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Create an executable from Python code with gmsh import

I'm trying to package up my Python package into an executable using pyinstaller. The script name is called "run-jointbuilder.py" The package has a number of dependancies (such as numpy), but importantly gmsh.
When using pyinstaller to compile my code, it appears to be successful, but then when I try to run the executable I get the following errors:
import gmsh # PyInstaller PYZ\
import ctypes.util # PyInstaller PYZ\
import 'ctypes.util' # <pyimod03_importers.FrozenImporter object at 0x000001BD783FC910>\
Traceback (most recent call last):\
File "PyInstaller\loader\pyiboot01_bootstrap.py", line 144, in __init__
File "ctypes\__init__.py", line 381, in __init__\
FileNotFoundError: Could not find module 'C:\Users\willber\Anaconda3\Scripts\gmsh' (or one of its dependencies). Try using the full path with constructor syntax.
I then get this error:
__main__.PyInstallerImportError: Failed to load dynlib/dll
'C:\\Users\\willber\\Anaconda3\\Scripts\\gmsh'. Most probably this dynlib/dll was not found when the application was frozen.
[18612] Failed to execute script run-jointbuilder
Has anybody tried to compile some Python code that imports the gmsh package? I'd really appreciate an example .spec file, for use with pyinstaller if so!

The gmsh python package wraps a bunch of compiled libraries which contain the implementations of the methods you call from python. When you import gmsh.py into your script then gmsh loads these libraries in the background giving you access to their functionality through python methods. So it's essential that these libraries are embedded in the pyinstaller output for your code to function as it does when you run it directly through the python interpreter.
It's difficult for pyinstaller to consistently find these libraries since they're not accessed in the same way as normal python imports, they are loaded using the cytpes package. There's some description of how pyinstaller does this in the docs. Since you're seeing a dynlib/dll loading error when you run the compiled python script, this suggests that pyinstaller isn't finding the gmsh library during compile and hence it is missing from the executable.
If you look in the gmsh.py source, you can see that gmsh.py loads up a .dll library called gmsh-4.9.dll for Windows OS. You can use the binaries input of the pyinstaller .spec file to point the compiler to the gmsh-4.9.dll.
Here's an example .spec file which dynamically locates the gmsh-4.9.dll at the time of compile so it picks up the right .dll for your active environment. You could make this more generic by filtering all *.dll in the gmsh directory, but I've hardcoded for clarity:
# -*- mode: python ; coding: utf-8 -*-
from pathlib import Path
import gmsh
# get the location of the gmsh dll which sits next to the gmsh.py file
libname = 'gmsh-4.9.dll'
libpath = Path(gmsh.__file__).parent / libname
print('Adding {} to binaries'.format(libpath))
block_cipher = None
a = Analysis(['gmsh-test.py'],
pathex=['C:\\Users\\user\\dev\\gmsh'],
# tell pyinstaller to add the binary to the compiled path
binaries=[(str(libpath), '.')],
datas=[],
hiddenimports=[],
hookspath=[],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher,
noarchive=False)
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
a.binaries,
a.zipfiles,
a.datas,
name='gmsh-test',
debug=False,
bootloader_ignore_signals=False,
strip=False,
upx=True,
console=True,
runtime_tmpdir=None,
)

How do I resolve a missing utility module preventing my executable from running when I already installed the parent module?

I've written a few Python scripts to create a tkinter GUI for a machine learning algorithm process. I originally coded everything in PyCharm, but I'd really like to put everything together into a stand-alone executable. I've moved my main script and its .py dependencies into their own directory and tested it out using the Command Prompt, and it works great. However, when I run pyinstaller, the executable is created but fails on startup.
The program is made up of three files, with GUI.py being the main script. As mentioned above, I moved the dependent files into a new directory and tested GUI.py in the Command Prompt, and it worked great. Executable is created (albeit with a lot of warnings about missing 'api-ms-win-crt' files) but can't be run.
I created the executable using the command:
pyinstaller --onefile GUI.py
When the executable is run from the command line after creation, I get a big long traceback ending in the following:
File "site-packages\sklearn\metrics\pairwise.py", line 32, in <module>
File "sklearn\metrics\pairwise_fast.pyx", line 1, in init
sklearn.metrics.pairwise_fast
ModuleNotFoundError: No module named 'sklearn.utils._cython_blas'
[3372] Failed to execute script GUI
I know I've already explicitly imported sklearn through the command prompt, but from the traceback, it seems I'm missing a utility module somewhere. I tried to import the missing module specifically, but I got an error that no distributed module was available.
I don't have much experience with pyinstaller, and I have no idea where to go from here. I'm using Windows 10 and Python 3.7.3.

