Remove legacy Cython features

Several Cython features have been deprecated in Cython 3.0 and will
generate errors in future Cython releases. This change removes .pxi
include files, all `IF` conditional statements, and cpdef functions.
Almost all Cython 3.0 deprecation warnings were addressed, a silent
API change from Python 3.11 was mitigated, and some of the custom
Cython code for type checking was replaced by equivalent C++ code.

.github/actions/build_and_check/action.yml

@@ -6,7 +6,7 @@ runs:
     - run: |
        brew install boost boost-mpi fftw
        brew install hdf5-mpi
-       pip3 install -c requirements.txt numpy cython h5py scipy
+       pip3 install -c requirements.txt numpy "cython<3.0" h5py scipy
       shell: bash
       if: runner.os == 'macOS'
     - run: |

CMakeLists.txt

@@ -247,7 +247,7 @@ endif()
 # Python interpreter and Cython interface library
 if(ESPRESSO_BUILD_WITH_PYTHON)
   find_package(Python 3.9 REQUIRED COMPONENTS Interpreter Development NumPy)
-  find_package(Cython 0.29.21...<3.0 REQUIRED)
+  find_package(Cython 0.29.21...<3.0.8 REQUIRED)
   find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
 endif()
 

maintainer/CI/build_cmake.sh

@@ -404,7 +404,7 @@ if [ "${with_coverage}" = true ] || [ "${with_coverage_python}" = true ]; then
         lcov --gcov-tool "${GCOV:-gcov}" -q --remove coverage.info '/usr/*' --output-file coverage.info # filter out system
         lcov --gcov-tool "${GCOV:-gcov}" -q --remove coverage.info '*/doc/*' --output-file coverage.info # filter out docs
         if [ -d _deps/ ]; then
-          lcov --gcov-tool "${GCOV:-gcov}" -q --remove coverage.info $(realpath _deps/)'/*' --output-file coverage.info # filter out docs
+          lcov --gcov-tool "${GCOV:-gcov}" -q --remove coverage.info $(realpath _deps/)'/*' --output-file coverage.info # filter out external projects
         fi
     fi
     if [ "${with_coverage_python}" = true ]; then

requirements.txt

@@ -1,5 +1,5 @@
 # build system
-cython>=0.29.21,<3.0
+cython>=0.29.21,<=3.0.7
 setuptools>=59.6.0
 # required scientific packages
 numpy>=1.23

src/core/electrostatics/icc.cpp

@@ -50,7 +50,6 @@
 #include <boost/mpi/operations.hpp>
 
 #include <algorithm>
-#include <cassert>
 #include <cmath>
 #include <limits>
 #include <stdexcept>
@@ -212,6 +211,8 @@ void ICCStar::iteration(CellStructure &cell_structure,
 }
 
 void icc_data::sanity_checks() const {
+  if (n_icc <= 0)
+    throw std::domain_error("Parameter 'n_icc' must be >= 1");
   if (convergence <= 0.)
     throw std::domain_error("Parameter 'convergence' must be > 0");
   if (relaxation < 0. or relaxation > 2.)
@@ -222,12 +223,14 @@ void icc_data::sanity_checks() const {
     throw std::domain_error("Parameter 'first_id' must be >= 0");
   if (eps_out <= 0.)
     throw std::domain_error("Parameter 'eps_out' must be > 0");
-
-  assert(n_icc >= 1);
-  assert(areas.size() == n_icc);
-  assert(epsilons.size() == n_icc);
-  assert(sigmas.size() == n_icc);
-  assert(normals.size() == n_icc);
+  if (areas.size() != n_icc)
+    throw std::invalid_argument("Parameter 'areas' has incorrect shape");
+  if (epsilons.size() != n_icc)
+    throw std::invalid_argument("Parameter 'epsilons' has incorrect shape");
+  if (sigmas.size() != n_icc)
+    throw std::invalid_argument("Parameter 'sigmas' has incorrect shape");
+  if (normals.size() != n_icc)
+    throw std::invalid_argument("Parameter 'normals' has incorrect shape");
 }
 
 ICCStar::ICCStar(icc_data data) {

src/python/espressomd/CMakeLists.txt

@@ -17,24 +17,6 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-add_custom_command(
-  OUTPUT gen_pxiconfig.cpp
-  COMMAND
-    ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/gen_pxiconfig.py
-    ${CMAKE_SOURCE_DIR}/src/config/features.def
-    ${CMAKE_CURRENT_BINARY_DIR}/gen_pxiconfig.cpp
-  DEPENDS ${CMAKE_SOURCE_DIR}/src/config/features.def)
-
-add_executable(gen_pxiconfig gen_pxiconfig.cpp)
-target_link_libraries(gen_pxiconfig espresso::config)
-set_target_properties(gen_pxiconfig PROPERTIES CXX_CLANG_TIDY
-                                               "${ESPRESSO_CXX_CLANG_TIDY}")
-
-add_custom_command(
-  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/myconfig.pxi
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/gen_pxiconfig >
-          ${CMAKE_CURRENT_BINARY_DIR}/myconfig.pxi DEPENDS gen_pxiconfig)
-
 add_custom_target(espressomd)
 
