libcasm-xtal 2.0.0__tar.gz

libcasm_xtal-2.0.0/CHANGELOG.md

@@ -0,0 +1,185 @@
+# Changelog
+
+All notable changes to `libcasm-xtal` will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [2.0.0] - 2025-05-02
+
+### Changed
+
+- Build for Python 3.13
+- Restrict requires-python to ">=3.9,<3.14"
+- Run CI tests using Python 3.13
+- Build MacOS arm64 wheels using MacOS 15
+- Build Linux wheels using Ubuntu 24.04
+
+
+## [2.0a12] - 2024-12-10
+
+### Fixed
+
+- Fixed `xtal::Lattice::_generate_voronoi_table()`. The acute angle test resulted in the FCC lattice missing a row for the normal that lies along a conventional unit cell lattice vector, so voronoi number was 4 instead of 5 for the octahedral interstitial coordinate).
+
+### Added
+
+- Added `Lattice.voronoi_table`, `Lattice.voronoi_number`, and `Lattice.voronoi_inner_radius`.
+
+### Changed
+
+- Build macos x86_64 wheels with macos-13 Github Actions runner
+
+
+## [2.0a11] - 2024-08-09
+
+### Added
+
+- Added `Lattice.copy`, `Lattice.__copy__`, `Lattice.__deepcopy__`, `Lattice.__repr__`,  `Lattice.to_dict`, and `Lattice.from_dict`
+- Added `AtomComponent.copy`, `AtomComponent.__copy__`, `AtomComponent.__deepcopy__`, `AtomComponent.__repr__`,  `AtomComponent.to_dict`, and `AtomComponent.from_dict`
+- Added `Occupant.copy`, `Occupant.__copy__`, `Occupant.__deepcopy__`, `Occupant.__repr__`,  `Occupant.to_dict`, and `Occupant.from_dict`
+- Added `DoFSetBasis.copy`, `DoFSetBasis.__copy__`, `DoFSetBasis.__deepcopy__`, `DoFSetBasis.__repr__`,  `DoFSetBasis.to_dict`, and `DoFSetBasis.from_dict`
+- Added `Prim.copy`, `Prim.__copy__`, `Prim.__deepcopy__`, and `Prim.__repr__`
+- Added `SymOp.copy`, `SymOp.__copy__`, `SymOp.__deepcopy__`, and `SymOp.__repr__`
+- Added `Structure.copy` and `Structure.__repr__`
+- Added `IntegralSiteCoordinate.copy`, `IntegralSiteCoordinate.__copy__`, and `IntegralSiteCoordinate.__deepcopy__`
+- Added `IntegralSiteCoordinateRep.copy`, `IntegralSiteCoordinateRep.__copy__`, `IntegralSiteCoordinateRep.__deepcopy__`, and `IntegralSiteCoordinateRep.__repr__`
+- Added usage documentation for Structure manipulation and input / output
+
+### Changed
+
+- Changed `IntegralSiteCoordinate.__str__` to `IntegralSiteCoordinate.__repr__` and changed the output from "b, i j k" to "[b, i, j, k]"
+- Changed `xtal::make_point_group` to remove the `symmetrized_with_fractional` step.
+- Changed construction of factor group translations to set components very close to zero (absolute value less than tol * 1e-5) to exactly zero.
+
+### Fixed
+
+- Make a user-defined CASM::xtal::SymInfo copy constructor so that member xtal::Coordinate have the correct "home" lattice
+
+
+## [2.0a10] - 2024-07-12
+
+### Changed
+
+- Clarified documentation for `libcasm.xtal.Lattice.is_equivalent_to`
+- Wheels compiled with numpy>=2.0.0
+- Run github actions on push, pull_request, and weekly
+- Use ruff NPY201
+
+
+## [2.0a9] - 2024-03-13
+
+### Fixed
+
+- Fix CASM::xtal::make_primitive, which was not copying unique_names. This also fixes the output of libcasm.xtal.make_primitive which was losing the occ_dof list as a result.
