I’ve created a flask executable using pyinstaller. The app has to read and write to a SQLite3 database. I am using flask-sqlalchemy and flask-migrate, flaskwebgui for opening in browser. The executable is unable to read the database.

Details:
Using the following spec file to create a standalone exe file

# -*- mode: python ; coding: utf-8 -*-

added_files = [
    ('main/templates/', 'templates'),
    ('main/static/', 'static')  
]

a = Analysis(
    ['run.py'],
    pathex=[],
    binaries=[],
    datas=added_files,
    hiddenimports=[],
    hookspath=[],
    hooksconfig={},
    runtime_hooks=[],
    excludes=[],
    noarchive=False,
    optimize=0,
)
pyz = PYZ(a.pure)

exe = EXE(
    pyz,
    a.scripts,
    a.binaries,
    a.datas,
    [],
    name='run',
    debug=False,
    bootloader_ignore_signals=False,
    strip=False,
    upx=True,
    upx_exclude=[],
    runtime_tmpdir=None,
    console=False,
    disable_windowed_traceback=False,
    argv_emulation=False,
    target_arch=None,
    codesign_identity=None,
    entitlements_file=None,
)

• The resulting /dist folder has an executable called run.exe. I am able to run the exe which opens a browser window (using Flaskwebgui) and the index page loads normally but as soon as I try to open ‘all loans’ view it gives error
  sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: loan.
• The flask app is able to read/write to the database when run normally (command line) but it give error when running from the executable.
• In the root directory, the database file called loansdb is stored inside /instance directory which was created by flask-migrate.
• folder structure (overview only, not exact)

project/
  |- main/
    |- routes.py
    |- __init__.py
    |- models.py
    |- templates/
       |- index.html
    |- static/
       |- style.css
  |- dist/
    |- run.exe
    |- logs/
  |- instance/
    |- loansdb

• The app reads the environment variables for the DATABASE_URL and I have verified that the executable is also able to read the environment variables.
• I put the loansdb file in the /dist folder like:

project
   |- dist
     |- run.exe
     |- loansdb

but it did not fix the problem.

• Similar to the above method, I put the whole /instance folder inside /dist but that also had no effect.
• I read up on this article talking about copying the temp files into the application’s directory but neither do I understand half of it and nor does it work.

Expected Behavior

• My understanding is that the database cannot be a part of the executable because that will make the database read-only because it runs in a ‘frozen’ state, which is not desired in this case.
• Being able to ship the program as a zip with the executable, database and other files such as a manual/readme would be most optimal for my use case.
• I am fairly new to flask and sqlalchemy and I would appreciate any alternative approach as well.