Segfault in REPL when importing a library

[KajWiik]

Affects: PythonCall

Describe the bug

$ julia --project=@temp
julia> import Pkg; Pkg.activate(temp = true); Pkg.add(["CondaPkg", "PythonCall"]);using CondaPkg; CondaPkg.add("python", version="3.13.*");CondaPkg.add("numpy");using PythonCall;
np = pyimport("numpy")
julia> np.
[33140] signal 11 (1): Segmentation fault```

Here is the full dump:

Details

[33140] signal 11 (1): Segmentation fault in expression starting at REPL[2]:1 _PyInterpreterState_GET at /usr/local/src/conda/python-3.13.9/Include/internal/pycore_pystate.h:214 [inlined] _PyType_LookupRef at /usr/local/src/conda/python-3.13.9/Objects/typeobject.c:5234 [inlined] _PyObject_LookupSpecial at /usr/local/src/conda/python-3.13.9/Objects/typeobject.c:2506 _dir_object at /usr/local/src/conda/python-3.13.9/Objects/object.c:1977 [inlined] PyObject_Dir at /usr/local/src/conda/python-3.13.9/Objects/object.c:2009 PyObject_Dir at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/C/pointers.jl:300 [inlined] macro expansion at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:118 [inlined] pydir at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/Core/builtins.jl:191 propertynames at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:270 unknown function (ip: 0x7b8401753beb) at (unknown file) #complete_symbol!#6 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:230 complete_symbol! at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:184 unknown function (ip: 0x7b840174bfd6) at (unknown file) completions at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:1150 #complete_line#66 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:809 complete_line at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:807 unknown function (ip: 0x7b840170e77c) at (unknown file) #complete_line_named#17 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:401 complete_line_named at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:400 [inlined] macro expansion at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:442 [inlined] macro expansion at ./lock.jl:376 [inlined] #check_show_hint##2 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:439 jfptr_YY.check_show_hintYY.YY.2_17954.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line) jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/task.c:1249 Allocations: 29426553 (Pool: 29424566; Big: 1987); GC: 22 Segmentation fault (core dumped)

julia> versioninfo()
Julia Version 1.12.1
Commit ba1e628ee49 (2025-10-17 13:02 UTC)
Build Info:
  Official https://julialang.org release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 4 × Intel(R) Core(TM) i5-4310U CPU @ 2.00GHz
  WORD_SIZE: 64
  LLVM: libLLVM-18.1.7 (ORCJIT, haswell)
  GC: Built with stock GC
Threads: 1 default, 1 interactive, 1 GC (on 4 virtual cores)

julia> CondaPkg.status()
CondaPkg Status /tmp/jl_UfA8Vd/CondaPkg.toml
Environment
  /tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default
Packages
  numpy v2.3.4
  python v3.13.9 (3.13.*)

julia> PythonCall.C.CTX
IOContext{REPL.LimitIO{Base.TTY}}:
  is_embedded = false
  is_initialized = true
  is_preinitialized = false
  lib_ptr = Ptr{Nothing}(0x00000000159f6d10)
  exe_path = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default/bin/python"
  lib_path = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default/lib/libpython3.13.so.1.0"
  dlopen_flags = 0x00000046
  pyprogname = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default/bin/python"
  pyprogname_w = MemoryRef{Int32}(Ptr{Nothing}(0x000070c8b541d520), Int32[47, 116, 109, 112, 47, 106, 108, 95, 85, 102  …  -1441332048, 28872, -599587392, 28872, -514150800, 28872, -514150800, 28872, -444150752, 28872])
  pyhome = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default:/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default"
  pyhome_w = MemoryRef{Int32}(Ptr{Nothing}(0x000070c8a23249e0), Int32[47, 116, 109, 112, 47, 106, 108, 95, 85, 102  …  0, 0, 0, -514153520, 28872, -677031280, 28872, 19, 0, 0])
  which = :CondaPkg
  version = v"3.13.9"

Occurs with both Python 3.13 and 3.14 and only in REPL. In script, everything works fine:

