PythonCall.jl
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JuliaPy
`Using PythonCall` results in a NumPy compilation error
Affects: PythonCall
Describe the bug
On doing using PythonCall, CondaPkg begins to set up a local Python environment. However, on reaching the installation of numpy, I receive the following compilation error:
Collecting numpy<1.19.0,>=1.15.4 (from ipfx)
Using cached numpy-1.18.5.zip (5.4 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [60 lines of output]
Running from numpy source directory.
<string>:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
required_version = LooseVersion('0.29.14')
/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py:77: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(cython_version) < required_version:
warning: /tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/numpy/__init__.pxd:17:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: /tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/numpy/__init__.pxd:17:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
Error compiling Cython file:
------------------------------------------------------------
...
def __init__(self, seed=None):
BitGenerator.__init__(self, seed)
self.rng_state.pcg_state = &self.pcg64_random_state
self._bitgen.state = <void *>&self.rng_state
self._bitgen.next_uint64 = &pcg64_uint64
^
------------------------------------------------------------
_pcg64.pyx:113:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/mtrand.pyx
Processing numpy/random/_pcg64.pyx
Traceback (most recent call last):
File "/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py", line 238, in <module>
main()
File "/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py", line 234, in main
find_process_files(root_dir)
File "/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py", line 225, in find_process_files
process(root_dir, fromfile, tofile, function, hash_db)
File "/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py", line 191, in process
processor_function(fromfile, tofile)
File "/tmp/pip-install-cgyfq94t/numpy_63725e2b74454648b28b02acfdf4db11/tools/cythonize.py", line 80, in process_pyx
subprocess.check_call(
File "/home/*/.julia/environments/v1.9/.CondaPkg/env/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/*/.julia/environments/v1.9/.CondaPkg/env/bin/python3.11', '-m', 'cython', '-3', '--fast-fail', '-o', '_pcg64.c', '_pcg64.pyx']' returned non-zero exit status 1.
Cythonizing sources
Traceback (most recent call last):
File "/home/*/.julia/environments/v1.9/.CondaPkg/env/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/*/.julia/environments/v1.9/.CondaPkg/env/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/*/.julia/environments/v1.9/.CondaPkg/env/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-ngmf88ne/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 380, in prepare_metadata_for_build_wheel
self.run_setup()
File "/tmp/pip-build-env-ngmf88ne/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 488, in run_setup
self).run_setup(setup_script=setup_script)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-ngmf88ne/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 488, in <module>
File "<string>", line 469, in setup_package
File "<string>", line 275, in generate_cython
RuntimeError: Running cythonize failed!
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
ERROR: InitError: failed process: Process(`/home/*/.julia/environments/v1.9/.CondaPkg/env/bin/pip install ipfx pyabf`, ProcessExited(1)) [1]
Stacktrace:
[1] pipeline_error
@ ./process.jl:565 [inlined]
[2] run(::Cmd; wait::Bool)
@ Base ./process.jl:480
[3] run(::Cmd)
@ Base ./process.jl:477
[4] _run(io::IO, cmd::Cmd, args::Any; flags::Any)
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:370
[5] (::CondaPkg.var"#29#30"{Base.TTY, Vector{String}, Vector{String}, Vector{String}})()
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:304
[6] withenv(f::Function)
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/env.jl:44
[7] _resolve_pip_install(io::Any, pip_specs::Any, load_path::Any)
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:301
[8] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:528
[9] resolve()
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:384
[10] envdir()
@ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/env.jl:70
[11] init_context()
@ PythonCall.C ~/.julia/packages/PythonCall/1f5yE/src/cpython/context.jl:63
[12] __init__()
@ PythonCall.C ~/.julia/packages/PythonCall/1f5yE/src/cpython/CPython.jl:21
[13] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1074
[14] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
@ Base ./loading.jl:1020
[15] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
@ Base ./loading.jl:1471
[16] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1748
[17] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1625
[18] macro expansion
@ ./loading.jl:1613 [inlined]
[19] macro expansion
@ ./lock.jl:267 [inlined]
[20] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1576
during initialization of module C
Your system Please provide detailed information about your system:
- OS: Arch Linux
- Versions: Julia 1.9.2, PythonCall 0.9.13
- Output of Pkg.status():
Status `~/.julia/environments/v1.9/Project.toml`
[7d9f7c33] Accessors v0.1.32
[28f2ccd6] ApproxFun v0.13.20
[13f3f980] CairoMakie v0.10.6
[861a8166] Combinatorics v1.0.2
[992eb4ea] CondaPkg v0.2.18
[d194a933] Conductor v0.0.6 `~/research/Conductor.jl`
[39dd38d3] Dierckx v0.5.3
[aae7a2af] DiffEqFlux v2.1.0
[77a26b50] DiffEqNoiseProcess v5.17.2
[0c46a032] DifferentialEquations v7.8.0
[31c24e10] Distributions v0.25.98
[61744808] DynamicalSystems v3.2.0
[eb9bf01b] FastDifferentiation v0.2.8
[f6369f11] ForwardDiff v0.10.35
[e9467ef8] GLMakie v0.8.6
[86223c79] Graphs v1.8.0
[34c5aeac] HSL v0.4.0
[09f84164] HypothesisTests v0.11.0
[7073ff75] IJulia v1.24.2
[a98d9a8b] Interpolations v0.14.7
[b6b21f68] Ipopt v1.4.1
[c8e1da08] IterTools v1.8.0
[4076af6c] JuMP v1.12.0
[2621e9c9] MadNLP v0.7.0 `https://github.com/MadNLP/MadNLP.jl.git#master`
[7fb6135f] MadNLPHSL v0.4.0
[961ee093] ModelingToolkit v8.62.0
[a4795742] NLPModels v0.20.0
[f4238b75] NLPModelsIpopt v0.10.1
[792afdf1] NLPModelsJuMP v0.12.1
[1dea7af3] OrdinaryDiffEq v6.53.3
[18e31ff7] Peaks v0.4.3
[91a5bcdd] Plots v1.38.16
[f27b6e38] Polynomials v3.2.13
[31e2f376] PredefinedDynamicalSystems v1.1.1
[c46f51b8] ProfileView v1.7.2
[92933f4c] ProgressMeter v1.7.2
[6099a3de] PythonCall v0.9.13
[274fc56d] PythonPlot v1.0.2
[90137ffa] StaticArrays v1.6.1
[81625895] StaticCompiler v0.5.3
[86c06d3c] StaticTools v0.8.8
⌅ [2913bbd2] StatsBase v0.33.21
[0c5d862f] Symbolics v5.5.0
[1986cc42] Unitful v1.15.0
[017b0a0e] HSL_jll v2023.5.26+0 `~/software/coinhsl/HSL_jll.jl-2023.5.26`
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated`
- Output of CondaPkg.status():
CondaPkg Status /home/*/.julia/environments/v1.9/CondaPkg.toml
Not Resolved (resolve first for more information)
Packages
sympy
Pip packages
ipfx
pyabf
What happens if you try to create an equivalent environment by hand, like this?
conda create -n test sympy
conda activate test
pip install ipfx pyabf
If that fails, then the issue lies with something else, not PythonCall.
Do you mean to run this through CondaPkg.jl or an external Conda installation? If the former, "conda create" doesn't seem to be a recognized command. If the latter, I don't actually have an external Conda installation outside Julia.
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