+- Fix JSON output of xtal::BasicStructure site label
+- Changed pseudoinverse calculation for basis changes to `completeOrthogonalDecomposition().pseudoInverse()`
+
+### Changed
+
+- Changed make_primitive to act on either Prim or Structure.
+- Changed default of `xtal.Structure.to_dict` to output in fractional coordinates
+- Added `excluded_species` and `frac` parameters to xtal.Structure.to_dict
+
+### Added
+
+- Add to libcasm.xtal: make_primitive_prim (equivalent to current make_primitive), make_primitive_structure, and make_canonical_structure. 
+- Add options to the BCC and FCC structure factory functions in libcasm.xtal.structures to make the conventional cubic unit cells.
+- Add to libcasm.xtal: StructureAtomInfo namedtuple, and methods sort_structure_by_atom_info, sort_structure_by_atom_type, sort_structure_by_atom_coordinate_frac, and sort_structure_by_atom_coordinate_cart
+- Add to libcasm.xtal: substitute_structure_species 
+- Add to libcasm.xtal.Prim: method labels, constructor parameter `labels`
+- Add to libcasm.xtal.Lattice: methods reciprocal, volume, lengths_and_angles, from_lengths_and_angles
+- Added `unit_cell`, `diagonal_only`, and `fixed_shape` parameters to libcasm.xtal.enumerate_superlattices.
+- Add to libcasm.xtal: combine_structures, filter_structure_by_atom_info, make_structure_atom_info, and make_structure_from_atom_info
+
+
+## [2.0a8] - 2023-11-15
+
+### Changed
+
+- Updated docs for PyData Sphinx Theme 0.14.3, particularly dark theme colors and logo
+
+### Fixed
+
+- Fixed broken docs links to xtal.SymOp
+- Fixed return type docs
+
+### Deprecated
+
+- The to_json and from_json methods of xtal.Prim, xtal.Structure, and xtal.SymInfo are deprecated in favor of the to_dict / from_dict methods and the builtin json module
+
+
+## [2.0a7] - 2023-11-14
+
+### Changed
+
+- Add py::is_operator() in the bindings of the `__mul__` operators xtal.SymOp and xtal.IntegralSiteCoordinateRep so it possible to add `__rmul__` operators to classes in other modules.
+
+
+## [2.0a6] - 2023-11-07
+
+### Changed
+
+- Allow integer array parameters to be either C or F ordered numpy arrays.
+- Added Lattice to CASM::xtal::SymInfo to avoid bad pointers in Coordinate members
+- Changed Prim.lattice and Structure.lattice docs to specify that the lattice is returned as a copy.
+
+
+## [2.0a5] - 2023-10-25
+
+### Added
+
+- Added SymOp.matrix_rep to get matrix representations for transforming CASM-supported properties in the standard basis
+
+### Changed
+
+- Do not allow automatic conversion from floating point arrays to integer Eigen objects.
+- Added a parameter, `mode`, to Structure.from_poscar and Structure.from_poscar_str to specify whether the POSCAR should be read as atoms, molecules, or both. The default was set to "atoms". Previous behavior was equivalent to using "both".
+
+### Fixed
+
+- Fixed the xtal::Site::dof error message thrown when the requested DoF type does not exist on the site
+- Updated documentation for the `local_dofs` parameters in libcasm.xtal.prims
+
+
+## [2.0a4] - 2023-09-29
+
+### Fixed
+
+- Fixed xtal::Site::has_dof to check for either occ or continuous DoF 
+
+
+## [2.0a3] - 2023-08-11
+
+This release separates out casm/crystallography from CASM v1, in particular removing remaining dependencies on casm/symmetry for constructing symmetry representations and getting basic symmetry operation info. It creates a Python package, libcasm.xtal, that enables using casm/crystallography and may be installed via pip install, using scikit-build, CMake, and pybind11. This release also includes usage and API documentation for using libcasm.xtal, built using Sphinx.
