Installation issues / segfault with brew-installed python 3.7, Julia 1.6

[alexlenail]

~ » python
Python 3.7.10 (default, Apr 27 2021, 08:49:44)
[Clang 12.0.0 (clang-1200.0.32.29)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import julia
>>> julia.install()
>>> import diffeqpy
>>> diffeqpy.install()
>>> from diffeqpy import ode
ERROR: [1]    33097 segmentation fault  python3

More:

(output of julia.install() I think? ran the above commands in a notebook -- this output was piped to shell)

    Updating registry at `~/.julia/registries/General`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`
   Resolving package versions...
   Installed FastBroadcast ─ v0.1.8
   Installed DiffEqBase ──── v6.62.2
    Updating `~/.julia/environments/v1.6/Project.toml`
  [2b5f629d] + DiffEqBase v6.62.2
    Updating `~/.julia/environments/v1.6/Manifest.toml`
  [2b5f629d] ↑ DiffEqBase v6.60.0 ⇒ v6.62.2
  [7034ab61] + FastBroadcast v0.1.8
Precompiling project...


20 dependencies successfully precompiled in 93 seconds (321 already precompiled)
   Resolving package versions...
   Installed PyCall ─ v1.92.3
    Updating `~/.julia/environments/v1.6/Project.toml`
  [438e738f] + PyCall v1.92.3
    Updating `~/.julia/environments/v1.6/Manifest.toml`
  [438e738f] + PyCall v1.92.3
    Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/169bb8ea6b1b143c5cf57df6d34d022a7b60c6db/build.log`

1 dependency successfully precompiled in 4 seconds (341 already precompiled)
    Updating registry at `~/.julia/registries/General`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`

(output of diffeqpy.install() I think?)

[ Info: Julia version info
Julia Version 1.6.0
Commit f9720dc2eb (2021-03-24 12:55 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.6.0)
  uname: Darwin 20.4.0 Darwin Kernel Version 20.4.0: Fri Mar  5 01:14:14 PST 2021; root:xnu-7195.101.1~3/RELEASE_X86_64 x86_64 i386
  CPU: Intel(R) Core(TM) i9-8950HK CPU @ 2.90GHz:
                 speed         user         nice          sys         idle          irq
       #1-12  2900 MHz    9615318 s          0 s    4074594 s  188383488 s          0 s

  Memory: 32.0 GB (1957.77734375 MB free)
  Uptime: 3.893959e6 sec
  Load Avg:  1.38916015625  1.18798828125  1.23046875
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake)
Environment:
  XPC_FLAGS = 0x0
  PATH = /usr/local/opt/[email protected]/bin:/usr/local/sbin:/Users/alex/.cargo/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
  TERM = xterm-color
  HOME = /Users/alex
[ Info: Julia executable: /Applications/Julia-1.6.app/Contents/Resources/julia/bin/julia
[ Info: Trying to import PyCall...
┌ Info: PyCall is already installed but not compatible with this Python
└ executable.  Re-building PyCall...
[ Info: Run `Pkg.build("PyCall"; verbose=true)`
    Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/299304989a5e6473d985212c28928899c74e9421/build.log`
    Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/169bb8ea6b1b143c5cf57df6d34d022a7b60c6db/build.log`
[ Info: PyCall is using /usr/local/opt/[email protected]/bin/python3.7 (Python 3.7.10) at /usr/local/opt/[email protected]/bin/python3.7, libpython = /usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7/Python
[ Info: /Users/alex/.julia/packages/PyCall/BD546/deps/deps.jl has been updated
[ Info: /Users/alex/.julia/prefs/PyCall has been updated

1 dependency successfully precompiled in 6 seconds (341 already precompiled)
[ Info: `/Users/alex/.julia/packages/PyCall/BD546/src/../deps/deps.jl`
const python = "/usr/local/opt/[email protected]/bin/python3.7"
const libpython = "/usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7/Python"
const pyprogramname = "/usr/local/opt/[email protected]/bin/python3.7"
const pyversion_build = v"3.7.10"
const PYTHONHOME = "/usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7:/usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7"

"True if we are using the Python distribution in the Conda package."
const conda = false

[ChrisRackauckas]

@tkf could we talk about some of the deployment issues of this library more generally? I would be interested to see if we could get a fix to JuliaPy/pyjulia#118 ?

[alexlenail]

Having done some digging, this appears to be an issue with julia 1.6:

xref: issue here: JuliaLang/julia#40246

Possible resolution of the issue here: JuliaLang/julia#40851

[alexlenail]

I am no longer having this issue in Julia 1.5.4. Closing...