Building python binding fails on Archlinux (solution known)
Aperta
Adatta ai principianti
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Valutazione
- Difficoltà
- 1/5
- Tempo stimato
- Meno di un'ora
- Idoneità per principianti
- 74/100
- Tipo di issue
- Bug
- Chiarezza
- Specificata chiaramente
- Stato di attività
- Ferma
- Ambito
- backend, build-system
Direzione di ricerca
Inizia da src/thermo/Thermodynamics.h, dove gli errori di compilazione segnalano che assert non è dichiarato negli accessor di specie ed elemento. Leggi gli include dell’header e aggiungi la dichiarazione di asserzione mancante indicata dal compilatore. Esegui di nuovo pip install . su Arch Linux e conferma che la compilazione C++ viene completata.
Scritto dal modello di indicizzazione a partire dal testo della issue.
Descrizione
My OS is: Linux 6.19.13-arch1-1 x86_64 GNU/Linux
OS Version: Well, its arch so rolling
Cmake Version: 4.3.2
Mutation++ origin: fresh git clone
Mutation++ build steps and steps to reproduce
pip install .fails with
`pip install .` output
Processing ./.
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy (from mutationpp==1.1.3)
Using cached numpy-2.4.4-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
Using cached numpy-2.4.4-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
Building wheels for collected packages: mutationpp
Building wheel for mutationpp (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for mutationpp (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [296 lines of output]
*** scikit-build-core 0.12.2 using CMake 4.3.2 (wheel)
*** Configuring CMake...
loading initial cache file /home/danielk/tmp/tmpo8hd87fl/build/CMakeInit.txt
-- The CXX compiler identification is GNU 15.2.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /sbin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python: /home/danielk/venvs/Mutationpp/bin/python (found version "3.13.11") found components: Interpreter Development.Module
-- Configuring done (0.3s)
-- Generating done (0.0s)
-- Build files have been written to: /home/danielk/tmp/tmpo8hd87fl/build
*** Building project with Ninja...
[1/91] Building CXX object interface/python/CMakeFiles/_mutationpp.dir/src/mutationpp_python.cpp.o
[2/91] Building CXX object interface/python/CMakeFiles/_mutationpp.dir/src/pyGlobalOptions.cpp.o
In file included from /home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/Python.h:14,
from /home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include/nanobind/nb_python.h:21,
from /home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include/nanobind/nanobind.h:32,
from /home/danielk/git/Mutationpp/interface/python/src/pyGlobalOptions.cpp:2:
/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/pyconfig.h:1967:9: warning: ‘_POSIX_C_SOURCE’ redefined
1967 | #define _POSIX_C_SOURCE 200809L
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/15.2.1/x86_64-pc-linux-gnu/bits/os_defines.h:39,
from /usr/include/c++/15.2.1/x86_64-pc-linux-gnu/bits/c++config.h:727,
from /usr/include/c++/15.2.1/cstdlib:46,
from /home/danielk/git/Mutationpp/src/general/GlobalOptions.h:25,
from /home/danielk/git/Mutationpp/interface/python/src/pyGlobalOptions.cpp:1:
/usr/include/features.h:319:10: note: this is the location of the previous definition
319 | # define _POSIX_C_SOURCE 202405L
| ^~~~~~~~~~~~~~~
/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/pyconfig.h:1988:9: warning: ‘_XOPEN_SOURCE’ redefined
1988 | #define _XOPEN_SOURCE 700
| ^~~~~~~~~~~~~
/usr/include/features.h:234:10: note: this is the location of the previous definition
234 | # define _XOPEN_SOURCE 800
| ^~~~~~~~~~~~~
[3/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/nb_static_property.cpp.o
[4/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/implicit.cpp.o
[5/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/trampoline.cpp.o