+
+### Added
+
+- Added xtal::SymOpSortKeyCompare for sorting xtal::SymOp
+- Added xtal::make_crystal_point_group to make the crystal point group from a sorted_factor_group (std::vector<xtal::SymOp>)
+- Added xtal::make_internal_translations to get translations from the factor group
+- Added standalone methods xtal::fast_pbc_displacement_cart and xtal::robust_pbc_displacement_cart using Eigen::Vector3d for coordinates
+- Added xtal::Molecule::identical overload for checking for identical Molecule up to a permutation
+- Added OccupantDoFIsEquivalent::atom_position_perm to get Molecule atom position permuation
+- Added xtal::make_simple_structure from a POSCAR stream
+- Added xtal::apply and xtal::copy_apply methods for transforming xtal::SimpleStructure including properties
+- Added xtal::make_inverse for xtal::SymOp
+- Added xtal::is_equivalent for comparing xtal::SimpleStructure
+- Added Python package libcasm.xtal to use CASM crystallography methods for building lattices, structures, and parent crystal structures and allowed degrees of freedom (prim); enumerating superlattices; creating superstructures; finding primitive and reduced cells; and determining symmetry operations.
+- Added scikit-build, CMake, and pybind11 build process
+- Added GitHub Actions for unit testing
+- Added GitHub Action build_wheels.yml for Python x86_64 wheel building using cibuildwheel
+- Added Cirrus-CI .cirrus.yml for Python aarch64 and arm64 wheel building using cibuildwheel
+- Added Python documentation
+
+
+### Changed
+
+- Moved StrainConverter into crystallography, removing symmetry dependencies
+- Moved SymInfo into crystallography from symmetry, using only xtal::SymOp
+- Moved class SymBasisPermute from symmetry to struct UnitCellCoordRep
+
+### Removed
+
+- Removed autotools build process
+- Removed boost dependencies

libcasm_xtal-2.0.0/CMakeLists.txt

@@ -0,0 +1,282 @@
+cmake_minimum_required(VERSION 3.20)
+set(CMAKE_OSX_DEPLOYMENT_TARGET "10.15" CACHE STRING "Minimum OS X deployment version")
+
+project(CASMcode_crystallography VERSION 2.0.0 LANGUAGES CXX)
+
+# set CMAKE_INSTALL_X variables
+include(GNUInstallDirs)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+# try to use ccache
+find_program(CCACHE_PROGRAM ccache)
+if(CCACHE_PROGRAM)
+    set(CMAKE_CXX_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
+endif()
+
+##############################################
+## Find dependencies
+
+# Should find ZLIB::ZLIB
+find_package(ZLIB)
+
+# Find CASM
+if(NOT DEFINED CASM_PREFIX)
+  message(STATUS "CASM_PREFIX not defined")
+  # try to find Python
+  find_package (Python COMPONENTS Interpreter Development)
+  if(DEFINED Python_EXECUTABLE)
+    # if Python found, obtain CASM_PREFIX from the libcasm.casmglobal
+    message(STATUS "found Python_EXECUTABLE: ${Python_EXECUTABLE}")
+    message(STATUS "checking for libcasm-global")
+    execute_process(
+      COMMAND pip show libcasm-global
+      RESULT_VARIABLE EXIT_CODE
+      OUTPUT_QUIET
+    )
+    if (${EXIT_CODE} EQUAL 0)
+      message(STATUS "found libcasm-global")
+      execute_process(COMMAND ${Python_EXECUTABLE} -m libcasm.casmglobal --prefix
+                      OUTPUT_VARIABLE CASM_PREFIX_RAW)
+      string(STRIP ${CASM_PREFIX_RAW} CASM_PREFIX)
+      message(STATUS "CASM_PREFIX: ${CASM_PREFIX}")
+    else()
+      message(STATUS "did not find libcasm-global")
+    endif()
+  endif()
+endif()
+if(DEFINED CASM_PREFIX)
+  set(CASMcode_global_ROOT ${CASM_PREFIX}/share/CASMcode_global/cmake)
+endif()
+find_package(CASMcode_global)
+if(NOT CASMcode_global_FOUND)
+  message(FATAL_ERROR "CMake failed to find CASMcode_global")
+endif()
+# if successful, we have CASM::casm_global
+
+# if no user CMAKE_INSTALL_PREFIX, use CASM_PREFIX if it exists
+IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  if(DEFINED CASM_PREFIX)
+    message(STATUS "CMAKE_INSTALL_PREFIX initialized to default, so updating CMAKE_INSTALL_PREFIX to CASM_PREFIX")
+    set(CMAKE_INSTALL_PREFIX ${CASM_PREFIX} CACHE PATH "set CMAKE_INSTALL_PREFIX to CASM_PREFIX" FORCE)
+    message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+  endif()
+ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+
+##############################################
+## Build libcasm_crystallography
+
+# create libcasm_crystallography
+set(
+  libcasm_crystallography_HEADERS