$ julia --project=@temp pythoncall.jl 
  Activating new project at `/tmp/jl_RvnsQJ`
   Resolving package versions...
    Updating `/tmp/jl_RvnsQJ/Project.toml`
  [992eb4ea] + CondaPkg v0.2.33
  [6099a3de] + PythonCall v0.9.28
    Updating `/tmp/jl_RvnsQJ/Manifest.toml`
  [992eb4ea] + CondaPkg v0.2.33
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [0f8b85d8] + JSON3 v1.14.3
  [1914dd2f] + MacroTools v0.5.16
  [0b3b1443] + MicroMamba v0.1.14
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [fa939f87] + Pidfile v1.3.0
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [6099a3de] + PythonCall v0.9.28
  [6c6a2e73] + Scratch v1.3.0
  [856f2bd8] + StructTypes v1.11.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [e17b2a0c] + UnsafePointers v1.0.0
⌅ [f8abcde7] + micromamba_jll v1.5.12+0
  [4d7b5844] + pixi_jll v0.41.3+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.12.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [deac9b47] + LibCURL_jll v8.11.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850ede] + nghttp2_jll v1.64.0+1
  [3f19e933] + p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    CondaPkg Found dependencies: /tmp/jl_RvnsQJ/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + libstdcxx
             + libstdcxx-ng
             + openssl
             + python
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_RvnsQJ/.CondaPkg
✔ Created /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = "3.13.*, >=3.9,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
✔ The default environment has been installed.
    CondaPkg Found dependencies: /tmp/jl_RvnsQJ/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + numpy
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_RvnsQJ/.CondaPkg
✔ Created /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ numpy = "*"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = "3.13.*, >=3.9,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
✔ The default environment has been installed.
[1 2 3 4 5]

Script:

import Pkg; Pkg.activate(temp = true); Pkg.add(["CondaPkg", "PythonCall"]);using CondaPkg; CondaPkg.add("numpy");using PythonCall;

np = pyimport("numpy")
println( np.array([1, 2, 3, 4, 5]))

[KajWiik]

I noticed that when using OhMyREPL I do not get a segfault. Is the bug in REPL?

[cjdoris]

I believe this is now fixed and released - please try with PythonCall 0.9.29.

[KajWiik]

I am sorry to report that it still segfaults when hitting after period (.)...

$ julia --project=@temp
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.12.1 (2025-10-17)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org release
|__/                   |

(jl_KolX4u) pkg> add PythonCall
   Resolving package versions...
    Updating `/tmp/jl_KolX4u/Project.toml`
  [6099a3de] + PythonCall v0.9.29
    Updating `/tmp/jl_KolX4u/Manifest.toml`
  [992eb4ea] + CondaPkg v0.2.33
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [0f8b85d8] + JSON3 v1.14.3
  [1914dd2f] + MacroTools v0.5.16
  [0b3b1443] + MicroMamba v0.1.14
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [fa939f87] + Pidfile v1.3.0
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [6099a3de] + PythonCall v0.9.29
  [6c6a2e73] + Scratch v1.3.0
  [856f2bd8] + StructTypes v1.11.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [e17b2a0c] + UnsafePointers v1.0.0
⌅ [f8abcde7] + micromamba_jll v1.5.12+0
  [4d7b5844] + pixi_jll v0.41.3+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.12.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [deac9b47] + LibCURL_jll v8.11.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850ede] + nghttp2_jll v1.64.0+1
  [3f19e933] + p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

julia> using PythonCall
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/Ds20G/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + libstdcxx
             + libstdcxx-ng
             + openssl
             + python
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_KolX4u/.CondaPkg
✔ Created /tmp/jl_KolX4u/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_KolX4u/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = ">=3.10,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_KolX4u/.CondaPkg/pixi.toml
✔ The default environment has been installed.

