pytraj
pytraj copied to clipboard
Amber-MD
Fails to build with Python 3.13
Noticed this when building AmberTools 24:
[ 75%] Building pytraj native library
sys.argv ['setup.py', 'build', '-b', '/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build']
Original compiler envs
CXX = /usr/bin/g++-13
CC = /usr/bin/gcc-13
COMPILER =
use_pip = False, cpptraj_home =
compile_c_extension = True
2.0.6
use_prebuilt_cythonized_files = False
pytraj is inside AMBERHOME
using environment: CC=/usr/bin/gcc-13, CXX=/usr/bin/g++-13
using CC=/usr/bin/gcc-13, CXX=/usr/bin/g++-13
Final compiler envs
CXX = /usr/bin/g++-13
CC = /usr/bin/gcc-13
COMPILER =
install = True
set rpath to /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/cpptraj/src
/usr/lib/python3.13/site-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2025-Mar-03, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
/usr/lib/python3.13/site-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
running build
running build_py
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/all_actions.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/io.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/version.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/context.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/convert.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/misc.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/get_common_objects.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/Timer.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/decorators.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/tools.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/c_commands.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/progress.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/check_and_assert.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/builder
copying pytraj/builder/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/builder
copying pytraj/builder/build.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/builder
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/water.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/topology_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/dssp_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/base_holder.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/nmr.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/dihedral_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/rmsd.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/matrix.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/energy_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/hbond_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/nucleic_acid_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/vector.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_action
copying pytraj/analysis/c_action/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_action
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_analysis
copying pytraj/analysis/c_analysis/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_analysis
copying pytraj/analysis/c_analysis/analysis_dict.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_analysis
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
copying pytraj/datasets/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
copying pytraj/datasets/array.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
copying pytraj/datasets/datasetlist.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
copying pytraj/externals/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
copying pytraj/externals/magic.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
copying pytraj/externals/wurlitzer.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/stripped_trajectory.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/shared_trajectory.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/frameiter.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/trajectory.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/shared_methods.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/trajectory_iterator.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory/c_traj
copying pytraj/trajectory/c_traj/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory/c_traj
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/topology
copying pytraj/topology/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/topology
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles
copying pytraj/datafiles/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles
copying pytraj/datafiles/load_samples.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/ala3
copying pytraj/datafiles/ala3/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/ala3
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/tz2
copying pytraj/datafiles/tz2/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/tz2
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/dpdp
copying pytraj/datafiles/dpdp/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/dpdp
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/trpcage
copying pytraj/datafiles/trpcage/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/trpcage
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/remd_ala2
copying pytraj/datafiles/remd_ala2/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/remd_ala2
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/math
copying pytraj/math/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/math
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
copying pytraj/core/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
copying pytraj/core/elements.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/multiprocess.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/mpi.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/dataset.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/base.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/cluster
copying pytraj/cluster/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/cluster
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/visualization
copying pytraj/visualization/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/visualization
copying pytraj/visualization/view.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/visualization
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/serialize
copying pytraj/serialize/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/serialize
copying pytraj/serialize/serialize.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/serialize