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/OccupantDoFIsEquivalent.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/BasicStructureTools.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Lattice.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/StrucMapCalculatorInterface.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Site.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/CanonicalForm.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SimpleStructure.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/HermiteCounter.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SimpleStrucMapCalculator.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/StrainConverter.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/DoFSet.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/DoFDecl.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SymInfo.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/LinearIndexConverter.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/AnisoValTraits.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Superlattice.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/LatticeMap.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/BasicStructure.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/IntegralCoordinateWithin.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Strain.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/UnitCellCoord.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/LatticeIsEquivalent.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Molecule.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/version.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/UnitCellCoordRep.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SymTools.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SuperlatticeEnumerator.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/StrucMapping.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Coordinate.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SimpleStructureTools.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/UnitCellCoordTraits.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Niggli.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SymRepBuilder.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/CoordinateSystems.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SymTypeComparator.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SpeciesProperty.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/SymType.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/Adapter.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/SimpleStructureIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/DoFSetIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/SymInfo_stream_io.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/LatticeIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/SuperlatticeEnumeratorIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/BasicStructureIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/UnitCellCoordIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/VaspIO.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/SymInfo_json_io.hh
+  ${PROJECT_SOURCE_DIR}/include/casm/crystallography/io/jsonStruc.hh
+)
+set(
+  libcasm_crystallography_SOURCES
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Superlattice.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/AnisoValTraits.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/LatticeMap.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/BasicStructure.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/IntegralCoordinateWithin.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Strain.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/UnitCellCoord.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/DoFSet.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/StrainConverter.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SymInfo.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/LinearIndexConverter.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/CanonicalForm.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Site.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SimpleStructure.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SimpleStrucMapCalculator.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/HermiteCounter.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/OccupantDoFIsEquivalent.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/BasicStructureTools.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Lattice.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/CoordinateSystems.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SymTypeComparator.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SpeciesProperty.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SymType.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SimpleStructureTools.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Coordinate.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/UnitCellCoordTraits.