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Deprecation ImportWarnings when precompiling
@ericphanson and I are working on an project which has PyMNE.jl has a dependency. When I precompile -- I get a large amount of deprecation warnings:
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3/dist-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3/dist-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
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Error when loading PyMNE
Not error were reported when I added and precompile PyMNE.
But when I tried to use it, I got the following error:
julia> using PyMNE
signal (11): Segmentation fault: 11
in expression starting at REPL[3]:1
_ZN4llvm17PMTopLevelManager16addImmutablePassEPNS_13ImmutablePassE at /Users/likanzhan/.julia/environments/v1.8/.CondaPkg/env/lib/libLLVM-11.dylib (unknown line)
Allocations: 5952326 (Pool: 5949181; Big: 3145); GC: 6
signal (11): Segmentation fault: 11
in expression starting at REPL[3]:1
_PyUnicode_FromId at /Users/likanzhan/.julia/environments/v1.8/.CondaPkg/env/lib/libpython3.10.dylib (unknown line)
wait_for_thread_shutdown at /Users/likanzhan/.julia/environments/v1.8/.CondaPkg/env/lib/libpython3.10.dylib (unknown line)
Py_FinalizeEx at /Users/likanzhan/.julia/environments/v1.8/.CondaPkg/env/lib/libpython3.10.dylib (unknown line)
Py_FinalizeEx at /Users/likanzhan/.julia/packages/PythonCall/dsECZ/src/cpython/pointers.jl:299 [inlined]
#36 at /Users/likanzhan/.julia/packages/PythonCall/dsECZ/src/cpython/context.jl:192
unknown function (ip: 0x14ea6432f)
ijl_apply_generic at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
_atexit at ./initdefs.jl:372
jfptr__atexit_29809 at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
ijl_atexit_hook at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
ijl_exit at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
jl_exit_thread0_cb at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
Allocations: 5952326 (Pool: 5949181; Big: 3145); GC: 6
And here is the version information of my Julia:
Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
OS: macOS (arm64-apple-darwin21.5.0)
CPU: 10 × Apple M1 Max
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
Threads: 4 on 8 virtual cores
Environment:
JULIA_NUM_THREADS = 4
JULIA_PKG_USE_CLI_GIT = true
Install MNE via Conda
Deprecation ImportWarnings when precompiling
Having issues with deprecation warnings:
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3/dist-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/lib/python3/dist-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
Tracking Issue: Initial Release
As part of the Julia industry Contributhon, we're going to package and release our code for interfacing with MNE-Python from Julia. Hooray! Here's what needs to happen.
Task list
- Make this tracking issue :)
- No private info in code
- Pre-make public commit:
- Add MIT license
- Add tests + CI badge to README
- Make sure repo follows best-practice settings
-
Make docs build -
Add docs badges to README - Just document usage in the README
- Add TagBot GitHub Action
- Add CompatHelper GitHub Action
- Make repo public
- Have @jrevels enable repo access for the general julia registrator
- Open PR in Julia registry
- Wait for it to auto-merge
Tiny thing: Update Release Notes
Could you update the release notes of 0.2.0 that get_info was removed?
Took us a while to figure that one out... :S
eval in __init__ breaks downstream precompilation
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.5.3 (2020-11-09)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(PyMNE_doodle) pkg> st
Project PyMNE_doodle v0.1.0
Status `~/src/tmp/PyMNE_doodle/Project.toml`
[6c5003b2] PyMNE v0.1.0
shell> cat src/PyMNE_doodle.jl
module PyMNE_doodle
using PyMNE
end
julia> using PyMNE
julia> using PyMNE_doodle
[ Info: Precompiling PyMNE_doodle [c51fb540-dcbe-4563-b378-fed5aac661c3]
ERROR: LoadError: InitError: Evaluation into the closed module `PyMNE` breaks incremental compilation because the side effects will not be permanent. This is likely due to some other module mutating `PyMNE` with `eval` during precompilation - don't do this.
Stacktrace:
[1] eval at ./boot.jl:331 [inlined]
[2] __init__() at /home/ubuntu/.julia/packages/PyMNE/pn9jE/src/PyMNE.jl:35
[3] _include_from_serialized(::String, ::Array{Any,1}) at ./loading.jl:697
[4] _require_search_from_serialized(::Base.PkgId, ::String) at ./loading.jl:782
[5] _require(::Base.PkgId) at ./loading.jl:1007
[6] require(::Base.PkgId) at ./loading.jl:928
[7] require(::Module, ::Symbol) at ./loading.jl:923
[8] include(::Function, ::Module, ::String) at ./Base.jl:380
[9] include(::Module, ::String) at ./Base.jl:368
[10] top-level scope at none:2
[11] eval at ./boot.jl:331 [inlined]
[12] eval(::Expr) at ./client.jl:467
[13] top-level scope at ./none:3
during initialization of module PyMNE
in expression starting at /home/ubuntu/src/tmp/PyMNE_doodle/src/PyMNE_doodle.jl:3
ERROR: Failed to precompile PyMNE_doodle [c51fb540-dcbe-4563-b378-fed5aac661c3] to /home/ubuntu/.julia/compiled/v1.5/PyMNE_doodle/zcqTA_V5NaD.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
[3] _require(::Base.PkgId) at ./loading.jl:1030
[4] require(::Base.PkgId) at ./loading.jl:928
[5] require(::Module, ::Symbol) at ./loading.jl:923So, I have a PyMNE_doodle project that just depends on PyMNE, that contains a module PyMNE_doodle that just imports PyMNE. I get that lovely error on precompilation of PyMNE_doodle, even though using PyMNE works fine.
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