[6/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/ReactionType.cpp.o
[7/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/error.cpp.o
[8/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/nb_internals.cpp.o
[9/91] Building CXX object interface/python/CMakeFiles/_mutationpp.dir/src/pyMixtureOptions.cpp.o
In file included from /home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/Python.h:14,
from /home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include/nanobind/nb_python.h:21,
from /home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include/nanobind/nanobind.h:32,
from /home/danielk/git/Mutationpp/interface/python/src/pyMixtureOptions.cpp:3:
/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/pyconfig.h:1967:9: warning: ‘_POSIX_C_SOURCE’ redefined
1967 | #define _POSIX_C_SOURCE 200809L
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/15.2.1/x86_64-pc-linux-gnu/bits/os_defines.h:39,
from /usr/include/c++/15.2.1/x86_64-pc-linux-gnu/bits/c++config.h:727,
from /usr/include/c++/15.2.1/bits/requires_hosted.h:31,
from /usr/include/c++/15.2.1/string:40,
from /home/danielk/git/Mutationpp/src/general/MixtureOptions.h:32,
from /home/danielk/git/Mutationpp/interface/python/src/pyMixtureOptions.cpp:1:
/usr/include/features.h:319:10: note: this is the location of the previous definition
319 | # define _POSIX_C_SOURCE 202405L
| ^~~~~~~~~~~~~~~
/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/pyconfig.h:1988:9: warning: ‘_XOPEN_SOURCE’ redefined
1988 | #define _XOPEN_SOURCE 700
| ^~~~~~~~~~~~~
/usr/include/features.h:234:10: note: this is the location of the previous definition
234 | # define _XOPEN_SOURCE 800
| ^~~~~~~~~~~~~
[10/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/nb_ndarray.cpp.o
[11/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/common.cpp.o
[12/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/JacobianManager.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/kinetics/JacobianManager.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/kinetics/JacobianManager.cpp.o -MF src/CMakeFiles/mutation++.dir/kinetics/JacobianManager.cpp.o.d -o src/CMakeFiles/mutation++.dir/kinetics/JacobianManager.cpp.o -c /home/danielk/git/Mutationpp/src/kinetics/JacobianManager.cpp
In file included from /home/danielk/git/Mutationpp/src/kinetics/JacobianManager.h:32,
from /home/danielk/git/Mutationpp/src/kinetics/JacobianManager.cpp:29:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
[13/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/nb_func.cpp.o
[14/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/Kinetics.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/kinetics/Kinetics.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/kinetics/Kinetics.cpp.o -MF src/CMakeFiles/mutation++.dir/kinetics/Kinetics.cpp.o.d -o src/CMakeFiles/mutation++.dir/kinetics/Kinetics.cpp.o -c /home/danielk/git/Mutationpp/src/kinetics/Kinetics.cpp
In file included from /home/danielk/git/Mutationpp/src/kinetics/Reaction.h:34,
from /home/danielk/git/Mutationpp/src/kinetics/RateLawGroup.h:42,
from /home/danielk/git/Mutationpp/src/kinetics/RateManager.h:31,
from /home/danielk/git/Mutationpp/src/kinetics/Kinetics.h:33,
from /home/danielk/git/Mutationpp/src/kinetics/Kinetics.cpp:28:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
[15/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/RateLaws.cpp.o
[16/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/StoichiometryManager.cpp.o
[17/91] Building CXX object src/CMakeFiles/mutation++.dir/general/Mixture.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/general/Mixture.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/general/Mixture.cpp.o -MF src/CMakeFiles/mutation++.dir/general/Mixture.cpp.o.d -o src/CMakeFiles/mutation++.dir/general/Mixture.cpp.o -c /home/danielk/git/Mutationpp/src/general/Mixture.cpp