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Niggli.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SuperlatticeEnumerator.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/SymTools.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/StrucMapping.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/LatticeIsEquivalent.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/Molecule.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/version.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/UnitCellCoordRep.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/SuperlatticeEnumeratorIO.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/LatticeIO.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/BasicStructureIO.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/SimpleStructureIO.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/DoFSetIO.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/SymInfo_stream_io.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/SymInfo_json_io.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/VaspIO.cc
+  ${PROJECT_SOURCE_DIR}/src/casm/crystallography/io/UnitCellCoordIO.cc
+)
+add_library(casm_crystallography SHARED ${libcasm_crystallography_SOURCES})
+target_include_directories(casm_crystallography
+  PUBLIC
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/casm/external>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/casm/external/gzstream>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/casm/external>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/casm/external/gzstream>
+)
+target_compile_options(casm_crystallography
+  PUBLIC
+    "-DCASM_XTAL_TXT_VERSION=\"${CMAKE_PROJECT_VERSION}\""
+    -DEIGEN_DEFAULT_DENSE_INDEX_TYPE=long
+    -DGZSTREAM_NAMESPACE=gz
+)
+target_link_libraries(casm_crystallography
+  ZLIB::ZLIB
+  ${CMAKE_DL_LIBS}
+  CASM::casm_global
+)
+if(APPLE)
+  set_target_properties(
+    casm_crystallography PROPERTIES INSTALL_RPATH "@loader_path")
+else()
+  set_target_properties(
+    casm_crystallography PROPERTIES INSTALL_RPATH "$ORIGIN")
+endif()
+
+##############################################
+## Install libcasm_crystallography
+
+# install header files in <prefix>/libcasm/include/,
+# while preserving directory structure
+foreach ( filevar ${libcasm_crystallography_HEADERS} )
+  file(RELATIVE_PATH relfile ${PROJECT_SOURCE_DIR}/include/ ${filevar})
+  get_filename_component( reldir ${relfile} DIRECTORY )
+  install( FILES ${filevar} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/${reldir} )
+endforeach()
+
+# install libcasm_crystallography in <prefix>/libcasm/lib/
+install(
+  TARGETS casm_crystallography
+  EXPORT CASMcode_crystallographyTargets
+  DESTINATION lib)
+
+##############################################
+## Python extensions
+
+# The CMake package config and target files are installed under the Python
+# package root. This is necessary to ensure that all the relative paths in the
+# helloTargets.cmake resolve correctly. It also provides encapsulation.
+#
+# The actual path used must be selected so that consuming projects can locate it
+# via `find_package`. To support finding CMake packages in the Python package
+# prefix, using `find_package`s default search path of
+# `<prefix>/<name>/share/<name>*/cmake/` is reasonable. Adding the Python
+# package installation prefix to CMAKE_PREFIX_PATH in combination with this path
+# will allow `find_package` to find this package and any other package installed
+# via a Python package if the CMake and Python packages are named the same.
+set(CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR "share/CASMcode_crystallography/cmake")
+
+install(
+  EXPORT CASMcode_crystallographyTargets
+  NAMESPACE CASM::
+  DESTINATION ${CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+include(CMakePackageConfigHelpers)
+
+write_basic_package_version_file(
+  CASMcode_crystallographyConfigVersion.cmake
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY SameMinorVersion)
+
+configure_package_config_file(
+  "${PROJECT_SOURCE_DIR}/cmake/CASMcode_crystallographyConfig.cmake.in" CASMcode_crystallographyConfig.cmake
+  INSTALL_DESTINATION ${CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+install(FILES "${PROJECT_BINARY_DIR}/CASMcode_crystallographyConfig.cmake"
+              "${PROJECT_BINARY_DIR}/CASMcode_crystallographyConfigVersion.cmake"
+        DESTINATION ${CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+# We are using the SKBUILD variable, which is defined when scikit-build is
+# running the CMake build, to control building the Python wrapper. This allows
+# the C++ project to be installed, standalone, when using the standard CMake
+# build flow.
