Backport fix from PR #494

actions/generate_recipe.py

@@ -31,7 +31,6 @@
     "git",
     "make",
     "libtool",
-    "pybind11",
     "sysroot_linux-64",
 }
 

doc/source/acknowledgements.rst

@@ -421,17 +421,14 @@ for parsing mmCIF files. This is used under the terms of the MIT
 or Boost Software License (the version bundled with gemmi is MIT,
 while the version on GitHub is BSL)
 
-pyboost11
----------
+zpp::serializer
+---------------
 
-Thanks to Yung-Yu's excellent
-`blog post <https://yyc.solvcon.net/en/latest/writing/2021/pyboost11/pyboost11.html>`__
-on how to interconvert between boost::python and pybind11, and for providing
-`pyboost11.hpp <https://yyc.solvcon.net/en/latest/writing/2021/pyboost11/code.html#pyboost11-code-pyboost11-hpp>`__
-as a header-only library to support interconversion. This was really useful
-to let me mix pybind11-wrapped gemmi objects with boost::python-wrapped sire.
-The code is used under the terms of the liberal open source license
-given at the top of the header file.
+:mod:`sire` bundles the header-only
+`zpp::serializer <https://github.com/eyalz800/serializer>`__ library (the
+copy distributed with gemmi) to exchange gemmi structures with the gemmi
+Python module using gemmi's own binary serialization. This is used under
+the terms of the MIT license.
 
 RDKit
 -----

pixi.toml

@@ -10,7 +10,6 @@ platforms = ["linux-64", "linux-aarch64", "osx-arm64", "win-64"]
 python = "*"
 cmake = ">=3.30.0"
 git = "*"
-pybind11 = "*"
 gsl = "*"
 libboost-devel = "*"
 libboost-python-devel = "*"
@@ -30,7 +29,7 @@ make = "*"
 libtool = "*"
 sysroot_linux-64 = "==2.17"
 kartograf = ">=1.0.0"
-gemmi = ">=0.6.4,<0.7.0"
+gemmi = ">=0.7.0,<0.8.0"
 
 # Host dependencies for local source builds (not used by generate_recipe.py)
 [target.linux-64.host-dependencies]
@@ -51,14 +50,14 @@ cxx-compiler = "*"
 make = "*"
 libtool = "*"
 kartograf = ">=1.0.0"
-gemmi = ">=0.6.4,<0.7.0"
+gemmi = ">=0.7.0,<0.8.0"
 
 [target.osx-arm64.host-dependencies]
 c-compiler = "*"
 cxx-compiler = "*"
 
 [target.win-64.dependencies]
-gemmi = ">=0.6.4,<0.7.0"
+gemmi = ">=0.7.0,<0.8.0"
 
 [target.win-64.host-dependencies]
 c-compiler = "*"
@@ -164,17 +163,17 @@ rdkit = ">=2023.0.0"
 
 [feature.test.target.linux-64.dependencies]
 kartograf = ">=1.0.0"
-gemmi = ">=0.6.4,<0.7.0"
+gemmi = ">=0.7.0,<0.8.0"
 
 [feature.test.target.linux-aarch64.dependencies]
 kartograf = ">=1.0.0"
 
 [feature.test.target.osx-arm64.dependencies]
 kartograf = ">=1.0.0"
-gemmi = ">=0.6.4,<0.7.0"
+gemmi = ">=0.7.0,<0.8.0"
 
 [feature.test.target.win-64.dependencies]
-gemmi = ">=0.6.4,<0.7.0"
+gemmi = ">=0.7.0,<0.8.0"
 
 # kartograf excluded from Windows test deps
 

wrapper/Convert/CMakeLists.txt

@@ -10,8 +10,7 @@ set( CMAKE_CXX_FLAGS "${OPTIMISED_CXX_FLAGS}" )
 
 add_subdirectory (SireRDKit)
 add_subdirectory (SireOpenMM)
-# SireGemmi currently disabled due to build issues
-# add_subdirectory (SireGemmi)
+add_subdirectory (SireGemmi)
 
