Some suggetions:

1.) Just accept it and modify sys.path ;-)

2.) make sure the environment variable PYTHONPATH points to the parent directory (be) and call your script only then

Example:

export PYTHONPATH=/absolute/path/to/be

3.) add an __init__.py file into the directory alembic and call your script from the be direcrory with. python -m alembic.env

4.) add the __init__.py like for 3.) and a small wrapper script to the be directory and call that script from be this script will then import alembic.env and call it's 'main' function.

Don't hesitate to contact me if my suggestions aren't clear enough.

I don't know your context but I often prefer 3.) and 4.) as nobody has to know about environment variables or sys path changes.

You must add the application dir to your path:

import sys
sys.path.append("/path/to/dir")
from app import object

Or from shell:

setenv PYTHONPATH $PYTHONPATH:"path/to/dir"

In case you use Windows: Adding variable to path in Windows.

Or from the command line:

set PYTHONPATH=%PYTHONPATH%;C:\path\to\dir

I posted a similar answer also to the question regarding imports from sibling packages. You can see it here.

Solution without sys.path hacks

Summary

• Wrap the code into one folder (e.g. packaged_stuff)
• Create a pyproject.toml (older alternative: setup.py)
• Pip install the package in editable state with pip install -e <myproject_folder>
• Import using from packaged_stuff.modulename import function_name

Setup

I assume the same folder structure as in the question

.
└── ptdraft
    ├── __init__.py
    ├── nib.py
    └── simulations
        ├── __init__.py
        └── life
            ├── __init__.py
            └── life.py

I call the . the root folder, and in my case it is located in C:\tmp\test_imports.

Steps

1) Add a pyproject.toml to the root folder

The contents of the pyproject.toml can be simply

[project]
name = "ptdraft"
version = "0.1.0"
description = "My small project"

[build-system]
build-backend = "flit_core.buildapi"
requires = ["flit_core >=3.2,<4"]

Basically "any" valid pyproject.toml would work. This is just a minimal working example, which uses flit as build backend.

2) Use a virtual environment

If you are familiar with virtual environments, activate one, and skip to the next step. Usage of virtual environments are not absolutely required, but they will really help you out in the long run (when you have more than 1 project ongoing..). The most basic steps are (run in the root folder)

• Create virtual env
  • python -m venv venv
• Activate virtual env
  • . venv/bin/activate (Linux) or ./venv/Scripts/activate (Win)
• Deactivate virtual env
  • deactivate (Linux)

To learn more about this, just Google out "python virtualenv tutorial" or similar. You probably never need any other commands than creating, activating and deactivating.

Once you have made and activated a virtual environment, your console should give the name of the virtual environment in parenthesis

PS C:\tmp\test_imports> python -m venv venv
PS C:\tmp\test_imports> .\venv\Scripts\activate
(venv) PS C:\tmp\test_imports>

3) pip install your project in editable state

Install your top level package (here ptdraft) using pip. The trick is to use the -e flag when doing the install. This way it is installed in an editable state, and all the edits made to the .py files will be automatically included in the installed package. Note that the -e flag with pyproject.toml requires pip 21.3 or newer.

In the root directory, run

pip install -e . (note the dot, it stands for "current directory")

You can also see that it is installed by using pip freeze

(venv) PS C:\tmp\test_imports> pip install -e .
Obtaining file:///home/user/projects/ptdraft
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
....
Successfully built ptdraft
Installing collected packages: ptdraft
Successfully installed ptdraft-0.1.0
(venv) PS C:\tmp\test_imports> pip freeze
ptdraft==0.1.0

4) Import by prepending mainfolder to every import

In this example, the mainfolder would be ptdraft. This has the advantage that you will not run into name collisions with other module names (from python standard library or 3rd party modules).

Example Usage

nib.py

def function_from_nib():
    print('I am the return value from function_from_nib!')

life.py

from ptdraft.nib import function_from_nib

if __name__ == '__main__':
    function_from_nib()

Running life.py

(venv) PS C:\tmp\test_imports> python .\ptdraft\simulations\life\life.py
I am the return value from function_from_nib!