+if(DEFINED SKBUILD)
+
+  # call pybind11-config to obtain the root of the cmake package
+  execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pybind11 --cmakedir
+                  OUTPUT_VARIABLE pybind11_ROOT_RAW)
+  string(STRIP ${pybind11_ROOT_RAW} pybind11_ROOT)
+  find_package(pybind11)
+
+  # The extension modules must load:
+  # - the casm_global library
+  # - the casm_crystallography library
+  # They can be found by setting a relative rpath
+
+  ### libcasm.xtal._xtal ###
+  pybind11_add_module(_xtal MODULE
+                      "${PROJECT_SOURCE_DIR}/python/src/xtal.cpp")
+  target_link_libraries(_xtal PRIVATE CASM::casm_global)
+  target_link_libraries(_xtal PRIVATE casm_crystallography)
+  install(TARGETS _xtal DESTINATION xtal)
+  if(APPLE)
+    set_target_properties(
+      _xtal PROPERTIES INSTALL_RPATH "@loader_path/../lib")
+  else()
+    set_target_properties(
+      _xtal PROPERTIES INSTALL_RPATH "$ORIGIN/../lib")
+  endif()
+
+endif()

libcasm_xtal-2.0.0/CMakeLists.txt.in

@@ -0,0 +1,191 @@
+cmake_minimum_required(VERSION 3.20)
+set(CMAKE_OSX_DEPLOYMENT_TARGET "10.15" CACHE STRING "Minimum OS X deployment version")
+
+project(CASMcode_crystallography VERSION 2.0.0 LANGUAGES CXX)
+
+# set CMAKE_INSTALL_X variables
+include(GNUInstallDirs)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+# try to use ccache
+find_program(CCACHE_PROGRAM ccache)
+if(CCACHE_PROGRAM)
+    set(CMAKE_CXX_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
+endif()
+
+##############################################
+## Find dependencies
+
+# Should find ZLIB::ZLIB
+find_package(ZLIB)
+
+# Find CASM
+if(NOT DEFINED CASM_PREFIX)
+  message(STATUS "CASM_PREFIX not defined")
+  # try to find Python
+  find_package (Python COMPONENTS Interpreter Development)
+  if(DEFINED Python_EXECUTABLE)
+    # if Python found, obtain CASM_PREFIX from the libcasm.casmglobal
+    message(STATUS "found Python_EXECUTABLE: ${Python_EXECUTABLE}")
+    message(STATUS "checking for libcasm-global")
+    execute_process(
+      COMMAND pip show libcasm-global
+      RESULT_VARIABLE EXIT_CODE
+      OUTPUT_QUIET
+    )
+    if (${EXIT_CODE} EQUAL 0)
+      message(STATUS "found libcasm-global")
+      execute_process(COMMAND ${Python_EXECUTABLE} -m libcasm.casmglobal --prefix
+                      OUTPUT_VARIABLE CASM_PREFIX_RAW)
+      string(STRIP ${CASM_PREFIX_RAW} CASM_PREFIX)
+      message(STATUS "CASM_PREFIX: ${CASM_PREFIX}")
+    else()
+      message(STATUS "did not find libcasm-global")
+    endif()
+  endif()
+endif()
+if(DEFINED CASM_PREFIX)
+  set(CASMcode_global_ROOT ${CASM_PREFIX}/share/CASMcode_global/cmake)
+endif()
+find_package(CASMcode_global)
+if(NOT CASMcode_global_FOUND)
+  message(FATAL_ERROR "CMake failed to find CASMcode_global")
+endif()
+# if successful, we have CASM::casm_global
+
+# if no user CMAKE_INSTALL_PREFIX, use CASM_PREFIX if it exists
+IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  if(DEFINED CASM_PREFIX)
+    message(STATUS "CMAKE_INSTALL_PREFIX initialized to default, so updating CMAKE_INSTALL_PREFIX to CASM_PREFIX")
+    set(CMAKE_INSTALL_PREFIX ${CASM_PREFIX} CACHE PATH "set CMAKE_INSTALL_PREFIX to CASM_PREFIX" FORCE)
+    message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+  endif()
+ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+
+##############################################
+## Build libcasm_crystallography
+
+# create libcasm_crystallography
+set(
+  libcasm_crystallography_HEADERS
+@header_files@)
+set(
+  libcasm_crystallography_SOURCES
+@source_files@)
+add_library(casm_crystallography SHARED ${libcasm_crystallography_SOURCES})
+target_include_directories(casm_crystallography
+  PUBLIC
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/casm/external>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/casm/external/gzstream>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/casm/external>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/casm/external/gzstream>
+)
+target_compile_options(casm_crystallography
+  PUBLIC