 # Make the cython_SRC, cython_HEADER and cython_AUX a cached variable to be able
@@ -93,8 +75,7 @@ foreach(cython_file ${cython_SRC})
         ${CMAKE_CURRENT_SOURCE_DIR} -I ${CMAKE_CURRENT_BINARY_DIR}
         ${cython_file} -o ${outputpath}
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/..
-      DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/myconfig.pxi ${cython_file}
-              ${cython_HEADER})
+      DEPENDS ${cython_file} ${cython_HEADER})
     set(target "espressomd_${basename}")
     add_library(${target} SHARED ${outputpath})
     if(NOT "${relpath}" STREQUAL "")

src/python/espressomd/electrostatic_extensions.py

@@ -17,10 +17,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-from . import utils
 from .script_interface import ScriptInterfaceHelper, script_interface_register
 from .code_features import has_features
-import numpy as np
 
 
 class ElectrostaticExtensions(ScriptInterfaceHelper):
@@ -33,7 +31,6 @@ def __init__(self, **kwargs):
         if 'sip' not in kwargs:
             params = self.default_params()
             params.update(kwargs)
-            self.validate_params(params)
             super().__init__(**params)
         else:
             super().__init__(**kwargs)
@@ -42,9 +39,6 @@ def _check_required_features(self):
         if not has_features("ELECTROSTATICS"):
             raise NotImplementedError("Feature ELECTROSTATICS not compiled in")
 
-    def validate_params(self, params):
-        raise NotImplementedError("Derived classes must implement this method")
-
     def default_params(self):
         raise NotImplementedError("Derived classes must implement this method")
 
@@ -93,43 +87,6 @@ class ICC(ElectrostaticExtensions):
     _so_name = "Coulomb::ICCStar"
     _so_creation_policy = "GLOBAL"
 
-    def validate_params(self, params):
-        utils.check_type_or_throw_except(
-            params["n_icc"], 1, int, "Invalid parameter 'n_icc'")
-        utils.check_type_or_throw_except(
-            params["first_id"], 1, int, "Invalid parameter 'first_id'")
-        utils.check_type_or_throw_except(
-            params["convergence"], 1, float, "Invalid parameter 'convergence'")
-        utils.check_type_or_throw_except(
-            params["relaxation"], 1, float, "Invalid parameter 'relaxation'")
-        utils.check_type_or_throw_except(
-            params["ext_field"], 3, float, "Invalid parameter 'ext_field'")
-        utils.check_type_or_throw_except(
-            params["max_iterations"], 1, int, "Invalid parameter 'max_iterations'")
-        utils.check_type_or_throw_except(
-            params["eps_out"], 1, float, "Invalid parameter 'eps_out'")
-
-        n_icc = params["n_icc"]
-        if n_icc <= 0:
-            raise ValueError("Parameter 'n_icc' must be >= 1")
-
-        if n_icc:
-            if np.shape(params["normals"]) != (n_icc, 3):
-                raise ValueError("Parameter 'normals' has incorrect shape")
-        utils.check_array_type_or_throw_except(
-            np.reshape(params["normals"], (-1,)), 3 * n_icc, float,
-            "Parameter 'normals' has incorrect type")
-
-        if "sigmas" not in params:
-            params["sigmas"] = np.zeros(n_icc)
-
-        for key in ("areas", "sigmas", "epsilons"):
-            if np.shape(params[key]) != (n_icc,):
-                raise ValueError(f"Parameter '{key}' has incorrect shape")
-            utils.check_array_type_or_throw_except(
-                np.reshape(params[key], (-1,)), n_icc, float,
-                f"Parameter '{key}' has incorrect type")
-
     def valid_keys(self):
         return {"n_icc", "convergence", "relaxation", "ext_field",
                 "max_iterations", "first_id", "eps_out", "normals",

src/python/espressomd/particle_data.py

@@ -22,7 +22,7 @@
 import functools
 from .interactions import BondedInteraction
 from .interactions import BondedInteractions
-from .utils import nesting_level, array_locked, is_valid_type, handle_errors
+from .utils import nesting_level, array_locked, is_valid_type
 from .utils import check_type_or_throw_except
 from .code_features import assert_features, has_features
 from .script_interface import script_interface_register, ScriptInterfaceHelper
@@ -598,7 +598,6 @@ def vs_auto_relate_to(self, rel_to, override_cutoff_check=False,
             "vs_relate_to",
             pid=rel_to,
             override_cutoff_check=override_cutoff_check)
-        handle_errors("vs_auto_relate_to")
         if self.propagation != Propagation.NONE:
             if couple_to_lb:
                 self.propagation |= Propagation.TRANS_LB_MOMENTUM_EXCHANGE

src/python/espressomd/script_interface.pxd

@@ -21,7 +21,7 @@ from libcpp.unordered_map cimport unordered_map
 from libcpp.string cimport string
 from libcpp.memory cimport shared_ptr
 from libcpp.vector cimport vector
-from libcpp cimport bool
+from libcpp cimport bool as cbool
 
 from boost cimport string_ref
 
@@ -37,8 +37,8 @@ cdef extern from "script_interface/ScriptInterface.hpp" namespace "ScriptInterfa
         Variant(const Variant & )
         Variant & operator = (const Variant &)
 