(jl_KolX4u) pkg> conda add scikit-rf
    CondaPkg Found dependencies: /tmp/jl_KolX4u/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/Ds20G/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + scikit-rf
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_KolX4u/.CondaPkg
✔ Created /tmp/jl_KolX4u/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_KolX4u/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ scikit-rf = "*"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = ">=3.10,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_KolX4u/.CondaPkg/pixi.toml
✔ The default environment has been installed.

julia> using PythonCall

julia> rf = pyimport("skrf")
Python: <module 'skrf' from '/tmp/jl_KolX4u/.CondaPkg/.pixi/envs/default/lib/python3.14/site-packages/skrf/__init__.py'>

julia> rf.Fatal Python error: _Py_CheckRecursiveCall: Unrecoverable stack overflow (used -598662 kB) while calling a Python object
Python runtime state: initialized

Current thread 0x00007b4bdaa1e140 [julia] (most recent call first):
  <no Python frame>

Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, _cyutility, scipy._cyutility, scipy.linalg.cython_lapack, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._pcg64, numpy.random._mt19937, numpy.random._generator, numpy.random._philox, numpy.random._sfc64, numpy.random.mtrand, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_schur_sqrtm, scipy.linalg._matfuncs_expm, scipy.linalg._linalg_pythran, scipy.linalg.cython_blas, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._slsqplib, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, scipy.special._ellip_harm_2, scipy.special._special_ufuncs, scipy.special._gufuncs, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._decomp_interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._hausdorff, scipy.spatial._distance_wrap, scipy.spatial.transform._rotation, scipy.spatial.transform._rigid_transform, scipy.optimize._direct, PIL._imaging, kiwisolver._cext, scipy.signal._sigtools, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal._spline, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._dierckx, scipy.interpolate._ppoly, scipy.interpolate._interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.ndimage._nd_image, scipy.ndimage._rank_filter_1d, _ni_label, scipy.ndimage._ni_label, scipy.signal._sosfilt, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._stats_pythran, scipy.stats._levy_stable.levyst, scipy.stats._ansari_swilk_statistics, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._rcont.rcont, scipy.stats._qmvnt_cy, scipy.signal._peak_finding_utils, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing (total: 144)

[503371] signal 6 (-6): Aborted
in expression starting at REPL[6]:1
pthread_kill at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
fatal_error_exit at /usr/local/src/conda/python-3.14.0/Python/pylifecycle.c:3250 [inlined]
fatal_error at /usr/local/src/conda/python-3.14.0/Python/pylifecycle.c:3396
_Py_FatalErrorFunc at /usr/local/src/conda/python-3.14.0/Python/pylifecycle.c:3482
_Py_CheckRecursiveCall at /usr/local/src/conda/python-3.14.0/Python/ceval.c:491
_Py_EnterRecursiveCallTstate at /usr/local/src/conda/python-3.14.0/Include/internal/pycore_ceval.h:216 [inlined]
method_enter_call at /usr/local/src/conda/python-3.14.0/Objects/descrobject.c:300 [inlined]
method_vectorcall_NOARGS at /usr/local/src/conda/python-3.14.0/Objects/descrobject.c:444
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.14.0/Include/internal/pycore_call.h:169 [inlined]
PyObject_VectorcallMethod at /usr/local/src/conda/python-3.14.0/Objects/call.c:856
PyObject_CallMethodNoArgs at /usr/local/src/conda/python-3.14.0/Include/cpython/abstract.h:65 [inlined]
_PyFile_Flush at /usr/local/src/conda/python-3.14.0/Objects/fileobject.c:542
flush_std_files at /usr/local/src/conda/python-3.14.0/Python/pylifecycle.c:1915
fatal_error at /usr/local/src/conda/python-3.14.0/Python/pylifecycle.c:3459
_Py_FatalErrorFunc at /usr/local/src/conda/python-3.14.0/Python/pylifecycle.c:3482
_Py_CheckRecursiveCall at /usr/local/src/conda/python-3.14.0/Python/ceval.c:491
_Py_EnterRecursiveCallTstate at /usr/local/src/conda/python-3.14.0/Include/internal/pycore_ceval.h:216 [inlined]
cfunction_enter_call at /usr/local/src/conda/python-3.14.0/Objects/methodobject.c:428 [inlined]
cfunction_vectorcall_NOARGS at /usr/local/src/conda/python-3.14.0/Objects/methodobject.c:504
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.14.0/Include/internal/pycore_call.h:169
_PyObject_CallNoArgs at /usr/local/src/conda/python-3.14.0/Include/internal/pycore_call.h:185 [inlined]
_dir_object at /usr/local/src/conda/python-3.14.0/Objects/object.c:2029 [inlined]
PyObject_Dir at /usr/local/src/conda/python-3.14.0/Objects/object.c:2052
PyObject_Dir at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/C/pointers.jl:300 [inlined]
macro expansion at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/Py.jl:118 [inlined]
pydir at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/builtins.jl:191
#4 at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/Py.jl:297
unknown function (ip: 0x7b4ba9b9150f) at (unknown file)
jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined]
jl_f_invokelatest at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/builtins.c:881
#setup_onfixedthread##1 at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/C/context.jl:44
unknown function (ip: 0x7b4ba9b125ff) at (unknown file)
jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined]
start_task at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/task.c:1249
Allocations: 35120552 (Pool: 35118507; Big: 2045); GC: 21
Aborted (core dumped)