In file included from /home/danielk/git/Mutationpp/src/general/Mixture.h:33,
from /home/danielk/git/Mutationpp/src/general/Mixture.cpp:28:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
[18/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/nb_enum.cpp.o
[19/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/RateManager.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/kinetics/RateManager.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/kinetics/RateManager.cpp.o -MF src/CMakeFiles/mutation++.dir/kinetics/RateManager.cpp.o.d -o src/CMakeFiles/mutation++.dir/kinetics/RateManager.cpp.o -c /home/danielk/git/Mutationpp/src/kinetics/RateManager.cpp
In file included from /home/danielk/git/Mutationpp/src/kinetics/Reaction.h:34,
from /home/danielk/git/Mutationpp/src/kinetics/RateLawGroup.h:42,
from /home/danielk/git/Mutationpp/src/kinetics/RateManager.h:31,
from /home/danielk/git/Mutationpp/src/kinetics/RateManager.cpp:31:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
In file included from /home/danielk/git/Mutationpp/src/kinetics/RateManager.cpp:33:
/home/danielk/git/Mutationpp/src/thermo/StateModel.h: In member function ‘void Mutation::Thermodynamics::StateModel::addTransferTerm(int, Mutation::Transfer::TransferModel*)’:
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:292:9: error: ‘assert’ was not declared in this scope
292 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:34:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
33 | #include "TransferModel.h"
+++ |+#include <cassert>
34 |
[20/91] Building CXX object interface/python/CMakeFiles/nanobind-static.dir/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/src/nb_type.cpp.o
[21/91] Building CXX object interface/python/CMakeFiles/_mutationpp.dir/src/pyMixture.cpp.o
FAILED: [code=1] interface/python/CMakeFiles/_mutationpp.dir/src/pyMixture.cpp.o
/sbin/c++ -pthread -D_mutationpp_EXPORTS -I/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13 -I/home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -O3 -DNDEBUG -fPIC -fvisibility=hidden -fno-stack-protector -Os -ffunction-sections -fdata-sections -MD -MT interface/python/CMakeFiles/_mutationpp.dir/src/pyMixture.cpp.o -MF interface/python/CMakeFiles/_mutationpp.dir/src/pyMixture.cpp.o.d -o interface/python/CMakeFiles/_mutationpp.dir/src/pyMixture.cpp.o -c /home/danielk/git/Mutationpp/interface/python/src/pyMixture.cpp
In file included from /home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/Python.h:14,
from /home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include/nanobind/nb_python.h:21,
from /home/danielk/tmp/pip-build-env-d0tr_1ba/overlay/lib/python3.13/site-packages/nanobind/include/nanobind/nanobind.h:32,
from /home/danielk/git/Mutationpp/interface/python/src/pyMixture.cpp:4:
/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/pyconfig.h:1967:9: warning: ‘_POSIX_C_SOURCE’ redefined
1967 | #define _POSIX_C_SOURCE 200809L
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/15.2.1/x86_64-pc-linux-gnu/bits/os_defines.h:39,
from /usr/include/c++/15.2.1/x86_64-pc-linux-gnu/bits/c++config.h:727,
from /usr/include/c++/15.2.1/bits/requires_hosted.h:31,
from /usr/include/c++/15.2.1/vector:62,
from /home/danielk/git/Mutationpp/src/general/Mixture.h:31,
from /home/danielk/git/Mutationpp/interface/python/src/pyMixture.cpp:1:
/usr/include/features.h:319:10: note: this is the location of the previous definition
319 | # define _POSIX_C_SOURCE 202405L
| ^~~~~~~~~~~~~~~
/home/danielk/.local/share/uv/python/cpython-3.13.11-linux-x86_64-gnu/include/python3.13/pyconfig.h:1988:9: warning: ‘_XOPEN_SOURCE’ redefined
1988 | #define _XOPEN_SOURCE 700
| ^~~~~~~~~~~~~
/usr/include/features.h:234:10: note: this is the location of the previous definition
234 | # define _XOPEN_SOURCE 800
| ^~~~~~~~~~~~~
