Installing on Apple M4 #452
Description
Hi!
I just tried installing BioSimSpace for my new Apple M4 (Sequoia 15.2). I first installed Miniforge, then created a new environment and then installed BioSimSpace with
conda install -c openbiosim biosimspace
The installation finished fine, but when I tried to import BioSimSpace in ipython as a quick test and got the below error.
Would really appreciate your help with this!
Thanks,
Jasmin
In [1]: import BioSimSpace as bss
INFO:numexpr.utils:NumExpr defaulting to 12 threads.
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ in <module>:1 │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/BioSimSpace/__init__.py:240 in │
│ <module> │
│ │
│ 237 from . import Align │
│ 238 from . import Box │
│ 239 from . import Convert │
│ ❱ 240 from . import FreeEnergy │
│ 241 from . import Gateway │
│ 242 from . import IO │
│ 243 from . import Metadynamics │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/BioSimSpace/FreeEnergy/__init__ │
│ .py:45 in <module> │
│ │
│ 42 │ getData │
│ 43 """ │
│ 44 │
│ ❱ 45 from ._relative import * │
│ 46 from ._utils import * │
│ 47 from ._atm import * │
│ 48 │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/BioSimSpace/FreeEnergy/_relativ │
│ e.py:94 in <module> │
│ │
│ 91 from .._SireWrappers import Molecules as _Molecules │
│ 92 from .._SireWrappers import System as _System │
│ 93 from .._Utils import cd as _cd │
│ ❱ 94 from .. import Process as _Process │
│ 95 from .. import Protocol as _Protocol │
│ 96 from .. import Types as _Types │
│ 97 from .. import Units as _Units │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/BioSimSpace/Process/__init__.py │
│ :94 in <module> │
│ │
│ 91 minimised = process.getSystem() │
│ 92 """ │
│ 93 │
│ ❱ 94 from ._amber import * │
│ 95 from ._gromacs import * │
│ 96 from ._namd import * │
│ 97 from ._openmm import * │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/BioSimSpace/Process/_amber.py:4 │
│ 6 in <module> │
│ │
│ 43 from sire.legacy import Mol as _SireMol │
│ 44 │
│ 45 from .. import _amber_home, _isVerbose │
│ ❱ 46 from ..Align._squash import _squash, _unsquash │
│ 47 from .._Config import Amber as _AmberConfig │
│ 48 from .._Exceptions import IncompatibleError as _IncompatibleError │
│ 49 from .._Exceptions import MissingSoftwareError as _MissingSoftwareError │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/BioSimSpace/Align/_squash.py:4 │
│ in <module> │
│ │
│ 1 import itertools as _it │
│ 2 import numpy as _np │
│ 3 import os as _os │
│ ❱ 4 import parmed as _pmd │
│ 5 import shutil as _shutil │
│ 6 import tempfile │
│ 7 │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/parmed/__init__.py:23 in │
│ <module> │
│ │
│ 20 from . import unit, utils │
│ 21 from .topologyobjects import * │
│ 22 from .structure import Structure, StructureView │
│ ❱ 23 from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta, tinker, entos │
│ 24 from . import formats │
│ 25 from .vec3 import Vec3 │
│ 26 from .parameters import ParameterSet │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/parmed/amber/__init__.py:14 in │
│ <module> │
│ │
│ 11 from .amberformat import AmberFormat, FortranFormat │
│ 12 from .asciicrd import AmberAsciiRestart, AmberMdcrd │
│ 13 from .mask import AmberMask │
│ ❱ 14 from .netcdffiles import NetCDFTraj, NetCDFRestart │
│ 15 from .offlib import AmberOFFLibrary │
│ 16 from .parameters import AmberParameterSet │
│ 17 from .readparm import AmberParm, ChamberParm, AmoebaParm, Rst7, BeemanRestart, ConvertFr │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/parmed/amber/netcdffiles.py:25 │
│ in <module> │
│ │
│ 22 from .. import __version__ │
│ 23 from ..formats.registry import FileFormatType │
│ 24 from .. import unit as u │
│ ❱ 25 from ..utils.netcdf import netcdf_file as NetCDFFile │
│ 26 import warnings │
│ 27 │
│ 28 class NetCDFRestart(metaclass=FileFormatType): │
│ │
│ /Users/af25016/miniforge3/envs/obss/lib/python3.11/site-packages/parmed/utils/netcdf.py:46 in │
│ <module> │
│ │
│ 43 import mmap as mm │
│ 44 │
│ 45 import numpy as np │
│ ❱ 46 from numpy.compat import asbytes, asstr │
│ 47 from numpy import frombuffer, dtype, empty, array, asarray │
│ 48 from numpy import little_endian as LITTLE_ENDIAN │
│ 49 from functools import reduce │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ModuleNotFoundError: No module named 'numpy.compat'