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/lazy.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/transform.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/TrajectoryBaseIterator.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/qm.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
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copying pytraj/core/parameter_types.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
copying pytraj/core/c_core.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
copying pytraj/topology/topology.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/topology
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copying pytraj/trajectory/c_traj/c_trajout.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory/c_traj
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creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils/progress-circle/css
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running build_ext
building 'pytraj.datasets.cast_dataset' extension
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.linux-x86_64-cpython-313/pytraj/datasets
/usr/bin/g++-13 -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -I/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/../cpptraj/src -I/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/pytraj -I/usr/include/python3.13 -c pytraj/datasets/cast_dataset.cpp -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.linux-x86_64-cpython-313/pytraj/datasets/cast_dataset.o -O0 -ggdb -fopenmp -Wl,-rpath=/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/cpptraj/src
In Datei, eingebunden von /usr/include/assert.h:35,
von /usr/include/python3.13/Python.h:19,
von pytraj/datasets/cast_dataset.cpp:20:
/usr/include/features.h:422:4: Warnung: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
422 | # warning _FORTIFY_SOURCE requires compiling with optimization (-O)
| ^~~~~~~
In Datei, eingebunden von /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/../cpptraj/src/Grid.h:3,
von pytraj/datasets/cast_dataset.cpp:799:
/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/../cpptraj/src/ArrayIterator.h:6:35: Warnung: »template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator« ist veraltet [-Wdeprecated-declarations]
6 | class ArrayIterator : public std::iterator<std::forward_iterator_tag, T> {
| ^~~~~~~~
In Datei, eingebunden von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/bits/stl_algobase.h:65,
von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/bits/specfun.h:43,
von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/cmath:3699,
von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/math.h:36,
von /usr/include/python3.13/Python.h:22:
/usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/bits/stl_iterator_base_types.h:127:34: Anmerkung: hier deklariert
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
pytraj/datasets/cast_dataset.cpp:1015:72: Warnung: »Py_UNICODE« ist veraltet [-Wdeprecated-declarations]
1015 | static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) {
| ^
In Datei, eingebunden von /usr/include/python3.13/unicodeobject.h:1014,
von /usr/include/python3.13/Python.h:79:
/usr/include/python3.13/cpython/unicodeobject.h:10:37: Anmerkung: hier deklariert
10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE;
| ^~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE*)«:
pytraj/datasets/cast_dataset.cpp:1016:23: Warnung: »Py_UNICODE« ist veraltet [-Wdeprecated-declarations]
1016 | const Py_UNICODE *u_end = u;
| ^~~~~
/usr/include/python3.13/cpython/unicodeobject.h:10:37: Anmerkung: hier deklariert
10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE;
| ^~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »int __Pyx_PyList_Extend(PyObject*, PyObject*)«:
pytraj/datasets/cast_dataset.cpp:4164:22: Fehler: »_PyList_Extend« wurde in diesem Gültigkeitsbereich nicht deklariert; meinten Sie »PyList_Extend«?
4164 | PyObject* none = _PyList_Extend((PyListObject*)L, v);
| ^~~~~~~~~~~~~~
| PyList_Extend
pytraj/datasets/cast_dataset.cpp: In Funktion »void __Pyx_init_assertions_enabled()«:
pytraj/datasets/cast_dataset.cpp:4202:39: Fehler: »_PyInterpreterState_GetConfig« wurde in diesem Gültigkeitsbereich nicht deklariert; meinten Sie »PyInterpreterState_GetID«?
4202 | __pyx_assertions_enabled_flag = ! _PyInterpreterState_GetConfig(__Pyx_PyThreadState_Current->interp)->optimization_level;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| PyInterpreterState_GetID
pytraj/datasets/cast_dataset.cpp: In Funktion »int __Pyx_PyInt_As_int(PyObject*)«:
pytraj/datasets/cast_dataset.cpp:24717:46: Fehler: zu wenige Argumente für Funktion »int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)«
24717 | int ret = _PyLong_AsByteArray((PyLongObject *)v,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
24718 | bytes, sizeof(val),
| ~~~~~~~~~~~~~~~~~~~
24719 | is_little, !is_unsigned);
| ~~~~~~~~~~~~~~~~~~~~~~~~
In Datei, eingebunden von /usr/include/python3.13/longobject.h:107,
von /usr/include/python3.13/Python.h:81:
/usr/include/python3.13/cpython/longobject.h:111:17: Anmerkung: hier deklariert
111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
| ^~~~~~~~~~~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »long int __Pyx_PyInt_As_long(PyObject*)«:
pytraj/datasets/cast_dataset.cpp:24913:46: Fehler: zu wenige Argumente für Funktion »int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)«
24913 | int ret = _PyLong_AsByteArray((PyLongObject *)v,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
24914 | bytes, sizeof(val),
| ~~~~~~~~~~~~~~~~~~~
24915 | is_little, !is_unsigned);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: Anmerkung: hier deklariert
111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
| ^~~~~~~~~~~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »char __Pyx_PyInt_As_char(PyObject*)«:
pytraj/datasets/cast_dataset.cpp:25185:46: Fehler: zu wenige Argumente für Funktion »int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)«
25185 | int ret = _PyLong_AsByteArray((PyLongObject *)v,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
25186 | bytes, sizeof(val),
| ~~~~~~~~~~~~~~~~~~~
25187 | is_little, !is_unsigned);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: Anmerkung: hier deklariert
111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
| ^~~~~~~~~~~~~~~~~~~
error: command '/usr/bin/g++-13' failed with exit code 1
make[2]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/build.make:535: AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Fehler 1
make[1]: *** [CMakeFiles/Makefile2:7341: AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Fehler 2
make[1]: *** Es wird auf noch nicht beendete Prozesse gewartet …
Thanks @vedranmiletic for the report. For now, please try lower version since 3.13 is too new. Thanks. I will have a look.