 # installation
 set( INSTALLDIR ${SIRE_PYTHON}/sire/legacy/Convert )

wrapper/Convert/SireGemmi/CMakeLists.txt

@@ -4,23 +4,19 @@
 #
 ##########################################
 
-# Find gemmi and pybind11 libraries
+# Find gemmi library
 find_package(gemmi)
-find_package(pybind11)
 
-if (${gemmi_FOUND} AND ${pybind11_FOUND})
+if (${gemmi_FOUND})
   # Only compile and install if we have gemmi
   message( STATUS "Compiling SireGemmi converter" )
 
   get_target_property(GEMMI_LOCATION gemmi::gemmi_cpp IMPORTED_LOCATION_RELEASE)
   message( STATUS "gemmi location: ${GEMMI_LOCATION}" )
-  message( STATUS "PYBIND11 INCLUDE ${pybind11_INCLUDE_DIR}")
-  message( STATUS "PYBIND11 LIBRARY ${pybind11_LIBRARIES}" )
   message( STATUS "ZLIB LIBRARIES ${ZLIB_LIBRARIES}" )
 
   # Third Party dependencies of this module
   include_directories( ${PYTHON_INCLUDE_DIR}
-                       ${pybind11_INCLUDE_DIR}
                        ${gemmi_INCLUDE_DIR} )
 
   # Sire include paths
@@ -59,7 +55,6 @@ if (${gemmi_FOUND} AND ${pybind11_FOUND})
                           SIRE_SireStream
                           SIRE_SireError
                           gemmi::gemmi_cpp
-                          ${pybind11_LIBRARIES}
                         )
 
   include( LimitSirePythonExportSymbols )

wrapper/Convert/SireGemmi/_SireGemmi.main.cpp

@@ -2,33 +2,51 @@
 // (C) Christopher Woods, GPL >= 3 License
 
 #include "boost/python.hpp"
-#include "boost/python/converter/registry.hpp"
 
 #include "sire_gemmi.h"
 
-#include "Helpers/pyboost11.hpp"
+#include <gemmi/version.hpp>
 
 namespace bp = boost::python;
 
 using namespace SireGemmi;
 
-#include <gemmi/model.hpp>
+bp::object sire_to_gemmi_state_py(const SireSystem::System &system,
+                                  const SireBase::PropertyMap &map)
+{
+    const auto state = sire_to_gemmi_state(system, map);
+
+    return bp::object(bp::handle<>(
+        PyBytes_FromStringAndSize(state.data(), state.size())));
+}
+
+SireSystem::System gemmi_state_to_sire_py(const bp::object &state,
+                                          const SireBase::PropertyMap &map)
+{
+    char *data = nullptr;
+    Py_ssize_t size = 0;
+
+    if (PyBytes_AsStringAndSize(state.ptr(), &data, &size) != 0)
+        bp::throw_error_already_set();
+
+    return gemmi_state_to_sire(std::string(data, size), map);
+}
 
 BOOST_PYTHON_MODULE(_SireGemmi)
 {
-    bp::def("sire_to_gemmi",
-            &sire_to_gemmi,
+    bp::def("_sire_to_gemmi_state",
+            &sire_to_gemmi_state_py,
             (bp::arg("mols"), bp::arg("map")),
-            "Convert sire system to a gemmi structure");
+            "Convert sire system to the pickle state of a gemmi Structure");
 
