Not installing under Python 3.11

[doccosmos]

Hi,

I'm trying to install under Python 3.11.4 on a Intel Mac running 13.5:

% python setup.py config_fc --fcompiler=gnu95 install /Users/mjg/Projects/packages/javelin/setup.py:5: DeprecationWarning:

numpy.distutils is deprecated since NumPy 1.23.0, as a result of the deprecation of distutils itself. It will be removed for Python >= 3.12. For older Python versions it will remain present. It is recommended to use setuptools < 60.0 for those Python versions. For more details, see: https://numpy.org/devdocs/reference/distutils_status_migration.html

from numpy.distutils.misc_util import Configuration running config_fc INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running install /opt/anaconda3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!! self.initialize_options() running build running config_cc INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options running build_src INFO: build_src INFO: building extension "javelin.gp.linalg_utils" sources INFO: f2py options: [] INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/fortranobject.c' to sources. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp' to include_dirs. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/javelin/gp/linalg_utils-f2pywrappers.f' to sources. INFO: building extension "javelin.gp.incomplete_chol" sources INFO: f2py options: [] INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/fortranobject.c' to sources. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp' to include_dirs. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/javelin/gp/incomplete_chol-f2pywrappers.f' to sources. INFO: building extension "javelin.gp.cov_funs.isotropic_cov_funs" sources INFO: f2py options: [] INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/cov_funs/fortranobject.c' to sources. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/cov_funs' to include_dirs. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/javelin/gp/cov_funs/isotropic_cov_funs-f2pywrappers.f' to sources. INFO: building extension "javelin.gp.cov_funs.distances" sources INFO: f2py options: [] INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/cov_funs/fortranobject.c' to sources. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/cov_funs' to include_dirs. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/javelin/gp/cov_funs/distances-f2pywrappers.f' to sources. INFO: building extension "javelin.spear_covfunc" sources INFO: f2py options: [] INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/fortranobject.c' to sources. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin' to include_dirs. INFO: adding 'build/src.macosx-10.9-x86_64-3.11/javelin/spear_covfunc-f2pywrappers2.f90' to sources. INFO: build_src: building npy-pkg config files running build_py running build_ext INFO: customize UnixCCompiler INFO: customize UnixCCompiler using build_ext INFO: CCompilerOpt.init[819] : load cache from file -> /Users/mjg/Projects/packages/javelin/build/temp.macosx-10.9-x86_64-cpython-311/ccompiler_opt_cache_ext.py INFO: CCompilerOpt.init[830] : hit the file cache WARN: resetting extension 'javelin.gp.linalg_utils' language from 'c' to 'f77'. WARN: resetting extension 'javelin.gp.incomplete_chol' language from 'c' to 'f77'. WARN: resetting extension 'javelin.gp.cov_funs.isotropic_cov_funs' language from 'c' to 'f77'. WARN: resetting extension 'javelin.gp.cov_funs.distances' language from 'c' to 'f77'. WARN: resetting extension 'javelin.spear_covfunc' language from 'c' to 'f77'. INFO: customize Gnu95FCompiler INFO: Found executable /usr/local/bin/gfortran INFO: customize Gnu95FCompiler using build_ext INFO: building 'javelin.gp.linalg_utils' extension INFO: compiling C sources INFO: C compiler: clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/anaconda3/include -fPIC -O2 -isystem /opt/anaconda3/include -ftrapping-math

INFO: compile options: '-DHAVE_CBLAS -Ibuild/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp -I/opt/anaconda3/lib/python3.11/site-packages/numpy/core/include -Ibuild/src.macosx-10.9-x86_64-3.11/numpy/distutils/include -I/opt/anaconda3/include/python3.11 -c' extra options: '-msse -msse2 -msse3' INFO: compiling Fortran sources INFO: Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops INFO: compile options: '-DHAVE_CBLAS -Ibuild/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp -I/opt/anaconda3/lib/python3.11/site-packages/numpy/core/include -Ibuild/src.macosx-10.9-x86_64-3.11/numpy/distutils/include -I/opt/anaconda3/include/python3.11 -c' INFO: gfortran:f77: javelin/gp/linalg_utils.f INFO: gfortran:f77: javelin/blas_wrap.f INFO: gfortran:f77: build/src.macosx-10.9-x86_64-3.11/javelin/gp/linalg_utils-f2pywrappers.f javelin/gp/linalg_utils.f:151:56:

151 | SUBROUTINE gp_array_logp(x, mu, sig, n, like, info) | 1 Warning: Unused dummy argument 'info' at (1) [-Wunused-dummy-argument] INFO: /usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-cpython-311/build/src.macosx-10.9-x86_64-3.11/javelin/gp/linalg_utilsmodule.o build/temp.macosx-10.9-x86_64-cpython-311/build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/fortranobject.o build/temp.macosx-10.9-x86_64-cpython-311/javelin/gp/linalg_utils.o build/temp.macosx-10.9-x86_64-cpython-311/javelin/blas_wrap.o build/temp.macosx-10.9-x86_64-cpython-311/build/src.macosx-10.9-x86_64-3.11/javelin/gp/linalg_utils-f2pywrappers.o -L/opt/anaconda3/lib -L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/../../.. -L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/../../.. -lopenblas -lopenblas -lgfortran -o build/lib.macosx-10.9-x86_64-cpython-311/javelin/gp/linalg_utils.cpython-311-darwin.so ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64 collect2: error: ld returned 1 exit status error: Command "/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-cpython-311/build/src.macosx-10.9-x86_64-3.11/javelin/gp/linalg_utilsmodule.o build/temp.macosx-10.9-x86_64-cpython-311/build/src.macosx-10.9-x86_64-3.11/build/src.macosx-10.9-x86_64-3.11/javelin/gp/fortranobject.o build/temp.macosx-10.9-x86_64-cpython-311/javelin/gp/linalg_utils.o build/temp.macosx-10.9-x86_64-cpython-311/javelin/blas_wrap.o build/temp.macosx-10.9-x86_64-cpython-311/build/src.macosx-10.9-x86_64-3.11/javelin/gp/linalg_utils-f2pywrappers.o -L/opt/anaconda3/lib -L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/../../.. -L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/../../.. -lopenblas -lopenblas -lgfortran -o build/lib.macosx-10.9-x86_64-cpython-311/javelin/gp/linalg_utils.cpython-311-darwin.so" failed with exit status 1 INFO: ########### EXT COMPILER OPTIMIZATION ########### INFO: Platform : Architecture: x64 Compiler : clang

CPU baseline : Requested : 'min' Enabled : SSE SSE2 SSE3 Flags : -msse -msse2 -msse3 Extra checks: none

CPU dispatch : Requested : 'max -xop -fma4' Enabled : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL Generated : none INFO: CCompilerOpt.cache_flush[863] : write cache to path -> /Users/mjg/Projects/packages/javelin/build/temp.macosx-10.9-x86_64-cpython-311/ccompiler_opt_cache_ext.py

[doccosmos]

Digging a bit, it looks like /usr/bin/ld has to be first in PATH rather than the Anaconda ld. It compiles fine, now, but then gives:

Python 3.11.4 (main, Jul 5 2023, 09:00:44) [Clang 14.0.6 ] on darwin Type "help", "copyright", "credits" or "license" for more information.

import javelin Traceback (most recent call last): File "", line 1, in File "/Users/mjg/Projects/packages/javelin/javelin/init.py", line 2, in from . import gp File "/Users/mjg/Projects/packages/javelin/javelin/gp/init.py", line 19, in from .GPutils import File "/Users/mjg/Projects/packages/javelin/javelin/gp/GPutils.py", line 17, in from javelin.gp.linalg_utils import ModuleNotFoundError: No module named 'javelin.gp.linalg_utils'

[nye17]

It seems like you are importing javelin from the source dir? Can you go to the example dir and run some of the test codes like plotcov.py, or jump out of the javelin source dir before importing javelin?

[lss-len]

I have similar problem with python 3.12

[lss-len]

from numpy.distutils.misc_util import Configuration ModuleNotFoundError: No module named 'numpy.distutils'