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Pyinstaller can not freeze SVD functions #4968

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Jerburi opened this issue Jul 3, 2020 · 6 comments
Closed

Pyinstaller can not freeze SVD functions #4968

Jerburi opened this issue Jul 3, 2020 · 6 comments
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@Jerburi
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Jerburi commented Jul 3, 2020

Welcome to the PyInstaller issue tracker! Before creating an issue, please heed the following:

  1. This tracker should only be used to report bugs and request features / enhancements to PyInstaller
  2. Use the search function before creating a new issue. Duplicates will be closed and directed to
    the original discussion.
  3. When making a bug report, make sure you provide all required information. The easier it is for
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Description of the issue

I have been trying to freeze a python script that contains an instance of an SVD function (single value decomposition) without success. Everytime the executable runs it, it crashes the program without any error message or exception that I can catch (nor any message appears with the --debug option of pyinstaller). However, when I remove this function of the code, everything works fine.

What is the most surprising of this problem, is that the executable works fine if I run it through the conda prompt. But fails if it is run by double-clicking it. Adding all the missing .dll dependancies that the build log mentions does not fix this issue.

I isolated the problem using a minimal script containing only the SVD. I tried three homologous functions from OpenCV (4.3.0), Numpy (1.18.5) and Scipy (1.5.0), and all three fail (although the OpenCV version seems to work sometimes).

Thanks for your support, and I hope this issue might just be something trivial.

I'm using:

  • Pyinstaller Version: 3.6
  • Version of Python: 3.7.7
  • Platform: Windows (English), Anaconda3

A minimal example program which shows the error

import numpy as np
import cv2
import scipy.linalg as scilin

np.random.seed(42)
a = np.random.random((15,20))

w = np.zeros(a.shape[0]); u = np.zeros((a.shape[0], a.shape[0])); vt = np.zeros(a.shape)
cv2.SVDecomp(a, w, u, vt)
print(w.shape, u.shape, vt.shape)

u2,w2,vt2 = np.linalg.svd(a, full_matrices=False, compute_uv=True)
print(w2.shape, u2.shape, vt2.shape)

u3,w3,vt3 = scilin.svd(a, full_matrices=False, compute_uv=True)
print(w3.shape, u3.shape, vt3.shape)

