arguments in gemmi program" ON)
 set(GEMMI_INSTALL_CMAKEDIR "${CMAKE_INSTALL_LIBDIR}/cmake/gemmi" CACHE STRING
@@ -106,7 +112,10 @@ else()
   message(STATUS "The build will use zlib code from third_party/zlib.")
   include_directories("${CMAKE_CURRENT_SOURCE_DIR}/third_party/zlib")
 endif()
-find_package(benchmark 1.3 QUIET)
+
+if (NOT DEFINED SKBUILD)
+  find_package(benchmark 1.3 QUIET)
+endif()
 if (benchmark_FOUND)
   message(STATUS "Found benchmark: ${benchmark_DIR}")
 else (NOT benchmark_FOUND)
@@ -379,6 +388,7 @@ endif()
 ### Python bindings ###
 if (USE_PYTHON)
   message(STATUS "The python module will be built.")
+  # CMake >=3.18 has subcomponent Development.Module
   find_package(Python ${PYTHON_VERSION} REQUIRED COMPONENTS Interpreter Development)
   if (EXISTS "${CMAKE_HOME_DIRECTORY}/pybind11")
     message(STATUS "Using ${CMAKE_HOME_DIRECTORY}/pybind11 (internal copy).")
@@ -422,6 +432,7 @@ write_basic_package_version_file(gemmi-config-version.cmake
 install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
 
 if (BUILD_GEMMI_PROGRAM)
+  # Is it useful to have the program location in gemmi-targets.cmake?
   install(TARGETS gemmi_prog EXPORT GemmiTargets)
 endif()
 install(TARGETS gemmi_cpp
@@ -439,24 +450,10 @@ if (USE_PYTHON)
   if (DEFINED PYTHON_INSTALL_DIR)
     message(STATUS "Install directory for Python module: ${PYTHON_INSTALL_DIR}")
     set(Python_SITEARCH "${PYTHON_INSTALL_DIR}")
-    set(Python_SITELIB "${PYTHON_INSTALL_DIR}")
   endif()
   file(TO_CMAKE_PATH "${Python_SITEARCH}" Python_SITEARCH)
-  file(TO_CMAKE_PATH "${Python_SITELIB}" Python_SITELIB)
-  # Using Python_SITEARCH and SITELIB is not good, because they are absolute
+  # Using Python_SITEARCH/SITELIB is not good, because they are absolute
   # and don't respect CMAKE_INSTALL_PREFIX.
   # https://discourse.cmake.org/t/findpython3-how-to-specify-local-installation-directory-for-python-module/3580/5
   install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}")
-  install(DIRECTORY examples/ DESTINATION "${Python_SITELIB}/gemmi-examples"
-          FILES_MATCHING PATTERN "*.py")
-  if (INSTALL_EGG_INFO)
-    install(CODE
-     "execute_process(COMMAND \"${Python_EXECUTABLE}\" setup.py install_egg_info --install-dir \"\$ENV{DESTDIR}${Python_SITELIB}\"
-                      WORKING_DIRECTORY \"${CMAKE_SOURCE_DIR}\"
-                      RESULT_VARIABLE EGG_STATUS)"
-    )
-    if (EGG_STATUS AND NOT EGG_STATUS EQUAL 0)
-      message(FATAL_ERROR "Failed to install egg-info. Use -D INSTALL_EGG_INFO=OFF to disable.")
-    endif()
-  endif()
 endif()

docs/cif.rst

@@ -1581,10 +1581,6 @@ Examples
 The examples here use C++11 or Python.
 Full working code code can be found in the examples__ directory.
 
-If you have the Python ``gemmi`` module installed you should also have
-the Python examples -- try ``python -m gemmi-examples`` if not sure
-where they are.
-
 The examples below can be run on one or more PDBx/mmCIF files.
 The ones that perform PDB-wide analysis are meant to be run on a
 `local copy <https://www.wwpdb.org/download/downloads>`_ of the mmCIF

docs/install.rst

@@ -84,9 +84,7 @@ If the compiler is not installed, pip shows a message with a download link.
 If gemmi is already installed, uninstall the old version first
 (``pip uninstall``) or add option ``--upgrade``.
 
-Setuptools compile only one unit at a time and the whole process
-takes several minutes. To make it faster, build in parallel with CMake.
-Clone the project and do::
+Alternatively, you can build a cloned project with CMake::
 
     cmake -D USE_PYTHON=1 .
     make -j4 py

pyproject.toml

@@ -0,0 +1,75 @@
+[build-system]
+requires = ["scikit-build-core==0.5.0", "pybind11>=2.6.2"]
+build-backend = "scikit_build_core.build"
+
+# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
+[project]
+name = "gemmi"
+dynamic = ["version"]
+requires-python = ">=3.7"
+description="library for structural biology"
+readme = "README.md"
+authors = [
+  { name = "Marcin Wojdyr", email = "[email protected]" },
+]
+urls.repository = "https://github.com/project-gemmi/gemmi"
+license = {text = "MPL-2.0"}  # or, at your option, LGPL-3.0
+keywords = ["structural bioinformatics", "structural biology",
+            "crystallography", "CIF", "mmCIF", "PDB", "CCP4", "MTZ"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)",
+  "Topic :: Software Development :: Libraries :: Python Modules",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Chemistry",
+  "Programming Language :: C++",
+  "Programming Language :: Python",
+]
+
+[tool.scikit-build]
+#build-dir = "/tmp/gemmi_build2/{wheel_tag}"
+experimental = true  # needed for install-dir
+wheel.install-dir = "/data"
+wheel.expand-macos-universal-tags = true  # not sure if this is useful
+wheel.packages = []
+sdist.exclude = ["*"]
+sdist.include = [
+  "/README.md",
+  "/LICENSE.txt",
+  "/CMakeLists.txt",
+  "/pyproject.toml",
+  "docs/code/*.cpp",
+  "examples/*.py",
+  "examples/*.cpp",
+  "include/gemmi/**/*.hpp",
+  "include/gemmi/third_party/*.h",
+  "include/gemmi/third_party/tao/**",
+  "src/*.cpp",
+  "prog/*.cpp",
+  "prog/*.h*",
+  "python/*.cpp",
+  "python/*.h*",
+  "third_party/README",
+  "third_party/*.h",
+  "third_party/zlib/*",
+  "tests/*",
+  "!tests/*.pyc",
+  "tools/gemmi-config.cmake.in"
+]
+cmake.build-type = "Release"
+cmake.verbose = true
+[tool.scikit-build.cmake.define]
+USE_PYTHON = "ON"
+#BUILD_GEMMI_PROGRAM = "OFF"
+
+[tool.scikit-build.metadata.version]
+provider = "scikit_build_core.metadata.regex"
+input = "include/gemmi/version.hpp"
+regex = "#define GEMMI_VERSION \"(?P<value>[0-9dev.-]+)\""
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "-q"]
+testpaths = ["tests"]

run-tests.sh

@@ -51,7 +51,7 @@ if [ -z "${NO_DOCTEST-}" ]; then
     (cd docs && make doctest SPHINXOPTS="-q -n -E")
 fi
 
-flake8 docs/ examples/ tests/ tools/ setup.py
+flake8 docs/ examples/ tests/ tools/
 pybind11-stubgen --dry-run --exit-code gemmi