+    "-DCASM_XTAL_TXT_VERSION=\"${CMAKE_PROJECT_VERSION}\""
+    -DEIGEN_DEFAULT_DENSE_INDEX_TYPE=long
+    -DGZSTREAM_NAMESPACE=gz
+)
+target_link_libraries(casm_crystallography
+  ZLIB::ZLIB
+  ${CMAKE_DL_LIBS}
+  CASM::casm_global
+)
+if(APPLE)
+  set_target_properties(
+    casm_crystallography PROPERTIES INSTALL_RPATH "@loader_path")
+else()
+  set_target_properties(
+    casm_crystallography PROPERTIES INSTALL_RPATH "$ORIGIN")
+endif()
+
+##############################################
+## Install libcasm_crystallography
+
+# install header files in <prefix>/libcasm/include/,
+# while preserving directory structure
+foreach ( filevar ${libcasm_crystallography_HEADERS} )
+  file(RELATIVE_PATH relfile ${PROJECT_SOURCE_DIR}/include/ ${filevar})
+  get_filename_component( reldir ${relfile} DIRECTORY )
+  install( FILES ${filevar} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/${reldir} )
+endforeach()
+
+# install libcasm_crystallography in <prefix>/libcasm/lib/
+install(
+  TARGETS casm_crystallography
+  EXPORT CASMcode_crystallographyTargets
+  DESTINATION lib)
+
+##############################################
+## Python extensions
+
+# The CMake package config and target files are installed under the Python
+# package root. This is necessary to ensure that all the relative paths in the
+# helloTargets.cmake resolve correctly. It also provides encapsulation.
+#
+# The actual path used must be selected so that consuming projects can locate it
+# via `find_package`. To support finding CMake packages in the Python package
+# prefix, using `find_package`s default search path of
+# `<prefix>/<name>/share/<name>*/cmake/` is reasonable. Adding the Python
+# package installation prefix to CMAKE_PREFIX_PATH in combination with this path
+# will allow `find_package` to find this package and any other package installed
+# via a Python package if the CMake and Python packages are named the same.
+set(CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR "share/CASMcode_crystallography/cmake")
+
+install(
+  EXPORT CASMcode_crystallographyTargets
+  NAMESPACE CASM::
+  DESTINATION ${CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+include(CMakePackageConfigHelpers)
+
+write_basic_package_version_file(
+  CASMcode_crystallographyConfigVersion.cmake
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY SameMinorVersion)
+
+configure_package_config_file(
+  "${PROJECT_SOURCE_DIR}/cmake/CASMcode_crystallographyConfig.cmake.in" CASMcode_crystallographyConfig.cmake
+  INSTALL_DESTINATION ${CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+install(FILES "${PROJECT_BINARY_DIR}/CASMcode_crystallographyConfig.cmake"
+              "${PROJECT_BINARY_DIR}/CASMcode_crystallographyConfigVersion.cmake"
+        DESTINATION ${CASM_CRYSTALLOGRAPHY_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+# We are using the SKBUILD variable, which is defined when scikit-build is
+# running the CMake build, to control building the Python wrapper. This allows
+# the C++ project to be installed, standalone, when using the standard CMake
+# build flow.
+if(DEFINED SKBUILD)
+
+  # call pybind11-config to obtain the root of the cmake package
+  execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pybind11 --cmakedir
+                  OUTPUT_VARIABLE pybind11_ROOT_RAW)
+  string(STRIP ${pybind11_ROOT_RAW} pybind11_ROOT)
+  find_package(pybind11)
+
+  # The extension modules must load:
+  # - the casm_global library
+  # - the casm_crystallography library
+  # They can be found by setting a relative rpath
+
+  ### libcasm.xtal._xtal ###
+  pybind11_add_module(_xtal MODULE
+                      "${PROJECT_SOURCE_DIR}/python/src/xtal.cpp")
+  target_link_libraries(_xtal PRIVATE CASM::casm_global)
+  target_link_libraries(_xtal PRIVATE casm_crystallography)
+  install(TARGETS _xtal DESTINATION xtal)
+  if(APPLE)
+    set_target_properties(
+      _xtal PROPERTIES INSTALL_RPATH "@loader_path/../lib")
+  else()
+    set_target_properties(
+      _xtal PROPERTIES INSTALL_RPATH "$ORIGIN/../lib")
+  endif()
+
+endif()