-    bool is_type[T](const Variant &)
-    bool is_none(const Variant &)
+    cbool is_type[T](const Variant &)
+    cbool is_none(const Variant &)
     ctypedef unordered_map[string, Variant] VariantMap
 
     Variant make_variant[T](const T & x)
@@ -71,7 +71,7 @@ cdef extern from "script_interface/initialize.hpp" namespace "ScriptInterface":
     void initialize(Factory[ObjectHandle] *)
 
 cdef extern from "script_interface/get_value.hpp" namespace "ScriptInterface":
-    T get_value[T](const Variant T)
+    T get_value[T](const Variant T) except +
 
 cdef extern from "script_interface/code_info/CodeInfo.hpp" namespace "ScriptInterface::CodeInfo":
     void check_features(const vector[string] & features) except +

src/python/espressomd/script_interface.pyx

@@ -23,6 +23,7 @@ from libcpp.memory cimport shared_ptr, make_shared
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.unordered_map cimport unordered_map
+from libcpp cimport bool as cbool
 
 cdef shared_ptr[ContextManager] _om
 
@@ -192,6 +193,7 @@ cdef class PScriptInterface:
         for name, value in kwargs.items():
             self.sip.get().set_parameter(utils.to_char_pointer(name),
                                          python_object_to_variant(value))
+            utils.handle_errors(f"while setting parameter '{name}'")
 
     def get_parameter(self, name):
         cdef Variant value = self.sip.get().get_parameter(utils.to_char_pointer(name))
@@ -299,7 +301,7 @@ cdef Variant python_object_to_variant(value) except *:
             vec_variant.push_back(python_object_to_variant(e))
         return make_variant[vector[Variant]](vec_variant)
     elif isinstance(value, (type(True), np.bool_)):
-        return make_variant[bool](value)
+        return make_variant[cbool](value)
     elif np.issubdtype(np.dtype(type(value)), np.signedinteger):
         return make_variant[int](value)
     elif np.issubdtype(np.dtype(type(value)), np.floating):
@@ -308,7 +310,7 @@ cdef Variant python_object_to_variant(value) except *:
         raise TypeError(
             f"No conversion from type '{type(value).__name__}' to 'Variant'")
 
-cdef variant_to_python_object(const Variant & value) except +:
+cdef variant_to_python_object(const Variant & value):
     """Convert C++ Variant objects to Python objects."""
 
     cdef vector[Variant] vec
@@ -324,8 +326,8 @@ cdef variant_to_python_object(const Variant & value) except +:
     cdef Vector4d vec4d
     if is_none(value):
         return None
-    if is_type[bool](value):
-        return get_value[bool](value)
+    if is_type[cbool](value):
+        return get_value[cbool](value)
     if is_type[int](value):
         return get_value[int](value)
     if is_type[double](value):

src/python/espressomd/system.py

@@ -38,8 +38,6 @@
 from . import thermostat
 
 from .code_features import has_features, assert_features
-from . import utils
-
 from .script_interface import script_interface_register, ScriptInterfaceHelper
 
 
@@ -152,16 +150,6 @@ class System(ScriptInterfaceHelper):
     _so_creation_policy = "GLOBAL"
     _so_bind_methods = _System._so_bind_methods
 
-    def __setattr__(self, attr, value):
-        if attr == "periodicity":
-            utils.check_type_or_throw_except(
-                value, 3, bool, "Attribute 'periodicity' must be a list of 3 bools")
-        if attr == "box_l":
-            utils.check_type_or_throw_except(
-                value, 3, float, "Attribute 'box_l' must be a list of 3 floats")
-        super().__setattr__(attr, value)
-        utils.handle_errors(f"while assigning system parameter '{attr}'")
-
     def __init__(self, **kwargs):
         if "sip" in kwargs:
             super().__init__(**kwargs)
@@ -428,14 +416,10 @@ def distance_vec(self, p1, p2):
         if isinstance(p1, particle_data.ParticleHandle):
             pos1 = p1.pos_folded
         else:
-            utils.check_type_or_throw_except(
-                p1, 3, float, "p1 must be a particle or 3 floats")
             pos1 = p1
         if isinstance(p2, particle_data.ParticleHandle):
             pos2 = p2.pos_folded
         else:
-            utils.check_type_or_throw_except(
-                p2, 3, float, "p2 must be a particle or 3 floats")
             pos2 = p2
 
         return self.call_method("distance_vec", pos1=pos1, pos2=pos2)