Build Log

57 INFO: PyInstaller: 3.6
57 INFO: Python: 3.7.7 (conda)
58 INFO: Platform: Windows-10-10.0.17763-SP0
59 INFO: UPX is not available.
60 INFO: Extending PYTHONPATH with paths
['C:\\Users\\Jorge Ramirez\\Documents',
 'C:\\Users\\Jorge Ramirez\\Documents\\Python Scripts']
60 INFO: checking Analysis
93 INFO: Building because C:\Users\Jorge Ramirez\Documents\Python Scripts\Test_SVD_pyinstaller.py changed
93 INFO: Initializing module dependency graph...
97 INFO: Caching module graph hooks...
103 INFO: Analyzing base_library.zip ...
2883 INFO: Processing pre-find module path hook   distutils
2884 INFO: distutils: retargeting to non-venv dir 'C:\\Anaconda3\\envs\\ephys\\lib'
3562 INFO: Caching module dependency graph...
3676 INFO: running Analysis Analysis-00.toc
3678 INFO: Adding Microsoft.Windows.Common-Controls to dependent assemblies of final executable
  required by C:\Anaconda3\envs\ephys\python.exe
3970 INFO: Analyzing Test_SVD_pyinstaller.py
5942 INFO: Processing pre-safe import module hook   setuptools.extern.six.moves
6327 INFO: Processing pre-find module path hook   site
6328 INFO: site: retargeting to fake-dir 'C:\\Anaconda3\\envs\\ephys\\lib\\site-packages\\PyInstaller\\fake-modules'
9634 INFO: Processing module hooks...
9634 INFO: Loading module hook "hook-cv2.py"...
9635 INFO: Loading module hook "hook-distutils.py"...
9636 INFO: Loading module hook "hook-encodings.py"...
9711 INFO: Loading module hook "hook-lib2to3.py"...
9713 INFO: Loading module hook "hook-numpy.core.py"...
9832 INFO: MKL libraries found when importing numpy. Adding MKL to binaries
9835 INFO: Loading module hook "hook-numpy.py"...
9836 INFO: Loading module hook "hook-pkg_resources.py"...
10141 INFO: Processing pre-safe import module hook   win32com
10403 INFO: Excluding import '__main__'
10404 INFO:   Removing import of __main__ from module pkg_resources
10404 INFO: Loading module hook "hook-pydoc.py"...
10405 INFO: Loading module hook "hook-pytest.py"...
11055 INFO: Loading module hook "hook-pythoncom.py"...
11296 INFO: Loading module hook "hook-pywintypes.py"...
11557 INFO: Loading module hook "hook-scipy.linalg.py"...
11558 INFO: Loading module hook "hook-scipy.py"...
11560 INFO: Loading module hook "hook-scipy.sparse.csgraph.py"...
11563 INFO: Loading module hook "hook-scipy.special._ellip_harm_2.py"...
14007 INFO: Processing pre-safe import module hook   six.moves
17161 INFO: Loading module hook "hook-scipy.special._ufuncs.py"...
17162 INFO: Loading module hook "hook-setuptools.py"...
C:\Anaconda3\envs\ephys\lib\site-packages\setuptools\distutils_patch.py:17: UserWarning: Setuptools is replacing distutils
  warnings.warn("Setuptools is replacing distutils")
17712 INFO: Loading module hook "hook-sysconfig.py"...
17714 INFO: Loading module hook "hook-win32com.py"...
18034 INFO: Loading module hook "hook-xml.dom.domreg.py"...
18035 INFO: Loading module hook "hook-xml.etree.cElementTree.py"...
18036 INFO: Loading module hook "hook-xml.py"...
18037 INFO: Loading module hook "hook-matplotlib.backends.py"...
18632 INFO:   Matplotlib backend "GTK3Agg": ignored
    backend Gtk3Agg requires cairo
18941 INFO:   Matplotlib backend "GTK3Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
19302 INFO:   Matplotlib backend "MacOSX": ignored
    cannot import name '_macosx' from 'matplotlib.backends' (C:\Anaconda3\envs\ephys\lib\site-packages\matplotlib\backends\__init__.py)
19612 INFO:   Matplotlib backend "nbAgg": ignored
    No module named 'IPython'
20144 INFO:   Matplotlib backend "Qt4Agg": added
20470 INFO:   Matplotlib backend "Qt4Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
20968 INFO:   Matplotlib backend "Qt5Agg": added
21273 INFO:   Matplotlib backend "Qt5Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
21756 INFO:   Matplotlib backend "TkAgg": added
22201 INFO:   Matplotlib backend "TkCairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
22656 INFO:   Matplotlib backend "WebAgg": added
23072 INFO:   Matplotlib backend "WX": ignored
    No module named 'wx'
23392 INFO:   Matplotlib backend "WXAgg": ignored
    No module named 'wx'
23733 INFO:   Matplotlib backend "WXCairo": ignored
    No module named 'wx'
24055 INFO:   Matplotlib backend "agg": added
24361 INFO:   Matplotlib backend "cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
24831 INFO:   Matplotlib backend "pdf": added
25262 INFO:   Matplotlib backend "pgf": added
25595 INFO:   Matplotlib backend "ps": added
25951 INFO:   Matplotlib backend "svg": added
26370 INFO:   Matplotlib backend "template": added
26917 INFO: Loading module hook "hook-matplotlib.py"...
