try/except works in pycharm but doesn't work in exe after compiling using pyinstaller

Question

Test code:

## file name: test.py
import scanpy as sc
print(sc.__version__)

Then install scanpy using pip

pip install scanpy==1.8.2
pip install pyinstaller==4.7

I generated the exe file using the command line below:

python -m PyInstaller --noupx test.py

I then tried to run test.exe . I got the error message:

Traceback (most recent call last):
  File "scanpy\_metadata.py", line 28, in <module>
  File "pathlib.py", line 1221, in read_text
  File "pathlib.py", line 1208, in open
  File "pathlib.py", line 1063, in _opener
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\xie186\\PycharmProjects\\pitaya\\test_exe\\dist\\test\\pyproject.toml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "test.py", line 1, in <module>
  File "PyInstaller\loader\pyimod03_importers.py", line 476, in exec_module
  File "scanpy\__init__.py", line 3, in <module>
  File "PyInstaller\loader\pyimod03_importers.py", line 476, in exec_module
  File "scanpy\_metadata.py", line 38, in <module>
  File "scanpy\_compat.py", line 25, in pkg_metadata
  File "importlib_metadata\__init__.py", line 984, in metadata
  File "importlib_metadata\__init__.py", line 561, in from_name
importlib_metadata.PackageNotFoundError: No package metadata was found for scanpy
[20028] Failed to execute script 'test' due to unhandled exception!

But when I run this script in pycharm, it works fine. I checked the code related to this error: https://github.com/theislab/scanpy/blob/16e62d1336a95966238113cdb5ab50f7d9f880ce/scanpy/_metadata.py#L24

In pycharm, the try part will fail and the code in except part will be executed. But in the exe file, it seems that the app will exit after the try part fails.

Any help will be appreciated!

Answer 1

Adding --recursive-copy-metadata scanpy solved my problem:

python -m PyInstaller --recursive-copy-metadata scanpy --noupx ..\test.py