It seems that Pyinstaller can't resolve sklearn import. So one easy way is to just bring the whole module directory which located in <path_to_python>/Lib/site-packages/sklearn/ with executable output. So use below spec file to generate your executable:
# -*- mode: python -*-
block_cipher = None
a = Analysis(['test.py'],
pathex=['<path to root of your project>'],
binaries=[],
datas=[],
hiddenimports=[],
hookspath=[],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher,
noarchive=False)
a.datas += Tree('<path_to_sklearn_in_python_dir>', prefix='sklearn')
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
a.binaries,
a.zipfiles,
a.datas,
[],
name='test',
debug=False,
bootloader_ignore_signals=False,
strip=False,
upx=False,
runtime_tmpdir=None,
console=True )
Finally generate your executable with
pyinstaller test.spec
This should resolve import errors for sklearn but if you face other NotFound imports add them like above to spec file.

Building up on M.R.'s answer, you can directly include the path to sklearn in your original pyinstaller command:
pyinstaller --onefile GUI.py --add-data "<path-to-python>\Lib\site-packages\sklearn;sklearn"
which results in the following line of code being added inside a = Analysis() in the automatically-generated GUI.spec file:
datas=[('<path-to-python>\\Lib\\site-packages\\sklearn', 'sklearn')]
Note that the --onefile option will result in an executable that is slower to start up than the default one-folder bundle (based on both the pyinstaller documentation and my own experience bundling up sklearn):
pyinstaller GUI.py --add-data "<path-to-python>\Lib\site-packages\sklearn;sklearn"

Pyinstaller exe conversion fail - using lightgbm and sklearn

I am trying to convert my code into an exe using pyinstaller spec. Pyinstaller initially failed with the following reason:
main__.PyInstallerImportError: Failed to load dynlib/dll
'C:\\Users\\...\\lightgbm\\../compile\\lib_lightgbm.dll'. Most probably this
dynlib/dll was not found when the application was frozen.
I tried to correct it by adding the following line to my pathex list in the spec:
'myenv\\lib\\site-packages\\lightgbm'
Note: myenv is my virtualenv created for this project.
Which led to ImportError for sklearn. I added sklearn to hidden imports. This is my final spec fie:
# -*- mode: python -*-
import sys
sys.setrecursionlimit(5000)
block_cipher = None
a = Analysis(['myscript.py'],
pathex=['C:\\project_folder', 'myenv\\lib\\site-packages\\lightgbm'],
binaries=[],
datas=[('lib_lightgbm.dll', '.')],
hiddenimports=['cython', 'sklearn', 'sklearn.feature_extraction','sklearn.pipeline', 'sklearn.ensemble', 'sklearn.neighbors.typedefs', 'sklearn.neighbors.quad_tree', 'sklearn.tree._utils'],
hookspath=[],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher,
noarchive=False)
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
[],
exclude_binaries=True,
name='myscript',
debug=False,
bootloader_ignore_signals=False,
strip=False,
upx=True,
console=True )
coll = COLLECT(exe,
a.binaries,
a.zipfiles,
a.datas,
strip=False,
upx=True,
name='myscript')
This leads to an error I find very weird:
File "myenv\lib\site-packages\lightgbm\sklearn.py", line 9, in <module>
ImportError: attempted relative import with no known parent package
[12692] Failed to execute script myscript
I have no idea why it would be searching for sklearn.py inside lightgbm?
There is sklearn.py inside lightgbm, but I am not sure how to fix this error. Also, there is no sklearn folder in the dist/myscript folder. Ideally it should have been present. I tried to manually copy the sklearn folder, although, as suspected, it made no difference. Could someone please let me know where the spec file is wrong?

Let's go back to the first error you had. That error suggests lib_lightgbm.dll was not seen when your application was frozen.
Assuming you run pyinstaller from Windows cmd.exe, you can fix this by passing a hook for lightgbm to pyinstaller, so that it knows where to get it from, e.g.
pyinstaller --additional-hooks-dir dir_with_lightgbm_hook --hidden-import lightgbm myscript.py
The name of the hook should be hook-lightgbm.py and for its contents, you can look here: https://github.com/pyinstaller/pyinstaller/blob/develop/PyInstaller/hooks/hook-numpy.py , it should be something similar. Just make sure that the library is added to the binaries list, i.e.
binaries.append((os.path.join(os.path.dirname(
get_module_file_attribute('lightgbm')), "lib_lightgbm.dll"), "lightgbm"))
The second "lightgbm" argument is the location where the .dll will be copied, relative to your distribution directory, so in your case it should end up as dist\myscript\lightgbm\lib_lightgbm.dll.
Note: Adding lib_lightgbm.dll through a hook will make pyinstaller add the dependencies for it to the distribution, so it is better to do it like this than just copying it manually.
Second note: When copying your distribution package to another machine, you might need to install the appropriate Visual Studio redistributable used by the library (e.g. VS 2015 redistributable).
EDIT: Forgot to mention that if you do it like this, you can remove the path you added to your pathex.