@hainm Thanks for the quick response.
By the way, I would, but it is not my choice to make. I am packaging AmberTools in Arch User Repository and Arch Linux recently moved to Python 3.13 as the default version.
I am not familiar with the Arch User Repository, but is there some way to "pin" python to a given version? As an additional example, parts of AmberTools (I'm not sure about pytraj), still require version 1.26 of numpy, rather than the current version 2. And we know you will find problems if/when Arch upgrades to gcc14.
Of course, this dependency issue is a big part of what makes package managers like conda so complex.
But in any event, thanks for your work in this area. If you find code changes that would make AmberTools more compatible with current upstream software, let us know -- that would help everyone, not just the Arch Linux folks.
I am not familiar with the Arch User Repository, but is there some way to "pin" python to a given version?
In theory, yes. In practice this means that each user has to compile Python 3.12 before compiling AmberTools, and for me this is no go. I am considering depending on Miniforge (which includes 3.12) instead of that, but I would prefer patching software.
As an additional example, parts of AmberTools (I'm not sure about pytraj), still require version 1.26 of numpy, rather than the current version 2.
If that is the asarray()/asanyarray() change in ParmEd, I already have that patched locally and will publish it in the next go.
And we know you will find problems if/when Arch upgrades to gcc14.
Arch Linux has already upgraded to GCC 14, but GCC 13 is provided as a binary since CUDA needs it so we can easily depend on that.
Of course, this dependency issue is a big part of what makes package managers like conda so complex.
True, it is what it is. Furthermore, Arch is rolling-release with all advantages and disadvantages of that.
But in any event, thanks for your work in this area. If you find code changes that would make AmberTools more compatible with current upstream software, let us know -- that would help everyone, not just the Arch Linux folks.
Great! I would be glad to upstream the patches so I don't have to carry them locally.
For a start I patched a CUDA CMake config file to allow using CUDA 12.6 (the only version provided by Arch), but that file is not part of AmberClassic. Where should I submit a patch?
FWIW, running python setup.py --cythonize seems to fix the issue. I will push an updated AmberTools PKGBUILD for Arch soon.
Hello there! I am the EasyBuild developer and I am working on installation of AmberTools25. I find some nice patches in AUR, thanks for that!
But still there is a lot of failing tests. I have 2025a toolchain with: Python3.13, Numpy 2.3 and GCC 14.