27190 INFO: Loading module hook "hook-PIL.Image.py"...
27540 INFO: Loading module hook "hook-PIL.py"...
27542 INFO: Excluding import 'PySide'
27545 INFO: Excluding import 'PyQt5'
27547 INFO:   Removing import of PyQt5.QtGui from module PIL.ImageQt
27547 INFO:   Removing import of PyQt5.QtCore from module PIL.ImageQt
27548 INFO: Import to be excluded not found: 'FixTk'
27548 INFO: Excluding import 'PyQt4'
27550 INFO: Excluding import 'tkinter'
27553 INFO:   Removing import of tkinter from module PIL.ImageTk
27553 INFO: Loading module hook "hook-PIL.SpiderImagePlugin.py"...
27555 INFO: Import to be excluded not found: 'FixTk'
27555 INFO: Excluding import 'tkinter'
27556 INFO: Loading module hook "hook-PyQt5.py"...
27973 INFO: Loading module hook "hook-PyQt5.QtCore.py"...
27987 INFO: Loading module hook "hook-PyQt5.QtGui.py"...
28000 INFO: Loading module hook "hook-PyQt5.QtWidgets.py"...
28016 INFO: Loading module hook "hook-_tkinter.py"...
28153 INFO: checking Tree
28188 INFO: checking Tree
28261 INFO: Looking for ctypes DLLs
28328 INFO: Analyzing run-time hooks ...
28338 INFO: Including run-time hook 'pyi_rth_multiprocessing.py'
28341 INFO: Including run-time hook 'pyi_rth_pkgres.py'
28342 INFO: Including run-time hook 'pyi_rth_win32comgenpy.py'
28343 INFO: Including run-time hook 'pyi_rth__tkinter.py'
28344 INFO: Including run-time hook 'pyi_rth_pyqt5.py'
28345 INFO: Including run-time hook 'pyi_rth_mplconfig.py'
28346 INFO: Including run-time hook 'pyi_rth_mpldata.py'
28365 INFO: Looking for dynamic libraries
28393 WARNING: lib not found: impi.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_blacs_intelmpi_ilp64.dll
28399 WARNING: lib not found: msmpi.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_blacs_msmpi_ilp64.dll
28432 WARNING: lib not found: impi.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_blacs_intelmpi_lp64.dll
28480 WARNING: lib not found: pgf90rtl.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_pgi_thread.dll
28482 WARNING: lib not found: pgc14.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_pgi_thread.dll
28483 WARNING: lib not found: pgf90.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_pgi_thread.dll
28835 WARNING: lib not found: mpich2mpi.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_blacs_mpich2_ilp64.dll
28922 WARNING: lib not found: mpich2mpi.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_blacs_mpich2_lp64.dll
29061 WARNING: lib not found: msmpi.dll dependency of C:\Anaconda3\envs\ephys\Library\bin\mkl_blacs_msmpi_lp64.dll
31264 INFO: Looking for eggs
31264 INFO: Using Python library C:\Anaconda3\envs\ephys\python37.dll
31265 INFO: Found binding redirects:
[]
31276 INFO: Warnings written to C:\Users\Jorge Ramirez\Documents\Python Scripts\build\Test_SVD_pyinstaller\warn-Test_SVD_pyinstaller.txt
31472 INFO: Graph cross-reference written to C:\Users\Jorge Ramirez\Documents\Python Scripts\build\Test_SVD_pyinstaller\xref-Test_SVD_pyinstaller.html
31549 INFO: checking PYZ
31567 INFO: Building because toc changed
31567 INFO: Building PYZ (ZlibArchive) C:\Users\Jorge Ramirez\Documents\Python Scripts\build\Test_SVD_pyinstaller\PYZ-00.pyz
33822 INFO: Building PYZ (ZlibArchive) C:\Users\Jorge Ramirez\Documents\Python Scripts\build\Test_SVD_pyinstaller\PYZ-00.pyz completed successfully.
33858 INFO: checking PKG
33859 INFO: Building because C:\Users\Jorge Ramirez\Documents\Python Scripts\build\Test_SVD_pyinstaller\PYZ-00.pyz changed
33860 INFO: Building PKG (CArchive) PKG-00.pkg
33896 INFO: Building PKG (CArchive) PKG-00.pkg completed successfully.
33899 INFO: Bootloader C:\Anaconda3\envs\ephys\lib\site-packages\PyInstaller\bootloader\Windows-64bit\run_d.exe
33899 INFO: checking EXE
33907 INFO: Rebuilding EXE-00.toc because pkg is more recent
33907 INFO: Building EXE from EXE-00.toc
33908 INFO: Appending archive to EXE C:\Users\Jorge Ramirez\Documents\Python Scripts\build\Test_SVD_pyinstaller\Test_SVD_pyinstaller.exe
33926 INFO: Building EXE from EXE-00.toc completed successfully.
33932 INFO: checking COLLECT
On your own risk, you can use the option `--noconfirm` to get rid of this question.
33954 INFO: Removing dir C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
34326 INFO: Building COLLECT COLLECT-00.toc
40073 INFO: Building COLLECT COLLECT-00.toc completed successfully.
@bwoodsend
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All 3 work for me using exactly the same (as far as I can tell) environment as you. Can we have the run-time traceback? Run your exe from cmd to see it without it closing immediately.

