diff --git a/CMakeLists.txt b/CMakeLists.txt index f35d368..7127220 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,13 +1,13 @@ -cmake_minimum_required(VERSION 3.20) +cmake_minimum_required(VERSION 3.22) project(diffpy_srreal LANGUAGES NONE) -# Keep this aligned with the pinned libdiffpy's src/SConscript. +# Keep this aligned with the pinned libdiffpy's CMakeLists.txt. set(CMAKE_CXX_STANDARD 23) set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_EXTENSIONS OFF) set(LIBDIFFPY_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/extern/libdiffpy") -if(NOT EXISTS "${LIBDIFFPY_SOURCE_DIR}/src/diffpy/version.tpl") +if(NOT EXISTS "${LIBDIFFPY_SOURCE_DIR}/CMakeLists.txt") message(FATAL_ERROR "Missing libdiffpy sources. Initialize the submodule with " "'git submodule update --init --recursive', or use a source distribution " @@ -15,42 +15,28 @@ if(NOT EXISTS "${LIBDIFFPY_SOURCE_DIR}/src/diffpy/version.tpl") ) endif() -# Read version information from the submodule; sdists carry the generated header. -set(LIBDIFFPY_VERSION_HEADER "${CMAKE_CURRENT_BINARY_DIR}/include/diffpy/version.hpp") -set(LIBDIFFPY_SDIST_VERSION_HEADER "${CMAKE_CURRENT_SOURCE_DIR}/_build/libdiffpy-version.hpp") -if(EXISTS "${LIBDIFFPY_SOURCE_DIR}/.git") - file(STRINGS "${LIBDIFFPY_SOURCE_DIR}/site_scons/fallback_version.py" - LIBDIFFPY_FALLBACK_VERSION REGEX "^FALLBACK_VERSION =") - if(NOT LIBDIFFPY_FALLBACK_VERSION MATCHES "([0-9]+)\\.([0-9]+)\\.([0-9]+)") - message(FATAL_ERROR "Cannot read the libdiffpy base version.") - endif() - set(DIFFPY_VERSION_MAJOR "${CMAKE_MATCH_1}") - set(DIFFPY_VERSION_MINOR "${CMAKE_MATCH_2}") - set(DIFFPY_VERSION_MICRO "${CMAKE_MATCH_3}") - set(DIFFPY_VERSION_PATCH 0) - set(DIFFPY_VERSION_STR "${DIFFPY_VERSION_MAJOR}.${DIFFPY_VERSION_MINOR}.${DIFFPY_VERSION_MICRO}") - math(EXPR DIFFPY_VERSION "${DIFFPY_VERSION_MAJOR} * 1000000000 + ${DIFFPY_VERSION_MINOR} * 1000000 + ${DIFFPY_VERSION_MICRO} * 1000") - set(DIFFPY_VERSION "${DIFFPY_VERSION}LL") - find_package(Git REQUIRED) - execute_process( - COMMAND "${GIT_EXECUTABLE}" -C "${LIBDIFFPY_SOURCE_DIR}" log -1 "--format=%H;%ci" - OUTPUT_VARIABLE LIBDIFFPY_COMMIT_INFO - OUTPUT_STRIP_TRAILING_WHITESPACE - COMMAND_ERROR_IS_FATAL ANY - ) - list(GET LIBDIFFPY_COMMIT_INFO 0 DIFFPY_GIT_SHA) - list(GET LIBDIFFPY_COMMIT_INFO 1 DIFFPY_VERSION_DATE) - configure_file("${LIBDIFFPY_SOURCE_DIR}/src/diffpy/version.tpl" - "${LIBDIFFPY_VERSION_HEADER}") -else() - configure_file("${LIBDIFFPY_SDIST_VERSION_HEADER}" - "${LIBDIFFPY_VERSION_HEADER}" COPYONLY) -endif() +# libdiffpy resolves its version from git unless src/diffpy/version.hpp exists, +# as in its own source distribution. The srreal sdist has no git, so write that +# header here and ship it. +set(LIBDIFFPY_SDIST_VERSION_HEADER "${LIBDIFFPY_SOURCE_DIR}/src/diffpy/version.hpp") if(SKBUILD_STATE STREQUAL "sdist") - configure_file("${LIBDIFFPY_VERSION_HEADER}" - "${LIBDIFFPY_SDIST_VERSION_HEADER}" COPYONLY) + # Refresh git checkouts; preserve the header when repacking an sdist. + if(EXISTS "${LIBDIFFPY_SOURCE_DIR}/.git" OR + NOT EXISTS "${LIBDIFFPY_SDIST_VERSION_HEADER}") + include("${LIBDIFFPY_SOURCE_DIR}/cmake/LibdiffpyVersion.cmake") + libdiffpy_resolve_version() + libdiffpy_write_version_header( + "${LIBDIFFPY_SOURCE_DIR}/src/diffpy/version.tpl" + "${LIBDIFFPY_SDIST_VERSION_HEADER}") + endif() return() endif() +# A header left over from a local sdist build would freeze the git checkout's +# version, so remove it. +if(EXISTS "${LIBDIFFPY_SOURCE_DIR}/.git" AND EXISTS "${LIBDIFFPY_SDIST_VERSION_HEADER}") + message(STATUS "Removing stale ${LIBDIFFPY_SDIST_VERSION_HEADER}") + file(REMOVE "${LIBDIFFPY_SDIST_VERSION_HEADER}") +endif() enable_language(CXX) # Conda is optional; system packages and CMAKE_PREFIX_PATH work as well. @@ -95,40 +81,30 @@ if(DEFINED _srreal_saved_suffixes) endforeach() endif() -set(DIFFPY_HAS_OBJCRYST 0) -configure_file("${LIBDIFFPY_SOURCE_DIR}/src/diffpy/features.tpl" - "include/diffpy/features.hpp") - -file(GLOB LIBDIFFPY_SOURCES CONFIGURE_DEPENDS - "${LIBDIFFPY_SOURCE_DIR}/src/diffpy/*.cpp" - "${LIBDIFFPY_SOURCE_DIR}/src/diffpy/srreal/*.cpp" -) +# Embed libdiffpy as an OBJECT library: every object is linked, so its static +# factory/serialization registrars are kept. +set(LIBDIFFPY_BUILD_OBJECT_LIB ON) +set(LIBDIFFPY_INSTALL OFF) # ObjCryst conversion uses the public Python API, so it does not depend on # pyobjcryst's private static library, compiler, REAL precision, or nanobind ABI. -list(FILTER LIBDIFFPY_SOURCES EXCLUDE REGEX "ObjCryst") -# Include every object: libdiffpy has static factory/serialization registrars -# that an ordinary static archive link can otherwise discard. -add_library(diffpy_core OBJECT ${LIBDIFFPY_SOURCES}) -set_target_properties(diffpy_core PROPERTIES +set(LIBDIFFPY_ENABLE_OBJCRYST OFF) +set(LIBDIFFPY_BUILD_TESTS OFF) +# Runtime data installs next to the extension, in diffpy/srreal/data. +set(LIBDIFFPY_RUNTIME_RELPATH data) +add_subdirectory("${LIBDIFFPY_SOURCE_DIR}" libdiffpy EXCLUDE_FROM_ALL) +set_target_properties(diffpy PROPERTIES POSITION_INDEPENDENT_CODE ON CXX_VISIBILITY_PRESET hidden VISIBILITY_INLINES_HIDDEN ON ) -target_include_directories(diffpy_core PUBLIC - "${CMAKE_CURRENT_BINARY_DIR}/include" - "${LIBDIFFPY_SOURCE_DIR}/src" -) -target_compile_definitions(diffpy_core PRIVATE DIFFPYRUNTIMERELPATH=data) -if(WIN32) - # libdiffpy and its Python wrappers are compiled into the same extension. - target_compile_definitions(diffpy_core PUBLIC BUILD_DLL _USE_MATH_DEFINES NOMINMAX) -endif() -target_link_libraries(diffpy_core PUBLIC Boost::serialization GSL::gsl GSL::gslcblas ${CMAKE_DL_LIBS}) file(GLOB SRREAL_SOURCES CONFIGURE_DEPENDS "src/extensions/*.cpp") # Retain CPython-specific wheels; stable-ABI packaging is a separate change. nanobind_add_module(srreal_ext NB_STATIC ${SRREAL_SOURCES}) -target_link_libraries(srreal_ext PRIVATE diffpy_core) +target_link_libraries(srreal_ext PRIVATE libdiffpy::diffpy) +if(WIN32) + target_compile_definitions(srreal_ext PRIVATE NOMINMAX) +endif() set_target_properties(srreal_ext PROPERTIES INSTALL_RPATH_USE_LINK_PATH ON) install(TARGETS srreal_ext LIBRARY DESTINATION diffpy/srreal) install(DIRECTORY "${LIBDIFFPY_SOURCE_DIR}/src/runtime/" diff --git a/devutils/generate_legacy_pickle_fixtures.py b/devutils/generate_legacy_pickle_fixtures.py deleted file mode 100644 index b2d982b..0000000 --- a/devutils/generate_legacy_pickle_fixtures.py +++ /dev/null @@ -1,136 +0,0 @@ -"""Regenerate fixtures using an installed Boost.Python diffpy.srreal -1.4.0. - -Run this script with the reference environment's Python, without placing -the migration checkout on PYTHONPATH. The fixture records the native -archive ABI. -""" - -import base64 -import json -import pickle -import struct -import sys -from importlib.metadata import version -from pathlib import Path - -import numpy as np - -import diffpy.srreal.srreal_ext as ext -from diffpy.srreal.bondcalculator import BondCalculator -from diffpy.srreal.bvscalculator import BVSCalculator -from diffpy.srreal.overlapcalculator import OverlapCalculator -from diffpy.srreal.pdfcalculator import DebyePDFCalculator, PDFCalculator -from diffpy.srreal.structureadapter import EMPTY -from diffpy.srreal.structureconverters import convertDiffPyStructure -from diffpy.structure import Atom, Structure - -assert any("Boost.Python" in str(c) for c in ext.Atom.