First - I recythonize all the pytraj cpp files and the build is ok. But the tests are not. As soon as I run serial or python tests (make test.serial) the pytraj test failing with Segmentation fault. Here is one failure example:
Testing serial pytraj
/software/Python/3.13.1-GCCcore-14.2.0/bin/python test.py
[node4234:2580124:0:2580124] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
<module 'pytraj' from '/scratch/gent/vo/001/gvo00117/easybuild/RHEL9/zen4-ib/software/AmberTools/25.2-foss-2
025a/lib/python3.13/site-packages/pytraj/__init__.py'>
[node4234:2818677:0:2818677] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
==== backtrace (tid:2818677) ====
0 0x000000000003e6f0 __GI___sigaction() :0
1 0x00000000001d5ad0 ActionList::SetupActions() ???:0
2 0x000000000002fa00 __pyx_pf_6pytraj_8analysis_8c_action_10actionlist_10ActionList_8setup() /tmp/vsc47063
/easybuild/build/AmberTools/25.2/foss-2025a/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp:23
944
3 0x000000000002eb90 __pyx_pw_6pytraj_8analysis_8c_action_10actionlist_10ActionList_9setup() /tmp/vsc47063
/easybuild/build/AmberTools/25.2/foss-2025a/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp:23
635
4 0x000000000004c7f8 __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS() /tmp/vsc47063/easybuild/build/AmberTo
ols/25.2/foss-2025a/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp:35590
5 0x0000000000182160 _PyObject_VectorcallTstate() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Pyt
hon-3.13.1/./Include/internal/pycore_call.h:168
6 0x0000000000182160 PyObject_VectorcallMethod() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Objects/call.c:856
7 0x000000000002feac __pyx_pf_6pytraj_8analysis_8c_action_10actionlist_10ActionList_10compute() /tmp/vsc47063/easybuild/build/AmberTools/25.2/foss-2025a/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp:24109
8 0x000000000002fcb9 __pyx_pw_6pytraj_8analysis_8c_action_10actionlist_10ActionList_11compute() /tmp/vsc47063/easybuild/build/AmberTools/25.2/foss-2025a/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp:24060
9 0x000000000004c7f8 __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS() /tmp/vsc47063/easybuild/build/AmberTools/25.2/foss-2025a/AmberTools/src/pytraj/pytraj/analysis/c_action/actionlist.cpp:35590
10 0x000000000017e9af _PyObject_VectorcallTstate() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/./Include/internal/pycore_call.h:168
11 0x000000000017e9af PyObject_Vectorcall() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Objects/call.c:327
12 0x000000000019066e _PyEval_EvalFrameDefault() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/generated_cases.c.h:813
13 0x000000000021841a PyEval_EvalCode() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/ceval.c:601
14 0x000000000021841a PyEval_EvalCode() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/ceval.c:602
15 0x0000000000235369 run_eval_code_obj() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/pythonrun.c:1337
16 0x00000000002306b1 run_mod() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/pythonrun.c:1422
17 0x00000000002306b1 Py_DECREF() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/./Include/object.h:944
18 0x00000000002306b1 run_mod() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/pythonrun.c:1423
19 0x000000000024de75 pyrun_file() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/pythonrun.c:1255
20 0x000000000024d4b2 _PyRun_SimpleFileObject() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/pythonrun.c:490
21 0x000000000024d7aa _PyRun_AnyFileObject() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/pythonrun.c:77
22 0x00000000002468e1 pymain_run_file_obj() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Modules/main.c:409
23 0x00000000002468e1 pymain_run_file() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Modules/main.c:428
24 0x00000000002468e1 pymain_run_python() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Modules/main.c:696
25 0x00000000002468e1 Py_RunMain() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Modules/main.c:775
26 0x00000000002091a7 Py_BytesMain() /tmp/vsc40003/easybuild/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Modules/main.c:829
27 0x0000000000029590 __libc_start_call_main() ???:0
28 0x0000000000029640 __libc_start_main_alias_2() :0
29 0x0000000000401065 _start() ???:0
=================================
Segmentation fault (core dumped)
This seems as a problem with new Cython after recythonize. Do you hit the same errors after the test? All of them failing for me. Most of the CPPTRAJ tests passing.