@Jerburi
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Jerburi commented Jul 21, 2020

Hi! I made a change on the code to be able to see more clearly the problem... I included a waiting time at the end as a message for the routine's ending:

import time

# The rest of the test code goes here

print('Waiting 10 seconds to check messages...')
time.sleep(10)

Now, when using the console there is no problem; all the three SVD functions work fine. However, the problem comes when you use the "frozen" application. It gets out before reaching the waiting time, for an unknown (ant not warned/printed) error.

Here is the run-time traceback by executing the frozen application on the console:

[7696] PyInstaller Bootloader 3.x
[7696] LOADER: executable is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\Test_SVD_pyinstaller.exe
[7696] LOADER: homepath is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[7696] LOADER: _MEIPASS2 is NULL
[7696] LOADER: archivename is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\Test_SVD_pyinstaller.exe
[7696] LOADER: No need to extract files to run; setting extractionpath to homepath
[7696] LOADER: SetDllDirectory(C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller)
[7696] LOADER: Already in the child - running user's code.
[7696] LOADER: Python library: C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\python37.dll
[7696] LOADER: Loaded functions from Python library.
[7696] LOADER: Manipulating environment (sys.path, sys.prefix)
[7696] LOADER: sys.prefix is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[7696] LOADER: Pre-init sys.path is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\base_library.zip;C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[7696] LOADER: Setting runtime options
[7696] LOADER: Initializing python
[7696] LOADER: Overriding Python's sys.path
[7696] LOADER: Post-init sys.path is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\base_library.zip;C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[7696] LOADER: Setting sys.argv
[7696] LOADER: setting sys._MEIPASS
[7696] LOADER: importing modules from CArchive
[7696] LOADER: extracted struct
[7696] LOADER: callfunction returned...
[7696] LOADER: extracted pyimod01_os_path
[7696] LOADER: callfunction returned...
[7696] LOADER: extracted pyimod02_archive
[7696] LOADER: callfunction returned...
[7696] LOADER: extracted pyimod03_importers
[7696] LOADER: callfunction returned...
[7696] LOADER: Installing PYZ archive with Python modules.
[7696] LOADER: PYZ archive: PYZ-00.pyz
[7696] LOADER: Running pyiboot01_bootstrap.py
[7696] LOADER: Running pyi_rth_multiprocessing.py
[7696] LOADER: Running pyi_rth_pkgres.py
[7696] LOADER: Running pyi_rth_win32comgenpy.py
[7696] LOADER: Running pyi_rth__tkinter.py
[7696] LOADER: Running pyi_rth_pyqt5.py
[7696] LOADER: Running pyi_rth_mplconfig.py
[7696] LOADER: Running pyi_rth_mpldata.py
[7696] LOADER: Running Test_SVD_pyinstaller.py
(15,) (15, 15) (15, 20)
(15,) (15, 15) (15, 20)
(15,) (15, 15) (15, 20)
Waiting 10 seconds to check messages...
[7696] LOADER: OK.
[7696] LOADER: Cleaning up Python interpreter.

.....And here I post the traceback I collected on the pop-up console while running the executable by itself:

[17120] PyInstaller Bootloader 3.x
[17120] LOADER: executable is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\Test_SVD_pyinstaller.exe
[17120] LOADER: homepath is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[17120] LOADER: _MEIPASS2 is NULL
[17120] LOADER: archivename is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\Test_SVD_pyinstaller.exe
[17120] LOADER: No need to extract files to run; setting extractionpath to homepath
[17120] LOADER: SetDllDirectory(C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller)
[17120] LOADER: Already in the child - running user's code.
[17120] LOADER: Python library: C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\python37.dll
[17120] LOADER: Loaded functions from Python library.
[17120] LOADER: Manipulating environment (sys.path, sys.prefix)
[17120] LOADER: sys.prefix is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[17120] LOADER: Pre-init sys.path is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\base_library.zip;C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[17120] LOADER: Setting runtime options
[17120] LOADER: Initializing python
[17120] LOADER: Overriding Python's sys.path
[17120] LOADER: Post-init sys.path is C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller\base_library.zip;C:\Users\Jorge Ramirez\Documents\Python Scripts\dist\Test_SVD_pyinstaller
[17120] LOADER: Setting sys.argv
[17120] LOADER: setting sys._MEIPASS
[17120] LOADER: importing modules from CArchive
[17120] LOADER: extracted struct
[17120] LOADER: callfunction returned...
[17120] LOADER: extracted pyimod01_os_path
[17120] LOADER: callfunction returned...
[17120] LOADER: extracted pyimod02_archive
[17120] LOADER: callfunction returned...
[17120] LOADER: extracted pyimod03_importers
[17120] LOADER: callfunction returned...
[17120] LOADER: Installing PYZ archive with Python modules.
[17120] LOADER: PYZ archive: PYZ-00.pyz
[17120] LOADER: Running pyiboot01_bootstrap.py
[17120] LOADER: Running pyi_rth_multiprocessing.py
[17120] LOADER: Running pyi_rth_pkgres.py
[17120] LOADER: Running pyi_rth_win32comgenpy.py
[17120] LOADER: Running pyi_rth__tkinter.py
[17120] LOADER: Running pyi_rth_pyqt5.py
[17120] LOADER: Running pyi_rth_mplconfig.py
[17120] LOADER: Running pyi_rth_mpldata.py
[17120] LOADER: Running Test_SVD_pyinstaller.py
(15,) (15, 15) (15, 20)