__mro__) - -fixtures = { - "producer": f"Boost.Python diffpy.srreal {version('diffpy.srreal')}", - "byteorder": sys.byteorder, - "pointer_size": struct.calcsize("P"), - "long_size": struct.calcsize("l"), - "cases": {}, -} - - -def record(name, obj, **expected): - fixtures["cases"][name] = { - "pickle": base64.b64encode(pickle.dumps(obj, protocol=4)).decode(), - **expected, - } - - -record("EMPTY", EMPTY, sites=0) -for cls in ( - ext.AtomicStructureAdapter, - ext.PeriodicStructureAdapter, - ext.CrystalStructureAdapter, -): - adapter = cls() - atom = ext.Atom() - atom.atomtype = "Ni" - atom.xyz_cartn = [1, 2, 3] - adapter.append(atom) - if hasattr(adapter, "setLatPar"): - adapter.setLatPar(4, 5, 6, 90, 90, 90) - if hasattr(adapter, "addSymOp"): - adapter.addSymOp(np.eye(3), np.zeros(3)) - record(cls.__name__, adapter, sites=1) - # Native C++ clones use a different reconstruction protocol. - record(cls.__name__ + "Clone", adapter.clone(), sites=1) - -structure = Structure([Atom("Ni", [1, 2, 3]), Atom("Ni", [2, 2, 3])]) -structure.Uisoequiv = 0.005 -record("DiffPyAdapter", convertDiffPyStructure(structure), sites=2) -for cls in ( - BondCalculator, - BVSCalculator, - OverlapCalculator, - PDFCalculator, - DebyePDFCalculator, -): - calc = cls(rmax=3) - record(cls.__name__ + "Empty", calc, sites=0, rmax=3) - calc.eval(structure) - record(cls.__name__, calc, sites=2, rmax=3, value=calc.value.tolist()) - - -def record_python_components(): - # Reuse importable Python components already exercised by the test suite. - sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "tests")) - from test_pdfbaseline import parabola_baseline - from test_pdfenvelope import parabola_envelope - from test_peakprofile import MySawTooth - from test_peakwidthmodel import MyPWM - from test_scatteringfactortable import LocalTable - - from diffpy.srreal.atomradiitable import CovalentRadiiTable - from diffpy.srreal.pdfbaseline import makePDFBaseline - from diffpy.srreal.pdfenvelope import makePDFEnvelope - - baseline = makePDFBaseline( - "legacy_parabola", parabola_baseline, a=1, b=2, c=3 - ) - for attribute, component in ( - ("peakprofile", MySawTooth()), - ("peakwidthmodel", MyPWM()), - ("scatteringfactortable", LocalTable()), - ("baseline", baseline), - ): - calc = PDFCalculator(rmax=3) - setattr(calc, attribute, component) - record( - "Python_" + attribute, - calc, - sites=0, - rmax=3, - component=attribute, - component_type=component.type(), - ) - calc = OverlapCalculator(rmax=3) - calc.atomradiitable = CovalentRadiiTable() - record( - "Python_atomradiitable", - calc, - sites=0, - rmax=3, - component="atomradiitable", - component_type="covalent", - ) - calc = PDFCalculator(rmax=3) - calc.envelopes = [ - makePDFEnvelope("legacy_envelope", parabola_envelope, a=1, b=2, c=3) - ] - record("Python_envelope", calc, sites=0, rmax=3) - - -record_python_components() - -path = ( - Path(__file__).resolve().parents[1] - / "tests/testdata/boost_python_pickles.json" -) -path.write_text(json.dumps(fixtures, indent=2) + "\n") diff --git a/extern/libdiffpy b/extern/libdiffpy index 427b5c6..e7b105e 160000 --- a/extern/libdiffpy +++ b/extern/libdiffpy @@ -1 +1 @@ -Subproject commit 427b5c658de4fa051f204cc17d2ac63165b46c5f +Subproject commit e7b105e492cd25e7c0b1a72cc1ec93f83267b07d diff --git a/news/cmake-libdiffpy.rst b/news/cmake-libdiffpy.rst new file mode 100644 index 0000000..7d80cb4 --- /dev/null +++ b/news/cmake-libdiffpy.rst @@ -0,0 +1,24 @@ +**Added:** + +* + +**Changed:** + +* Build the embedded libdiffpy through its own CMake project + (``add_subdirectory``) instead