In file included from /home/danielk/git/Mutationpp/src/general/Mixture.h:33:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
[22/91] Building CXX object src/CMakeFiles/mutation++.dir/general/MixtureOptions.cpp.o
[23/91] Building CXX object src/CMakeFiles/mutation++.dir/thermo/ChemNonEqStateModel.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/thermo/ChemNonEqStateModel.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/thermo/ChemNonEqStateModel.cpp.o -MF src/CMakeFiles/mutation++.dir/thermo/ChemNonEqStateModel.cpp.o.d -o src/CMakeFiles/mutation++.dir/thermo/ChemNonEqStateModel.cpp.o -c /home/danielk/git/Mutationpp/src/thermo/ChemNonEqStateModel.cpp
In file included from /home/danielk/git/Mutationpp/src/kinetics/Reaction.h:34,
from /home/danielk/git/Mutationpp/src/kinetics/RateLawGroup.h:42,
from /home/danielk/git/Mutationpp/src/kinetics/RateManager.h:31,
from /home/danielk/git/Mutationpp/src/kinetics/Kinetics.h:33,
from /home/danielk/git/Mutationpp/src/thermo/StateModel.h:32,
from /home/danielk/git/Mutationpp/src/thermo/ChemNonEqStateModel.cpp:28:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
/home/danielk/git/Mutationpp/src/thermo/StateModel.h: In member function ‘void Mutation::Thermodynamics::StateModel::addTransferTerm(int, Mutation::Transfer::TransferModel*)’:
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:292:9: error: ‘assert’ was not declared in this scope
292 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:34:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
33 | #include "TransferModel.h"
+++ |+#include <cassert>
34 |
[24/91] Building CXX object src/CMakeFiles/mutation++.dir/thermo/Composition.cpp.o
[25/91] Building CXX object src/CMakeFiles/mutation++.dir/thermo/ChemNonEqTTvStateModel.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/thermo/ChemNonEqTTvStateModel.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/thermo/ChemNonEqTTvStateModel.cpp.o -MF src/CMakeFiles/mutation++.dir/thermo/ChemNonEqTTvStateModel.cpp.o.d -o src/CMakeFiles/mutation++.dir/thermo/ChemNonEqTTvStateModel.cpp.o -c /home/danielk/git/Mutationpp/src/thermo/ChemNonEqTTvStateModel.cpp
In file included from /home/danielk/git/Mutationpp/src/kinetics/Reaction.h:34,
from /home/danielk/git/Mutationpp/src/kinetics/RateLawGroup.h:42,
from /home/danielk/git/Mutationpp/src/kinetics/RateManager.h:31,
from /home/danielk/git/Mutationpp/src/kinetics/Kinetics.h:33,
from /home/danielk/git/Mutationpp/src/thermo/StateModel.h:32,
from /home/danielk/git/Mutationpp/src/thermo/ChemNonEqTTvStateModel.cpp:28:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
/home/danielk/git/Mutationpp/src/thermo/StateModel.h: In member function ‘void Mutation::Thermodynamics::StateModel::addTransferTerm(int, Mutation::Transfer::TransferModel*)’:
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:292:9: error: ‘assert’ was not declared in this scope
292 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:34:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
33 | #include "TransferModel.h"
+++ |+#include <cassert>
34 |
[26/91] Building CXX object src/CMakeFiles/mutation++.dir/thermo/HarmonicOscillator.cpp.o
[27/91] Building CXX object src/CMakeFiles/mutation++.dir/thermo/EquilStateModel.cpp.o
FAILED: [code=1] src/CMakeFiles/mutation++.dir/thermo/EquilStateModel.cpp.o
/sbin/c++ -pthread -I/home/danielk/git/Mutationpp/src/general -I/home/danielk/git/Mutationpp/src/kinetics -I/home/danielk/git/Mutationpp/src/numerics -I/home/danielk/git/Mutationpp/src/thermo -I/home/danielk/git/Mutationpp/src/transfer -I/home/danielk/git/Mutationpp/src/transport -I/home/danielk/git/Mutationpp/src/utilities -I/home/danielk/git/Mutationpp/src/gsi -isystem /usr/include/eigen3 -g -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT src/CMakeFiles/mutation++.dir/thermo/EquilStateModel.cpp.o -MF src/CMakeFiles/mutation++.dir/thermo/EquilStateModel.cpp.o.d -o src/CMakeFiles/mutation++.dir/thermo/EquilStateModel.cpp.o -c /home/danielk/git/Mutationpp/src/thermo/EquilStateModel.cpp