** It terminates suddenly after this line and no error message is displayed

@bwoodsend
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bwoodsend commented Jul 21, 2020

I think I know what this is. The numpy hooks are missing a dll called libiomp5md which causes this crash with no error message on Conda numpy. Just to confirm this - If you run the following from cmd:

python -c "from ctypes.util import find_library; print(find_library('libiomp5md'))"

This should print a filename. Copy that file into you app (in the same folder as the .exe file). It should run then normally?


Edit: We seem to be referring to this answer a lot so it's worth elaborating. You can just copy and paste the file into your app as a proof of concept fix but the proper way to add it is using --add-binaries=C:\full\path\to\libiomp5md.dll;., or if you use the spec file you can avoid the hard-coded full path by letting ctypes find it for you:

from ctypes.util import find_library
...
a = Analysis(
    ...,
    binaries=[find_library("libiomp5md", ".")]
    ...
)

It's also worth pointing out that there are a long list of other DLLs which also aren't found. You tend not to get a crash for these because they come with a lot of standard developer tools e.g. git-bash for Windows. So your broken app, instead of crashing, finds these other copies of those DLLs and appears to work. But if you put that program on a machine which doesn't have git-bash or clang or various other tools it'll break. We've had no success fixing this as there are too many of these DLLs to track. The only way to avoid this issue is to not use conda, or failing that, install numpy with pip.

@bwoodsend bwoodsend self-assigned this Jul 21, 2020
@Jerburi
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Jerburi commented Jul 21, 2020

Hi,

I copied the binary as you said, and the program runs without a problem.

I will add this binary into the spec file of my original project and hopefully it will run all!

Thanks a lot!

@Jerburi Jerburi closed this as completed Jul 21, 2020
@bwoodsend bwoodsend mentioned this issue Jul 22, 2020
6 tasks
bwoodsend added a commit to bwoodsend/pyinstaller that referenced this issue Sep 14, 2020
Whilst I'm here also:

- Exclude numpy's testing and C/Fortran compiling code, and
  everything else it drags with it (namely scipy).
- Try to fix Conda support.
- Avoid dragging 400MB of unused MKL DLLs on Conda.

They're all closed due to our no-conda policy but, (for now) fixes
 pyinstaller#4935, pyinstaller#4968, pyinstaller#5075, pyinstaller#5082, pyinstaller#5019 and pyinstaller#5019. Although likely at
the expense of junk DLLs being dragged in.
bwoodsend added a commit to bwoodsend/pyinstaller that referenced this issue Sep 17, 2020
Whilst I'm here also:

- Exclude numpy's testing and C/Fortran compiling code, and
  everything else it drags with it (namely scipy).
- Try to fix Conda support.
- Avoid dragging 400MB of unused MKL DLLs on Conda.

They're all closed due to our no-conda policy but, (for now) fixes
 pyinstaller#4935, pyinstaller#4968, pyinstaller#5075, pyinstaller#5082, pyinstaller#5019 and pyinstaller#5019. Although likely at
the expense of junk DLLs being dragged in.
@caro314
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caro314 commented Jul 1, 2022

Hi,
I experience something similar, like program silently crashes within savefig without any error message printed. This happens only when running the .exe (tried both, clicking it in the explorer and running from terminal- yes, also in the correct venv).

I am not using conda, I am using venv on windows10.

When I pass the line mentioned above to hit the dll file, I would receive "None".

Do you have any other suggestions where this error arises from? I was able to combine numpy, conda and savefig in another application a year ago.

Bests, Cati

@bwoodsend
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Open a new issue then. If you're not using conda then your issue isn't this issue.

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