Also the the tests for gem.pmemd exec with GEM failing for me. Either serial and parallel test from 2048_wat_gem - all failing with a big difference in potential energy (Etot) and electrostatic energy (EELEC). An example:
mdout.2048_wat_nvt_gem.pmemd.gemstar.dif:
106c106
< Etot = -12251.1470 EKtot = 5463.3015 EPtot = -17714.4486
> Etot = 61235.8878 EKtot = 5463.3015 EPtot = 55772.5862
109c109
< EELEC = 608.9507 EHBOND = 0. RESTRAINT = 0.
> EELEC = 74095.9856 EHBOND = 0. RESTRAINT = 0.
114c114
< Etot = -12250.2628 EKtot = 5421.8168 EPtot = -17672.0796
> Etot = 61236.7720 EKtot = 5421.8168 EPtot = 55814.9553
117c117
< EELEC = 664.4617 EHBOND = 0. RESTRAINT = 0.
> EELEC = 74151.4965 EHBOND = 0. RESTRAINT = 0.
122c122
< Etot = -12251.3036 EKtot = 5390.0242 EPtot = -17641.3278
> Etot = 61235.7312 EKtot = 5390.0242 EPtot = 55845.7070
125c125
< EELEC = 704.6328 EHBOND = 0. RESTRAINT = 0.
> EELEC = 74191.6676 EHBOND = 0. RESTRAINT = 0.
130c130
< Etot = -12250.0696 EKtot = 5382.6170 EPtot = -17632.6865
> Etot = 61236.9653 EKtot = 5382.6170 EPtot = 55854.3483
133c133
< EELEC = 686.2669 EHBOND = 0. RESTRAINT = 0.
> EELEC = 74173.3017 EHBOND = 0. RESTRAINT = 0.
138c138
< Etot = -12249.8613 EKtot = 5464.8264 EPtot = -17714.6877
> Etot = 61237.1735 EKtot = 5464.8264 EPtot = 55772.3471
141c141
< EELEC = 660.7993 EHBOND = 0. RESTRAINT = 0.
> EELEC = 74147.8341 EHBOND = 0. RESTRAINT = 0.
147c147
< Etot = -12250.3073 EKtot = 5416.4765 EPtot = -17666.7839
> Etot = 61236.7275 EKtot = 5416.4765 EPtot = 55820.2510
150c150
< EELEC = 673.1005 EHBOND = 0. RESTRAINT = 0.
> EELEC = 74160.1353 EHBOND = 0. RESTRAINT = 0.
### Maximum absolute error in matching lines = 7.35e+04 at line 109 field 3
### Maximum relative error in matching lines = 1.21e+02 at line 109 field 3
gem.pmemd test for AMOEBA are ok. This seems as problem with new Numpy. Do yours gem.pmemd tests are ok?
Thank you for pointing to this, so I skip the pytraj tests them.
@vedranmiletic I think you miss one patch for parmed in 0002-NumPy-2-compatibility.patch:
--- a/AmberTools/src/parmed/parmed/utils/netcdf.py 2025-03-24 15:55:38.000000000 +0100
+++ b/AmberTools/src/parmed/parmed/utils/netcdf.py 2025-07-15 14:14:34.000940000 +0200
@@ -39,15 +39,25 @@
from operator import mul
from collections import OrderedDict
from platform import python_implementation
+from typing import Any
import mmap as mm
import numpy as np
-from numpy.compat import asbytes, asstr
from numpy import frombuffer, dtype, empty, array, asarray
from numpy import little_endian as LITTLE_ENDIAN
from functools import reduce
+def asbytes(s: Any) -> bytes:
+ """Ensures input is in bytes format. Mimics numpy.compat.asbytes"""
+ return str(s).encode("latin1") if isinstance(s, str) else s
+
+
+def asstr(b: Any) -> str:
+ """Ensures input is in string format. Mimics numpy.compat.asstr"""
+ return b.decode("latin1") if isinstance(b, bytes) else str(b)
+
+
IS_PYPY = python_implementation() == 'PyPy'
New numpy has no numpy.compat