of duplicating its build logic. + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/pyproject.toml b/pyproject.toml index c06b940..c98f744 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,8 @@ cmake.build-type = "Release" wheel.packages = ["src/diffpy"] sdist.cmake = true sdist.include = [ - "_build/libdiffpy-version.hpp", + "extern/libdiffpy/CMakeLists.txt", + "extern/libdiffpy/cmake/**", "extern/libdiffpy/src/diffpy/**", "extern/libdiffpy/src/runtime/**", "extern/libdiffpy/LICENSE.rst", diff --git a/tests/test_saved_calculations.py b/tests/test_saved_calculations.py index 90eba55..6746f25 100644 --- a/tests/test_saved_calculations.py +++ b/tests/test_saved_calculations.py @@ -1,18 +1,10 @@ """Saved calculations retain structures, components, and Python state.""" -import base64 import copy -import json import pickle -import struct -import sys -from importlib import import_module -from pathlib import Path -import numpy as np import pytest -from test_python_interfaces import CALCULATOR_MODULES from test_structure_lifetimes import make_structure from diffpy.srreal import srreal_ext as ext @@ -84,84 +76,6 @@ def test_unmanaged_dictionary_is_still_rejected(): assert calc.getStructure() is not None -_legacy = json.loads( - (Path(__file__).parent / "testdata/boost_python_pickles.json").read_text() -) - - -@pytest.fixture(scope="module") -def legacy_component_registry(): - # Registered-function pickles require their type to be registered in the - # receiving process under both bindings. - from test_pdfbaseline import parabola_baseline - from test_pdfenvelope import parabola_envelope - - from diffpy.srreal.pdfbaseline import makePDFBaseline - from diffpy.srreal.pdfenvelope import makePDFEnvelope - - makePDFBaseline("legacy_parabola", parabola_baseline, a=1, b=2, c=3) - makePDFEnvelope("legacy_envelope", parabola_envelope, a=1, b=2, c=3) - yield - ext.PDFBaseline._deregisterType("legacy_parabola") - ext.PDFEnvelope._deregisterType("legacy_envelope") - - -@pytest.mark.parametrize("name,case", _legacy["cases"].items()) -def test_boost_python_pickle_compatibility( - name, case, legacy_component_registry -): - if (sys.byteorder, struct.calcsize("P"), struct.calcsize("l")) != ( - _legacy["byteorder"], - _legacy["pointer_size"], - _legacy["long_size"], - ): - pytest.skip("Boost binary archive uses a different native ABI") - obj = pickle.loads(base64.b64decode(case["pickle"])) - # The restored object must itself remain serializable with this binding. - for restored in [obj, pickle.loads(pickle.dumps(obj))]: - if "rmax" in case: - assert restored.rmax == case["rmax"] - assert callable(restored) - adapter = restored.getStructure() - if "component" in case: - component = getattr(restored, case["component"]) - assert component.type() == case["component_type"] - if name == "Python_envelope": - assert restored.getEnvelope("legacy_envelope")(2) == 11 - if "value" in case: - np.testing.assert_allclose( - restored.value, case["value"], atol=1e-12 - ) - np.testing.assert_allclose( - restored.eval(), case["value"], atol=1e-12 - ) - # Old pickles name srreal_ext classes and must also retain - # their normal public calling interface after restoration. - module = import_module( - "diffpy.srreal." + CALCULATOR_MODULES[name] - ) - assert type(restored) is getattr(module, name) - result = restored() - if "PDFCalculator" in name: - np.testing.assert_allclose(result[0], restored.rgrid) - np.testing.assert_allclose(result[1], restored.pdf) - else: - expected = ( - restored.sitesquareoverlaps - if name == "OverlapCalculator" - else restored.value - ) - 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