[cjdoris]

Actually now you're seeing a different issue #694 which is caused by some internal changes in python 3.14. For now you can work around it by restricting to python 3.13 or older (CondaPkg.add("python", version="<3.14")).

[KajWiik]

Hm, with 3.13.9 (should I try 3.13.0?) I get right after pyimport():

$ julia --project=@temp
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.12.1 (2025-10-17)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org release
|__/                   |

julia> using PythonCall
 │ Package PythonCall not found, but a package named PythonCall is available from a registry. 
 │ Install package?
 │   (jl_A5OqBg) pkg> add PythonCall 
 └ (y/n/o) [y]: 
   Resolving package versions...
    Updating `/tmp/jl_A5OqBg/Project.toml`
  [6099a3de] + PythonCall v0.9.29
    Updating `/tmp/jl_A5OqBg/Manifest.toml`
  [992eb4ea] + CondaPkg v0.2.33
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [0f8b85d8] + JSON3 v1.14.3
  [1914dd2f] + MacroTools v0.5.16
  [0b3b1443] + MicroMamba v0.1.14
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [fa939f87] + Pidfile v1.3.0
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [6099a3de] + PythonCall v0.9.29
  [6c6a2e73] + Scratch v1.3.0
  [856f2bd8] + StructTypes v1.11.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [e17b2a0c] + UnsafePointers v1.0.0
⌅ [f8abcde7] + micromamba_jll v1.5.12+0
  [4d7b5844] + pixi_jll v0.41.3+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.12.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [deac9b47] + LibCURL_jll v8.11.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850ede] + nghttp2_jll v1.64.0+1
  [3f19e933] + p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/Ds20G/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + libstdcxx
             + libstdcxx-ng
             + openssl
             + python
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_A5OqBg/.CondaPkg
✔ Created /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = ">=3.10,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
✔ The default environment has been installed.

julia> using CondaPkg
 │ Package CondaPkg not found, but a package named CondaPkg is available from a registry. 
 │ Install package?
 │   (jl_A5OqBg) pkg> add CondaPkg 
 └ (y/n/o) [y]: 
   Resolving package versions...
    Updating `/tmp/jl_A5OqBg/Project.toml`
  [992eb4ea] + CondaPkg v0.2.33
    Manifest No packages added to or removed from `/tmp/jl_A5OqBg/Manifest.toml`

julia> CondaPkg.add("python", version="<3.14")
    CondaPkg Found dependencies: /tmp/jl_A5OqBg/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/Ds20G/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             ~ python
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_A5OqBg/.CondaPkg
✔ Created /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = "<3.14, >=3.10,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
✔ The default environment has been installed.