-    bp::def("gemmi_to_sire",
-            &gemmi_to_sire,
-            (bp::arg("mols"), bp::arg("map")),
-            "Convert a gemmi Structure to a sire system");
+    bp::def("_gemmi_state_to_sire",
+            &gemmi_state_to_sire_py,
+            (bp::arg("state"), bp::arg("map")),
+            "Convert the pickle state of a gemmi Structure to a sire system");
+
+    bp::scope().attr("_gemmi_version") = GEMMI_VERSION;
 
     bp::def("_register_pdbx_loader",
             &register_pdbx_loader,
             "Internal function called once used to register PDBx support");
-
-    pyboost11::converter<gemmi::Structure>();
 }

wrapper/Convert/SireGemmi/sire_gemmi.cpp

@@ -2,24 +2,29 @@
 #include "sire_gemmi.h"
 
 #include "gemmi/cif.hpp"
+#include "gemmi/mmcif.hpp"
 #include "gemmi/modify.hpp"
 #include "gemmi/polyheur.hpp"
+#include "gemmi/read_cif.hpp"
 #include "gemmi/to_cif.hpp"
 #include "gemmi/to_mmcif.hpp"
-#include "gemmi/mmcif.hpp"
+
+// gemmi/serialize.hpp requires the zpp serializer to be included first
+#include "gemmi/serialize.hpp"
+#include "third_party/serializer.h"
 
 #include "SireIO/pdbx.h"
 
 #include "SireMol/core.h"
-#include "SireMol/moleditor.h"
 #include "SireMol/element.h"
+#include "SireMol/moleditor.h"
 
-#include "SireMol/atomproperty.hpp"
-#include "SireMol/atomelements.h"
-#include "SireMol/atomcoords.h"
 #include "SireMol/atomcharges.h"
-#include "SireMol/connectivity.h"
+#include "SireMol/atomcoords.h"
+#include "SireMol/atomelements.h"
+#include "SireMol/atomproperty.hpp"
 #include "SireMol/bondhunter.h"
+#include "SireMol/connectivity.h"
 
 #include "SireMol/iswater.h"
 
@@ -30,9 +35,9 @@
 
 #include "SireError/errors.h"
 
-#include <string>
-#include <sstream>
 #include <iostream>
+#include <sstream>
+#include <string>
 
 namespace cif = gemmi::cif;
 
@@ -1265,6 +1270,30 @@ namespace SireGemmi
         return lines;
     }
 
+    SireSystem::System gemmi_state_to_sire(const std::string &state,
+                                           const SireBase::PropertyMap &map)
+    {
+        gemmi::Structure structure;
+
+        zpp::serializer::memory_view_input_archive in(
+            reinterpret_cast<const unsigned char *>(state.data()), state.size());
+        in(structure);
+
+        return gemmi_to_sire(structure, map);
+    }
+
+    std::string sire_to_gemmi_state(const SireSystem::System &system,
+                                    const SireBase::PropertyMap &map)
+    {
+        const auto structure = sire_to_gemmi(system, map);
+
+        std::vector<unsigned char> data;
+        zpp::serializer::memory_output_archive out(data);
+        out(structure);
+
+        return std::string(data.begin(), data.end());
+    }
+
     void register_pdbx_loader()
     {
         SireIO::PDBxReaderFunction reader_function(&pdbx_reader_function);

wrapper/Convert/SireGemmi/sire_gemmi.h

@@ -11,6 +11,7 @@ namespace gemmi
 #include "SireBase/propertymap.h"
 
 #include <memory>
+#include <string>
 
 namespace SireGemmi
 {
@@ -21,6 +22,13 @@ namespace SireGemmi
     gemmi::Structure sire_to_gemmi(const SireSystem::System &system,
                                    const SireBase::PropertyMap &map);
 
+    // Structures cross to Python as gemmi's pickle state (zpp serialized)
+    SireSystem::System gemmi_state_to_sire(const std::string &state,
+                                           const SireBase::PropertyMap &map);
+
+    std::string sire_to_gemmi_state(const SireSystem::System &system,
+                                    const SireBase::PropertyMap &map);
+
     void register_pdbx_loader();
 }
 

wrapper/Convert/SireGemmi/third_party/LICENSE.zpp_serializer

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 Eyal Z
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.