PyInstaller: cannot exclude a module

I have compiled the exe of a .py file but the problem is that it is 200mb+
I would like to remove useless packages (for instance scipy that I am not using).
Still I have not clear the proper syntax of PyInstaller.
Let's start from the beginning...usually I do on cmd:
cd myFolder
C:\Python27\Scripts\Pyinstaller.exe MyFile.py
and it gives me the exe file in the dist folder.
If I want to set some configuration which is the proper way?
C:\Python27\Scripts\Pyinstaller.exe MyFile.py Config.py
or
C:\Python27\Scripts\Pyinstaller.exe Config.py
because online I found both of them but I could not distinguish.
If it is the last one I tried to run:
lock_cipher = None
a = Analysis(['Main.py'],
pathex=['C:\Users\myname\Desktop\myFolder'],
binaries=None,
datas=None,
hiddenimports=[],
hookspath=None,
runtime_hooks=None,
excludes=None,
cipher=block_cipher)
a.binaries = [x for x in a.binaries if not x[0].startswith("scipy")]
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz)
coll = COLLECT(exe)
But it does not work. Where am I wrong?

My suggestion is that you use a virtual env containing only the required modules. It is a better development practice.
Also, you can use --exclude-module flag to list all the modules you want to exclude. (Pyinstaller automatically includes unneeded modules)

How to compile python script to binary executable

I need to convert a Python script to a Windows executable.
I have Python 2.6 installed to python26.
I have created one script and kept it in C:\pythonscript. Inside this folder there are two files
Setup.py and oldlogs.py (this file need coversion)
setup.py code is
from distutils.core import setup
import py2exe
setup(console=['oldlogs.py'])
How can I convert oldlogs.py to an exe file?

Or use PyInstaller as an alternative to py2exe. Here is a good starting point. PyInstaller also lets you create executables for linux and mac...
Here is how one could fairly easily use PyInstaller to solve the issue at hand:
pyinstaller oldlogs.py
From the tool's documentation:
PyInstaller analyzes myscript.py and:
Writes myscript.spec in the same folder as the script.
Creates a folder build in the same folder as the script if it does not exist.
Writes some log files and working files in the build folder.
Creates a folder dist in the same folder as the script if it does not exist.
Writes the myscript executable folder in the dist folder.
In the dist folder you find the bundled app you distribute to your users.

I recommend PyInstaller, a simple python script can be converted to an exe with the following commands:
utils/Makespec.py [--onefile] oldlogs.py
which creates a yourprogram.spec file which is a configuration for building the final exe. Next command builds the exe from the configuration file:
utils/Build.py oldlogs.spec
More can be found here

Since other SO answers link to this question it's worth noting that there is another option now in PyOxidizer.
It's a rust utility which works in some of the same ways as pyinstaller, however has some additional features detailed here, to summarize the key ones:
Single binary of all packages by default with the ability to do a zero-copy load of modules into memory, vs pyinstaller extracting them to a temporary directory when using onefile mode
Ability to produce a static linked binary
(One other advantage of pyoxidizer is that it does not seem to suffer from the GLIBC_X.XX not found problem that can crop up with pyinstaller if you've created your binary on a system that has a glibc version newer than the target system).
Overall pyinstaller is much simpler to use than PyOxidizer, which often requires some complexity in the configuration file, and it's less Pythony since it's written in Rust and uses a configuration file format not very familiar in the Python world, but PyOxidizer does some more advanced stuff, especially if you are looking to produce single binaries (which is not pyinstaller's default).

# -*- mode: python -*-
block_cipher = None
a = Analysis(['SCRIPT.py'],
pathex=[
'folder path',
'C:\\Windows\\WinSxS\\x86_microsoft-windows-m..namespace-downlevel_31bf3856ad364e35_10.0.17134.1_none_50c6cb8431e7428f',
'C:\\Windows\\WinSxS\\x86_microsoft-windows-m..namespace-downlevel_31bf3856ad364e35_10.0.17134.1_none_c4f50889467f081d'
],
binaries=[(''C:\\Users\\chromedriver.exe'')],
datas=[],
hiddenimports=[],
hookspath=[],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher)
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
a.binaries,
a.zipfiles,
a.datas,
name='NAME OF YOUR EXE',
debug=False,
strip=False,
upx=True,
runtime_tmpdir=None,
console=True )