In file included from /home/danielk/git/Mutationpp/src/kinetics/Reaction.h:34,
from /home/danielk/git/Mutationpp/src/kinetics/RateLawGroup.h:42,
from /home/danielk/git/Mutationpp/src/kinetics/RateManager.h:31,
from /home/danielk/git/Mutationpp/src/kinetics/Kinetics.h:33,
from /home/danielk/git/Mutationpp/src/thermo/StateModel.h:32,
from /home/danielk/git/Mutationpp/src/thermo/EquilStateModel.cpp:28:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Species& Mutation::Thermodynamics::Thermodynamics::species(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:200:9: error: ‘assert’ was not declared in this scope
200 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:42:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
41 | #include <Eigen/Dense>
+++ |+#include <cassert>
42 |
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h: In member function ‘const Mutation::Thermodynamics::Element& Mutation::Thermodynamics::Thermodynamics::element(int) const’:
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: error: ‘assert’ was not declared in this scope
213 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/Thermodynamics.h:213:9: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
/home/danielk/git/Mutationpp/src/thermo/StateModel.h: In member function ‘void Mutation::Thermodynamics::StateModel::addTransferTerm(int, Mutation::Transfer::TransferModel*)’:
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:292:9: error: ‘assert’ was not declared in this scope
292 | assert(i >= 0);
| ^~~~~~
/home/danielk/git/Mutationpp/src/thermo/StateModel.h:34:1: note: ‘assert’ is defined in header ‘<cassert>’; this is probably fixable by adding ‘#include <cassert>’
33 | #include "TransferModel.h"
+++ |+#include <cassert>
34 |
[28/91] Building CXX object src/CMakeFiles/mutation++.dir/kinetics/Reaction.cpp.o
[29/91] Building CXX object src/CMakeFiles/mutation++.dir/numerics/Interpolators.cpp.o
ninja: build stopped: subcommand failed.
*** CMake build failed
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mutationpp
Failed to build mutationpp
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> mutationpp
however, reading the build errors and the cmake files a bit, it seemed to be an issue with asserts being used without proper header inclusion so i kinda hacked in a cmake command in the pyproject.toml like so
diff --git a/pyproject.toml b/pyproject.toml
index 4fa3725..ce45a0a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,6 +41,9 @@ test = ["pytest"]
experimental = true
sdist.cmake = false
sdist.exclude = [".*"]
+cmake.args = [
+ "-DCMAKE_CXX_FLAGS_RELEASE='-O3 -DNDEBUG -include cassert'",
+]
[tool.scikit-build.metadata.version]
provider = "scikit_build_core.metadata.regex"
regex = '^project\(mutation\+\+\s*\n^\s*VERSION\s*(?P<value>\d+\.\d+\.\d+)\s*$'
and that seems to have fixed the issue - tests run fine:
pytest
==================== test session starts =====================
platform linux -- Python 3.13.11, pytest-9.0.3, pluggy-1.6.0
rootdir: /home/danielk/git/Mutationpp
configfile: pyproject.toml
testpaths: tests/python
collected 68 items
tests/python/test_mutation.py ............................................................... [ 92%]
tests/python/test_options.py ..... [100%]
===================== 68 passed in 0.16s =====================
Just wanted to let you know in case there is some quick fix that is possible to avoid this patch because i guess it would not be desirable to have these extra flags on every system if it runs without them :) im not familiar enough with your setup to try to suggest the proper way of doing it I'm afraid
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