(jl_A5OqBg) pkg> conda add scikit-rf
    CondaPkg Found dependencies: /tmp/jl_A5OqBg/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/Ds20G/CondaPkg.toml
    CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + scikit-rf
    CondaPkg Initialising pixi
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_A5OqBg/.CondaPkg
✔ Created /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx = ">=3.4,<15.0"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ scikit-rf = "*"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = "<3.14, >=3.10,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_A5OqBg/.CondaPkg/pixi.toml
✔ The default environment has been installed.

(jl_A5OqBg) pkg> st
Status `/tmp/jl_A5OqBg/Project.toml`
  [992eb4ea] CondaPkg v0.2.33
  [6099a3de] PythonCall v0.9.29

(jl_A5OqBg) pkg> conda st
CondaPkg Status /tmp/jl_A5OqBg/CondaPkg.toml
Environment
  /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default
Packages
  python v3.13.9 (<3.14)
  scikit-rf v1.8.0

julia> using PythonCall

julia> rf = pyimport("skrf")
ERROR: Python: Fatal Python error: _Py_CheckRecursiveCall: Unrecoverable stack overflow (used 445562 kB) while calling a Python object
Python runtime state: initialized

Current thread 0x00007c0f3e3cf140 [julia] (most recent call first):
  <no Python frame>

[557363] signal 6 (-6): Aborted
in expression starting at REPL[9]:1
pthread_kill at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7c0ee998f4ae) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
_Py_FatalErrorFunc at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0 (unknown line)
unknown function (ip: 0x7c0ee98addf8) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
unknown function (ip: 0x7c0ee98be0da) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
PyObject_VectorcallMethod at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0 (unknown line)
unknown function (ip: 0x7c0ee9ae5a59) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
unknown function (ip: 0x7c0ee9b0272a) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
unknown function (ip: 0x7c0ee998f7ba) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
_Py_FatalErrorFunc at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0 (unknown line)
unknown function (ip: 0x7c0ee98addf8) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
unknown function (ip: 0x7c0ee98b1d60) at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0
PyObject_CallFunction at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0 (unknown line)
PyImport_Import at /tmp/jl_A5OqBg/.CondaPkg/.pixi/envs/default/lib/libpython3.14.so.1.0 (unknown line)
PyImport_Import at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/C/pointers.jl:300 [inlined]
macro expansion at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/Py.jl:118 [inlined]
pyimport at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/builtins.jl:1458
#_showerror#15 at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/err.jl:110
_showerror at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/err.jl:97 [inlined]
#showerror#14 at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/err.jl:94 [inlined]
showerror at /home/kjwiik/.julia/packages/PythonCall/Ds20G/src/Core/err.jl:94
unknown function (ip: 0x7c0f0212aa42) at (unknown file)
show_exception_stack at ./errorshow.jl:1016
display_error at ./client.jl:110
jfptr_display_error_16923.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line)
jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined]
jl_f_invokelatest at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/builtins.c:881
repl_display_error at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:567
print_response at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:584
#print_response##0 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:558
jfptr_YY.print_responseYY.YY.0_18324.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line)
with_repl_linfo at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:833
jfptr_with_repl_linfo_18268.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line)
print_response at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:556
do_respond at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:1192
jfptr_do_respond_17885.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line)
jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined]
jl_f_invokelatest at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/builtins.c:881
run_interface at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2854
run_frontend at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:1663
#61 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:650
jfptr_YY.61_17990.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line)
jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined]
start_task at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/task.c:1249
Allocations: 58101029 (Pool: 58098907; Big: 2122); GC: 28
Aborted (core dumped)

[KajWiik]

Hm, the error message has references to libpython3.14.so.1.0 even when conda st gives 3.13.9, maybe 3.14 is still used? How to ensure <3.14?

[cjdoris]

You need to do the CondaPkg commands before importing PythonCall otherwise you'll get the old Python version.

[KajWiik]

Doh! Indeed, now it is working fine, many thanks! This makes my life so much easier :-)!