Poetry install of the package also installed old deprecated files...

Using poetry to install dynode in a venv, and then looking into the dynode package folder (e.g., inside .venv/lib/python3.10/site-packages/dynode, you will see a bunch of deprecated files also being installed:

-rw-r--r-- 1 tjk3 domain users 2.7K Dec  2 12:14 abstract_initializer.py
-rw-r--r-- 1 tjk3 domain users 3.3K Dec  2 12:14 _simulation_date.py
-rw-r--r-- 1 tjk3 domain users 3.4K Dec  2 12:14 __init__.py
-rw-r--r-- 1 tjk3 domain users  31K Dec  2 12:14 abstract_parameters.py
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 config
-rw-r--r-- 1 tjk3 domain users  28K Dec  2 12:14 dynode_runner.py
-rw-r--r-- 1 tjk3 domain users  19K Dec  2 12:14 covid_sero_initializer.py
-rw-r--r-- 1 tjk3 domain users  35K Dec  2 12:14 config.py
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 infer
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 logging
-rw-r--r-- 1 tjk3 domain users 4.7K Dec  2 12:14 mechanistic_runner.py
-rw-r--r-- 1 tjk3 domain users  20K Dec  2 12:14 mechanistic_inferer.py
drwxr-xr-x 3 tjk3 domain users 4.0K Dec  2 12:14 model_configuration
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 model_odes
-rw-r--r-- 1 tjk3 domain users 4.2K Dec  2 12:14 odes.py
-rw-r--r-- 1 tjk3 domain users    0 Dec  2 12:14 py.typed
-rw-r--r-- 1 tjk3 domain users  11K Dec  2 12:14 sample.py
-rw-r--r-- 1 tjk3 domain users 1.8K Dec  2 12:14 static_value_parameters.py
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 simulation
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 typing
-rw-r--r-- 1 tjk3 domain users 4.6K Dec  2 12:14 typing.py
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:14 utils
-rw-r--r-- 1 tjk3 domain users  61K Dec  2 12:14 utils.py
-rw-r--r-- 1 tjk3 domain users  25K Dec  2 12:14 vis_utils.py

However, if you use pip to install dynode into the venv, you only get these:

-rw-r--r-- 1 tjk3 domain users 3.4K Dec  2 12:11 __init__.py
-rw-r--r-- 1 tjk3 domain users    0 Dec  2 12:11 py.typed
drwxr-xr-x 3 tjk3 domain users 4.0K Dec  2 12:11 config
drwxr-xr-x 2 tjk3 domain users 4.0K Dec  2 12:11 __pycache__
drwxr-xr-x 3 tjk3 domain users 4.0K Dec  2 12:11 infer
drwxr-xr-x 3 tjk3 domain users 4.0K Dec  2 12:11 simulation
drwxr-xr-x 3 tjk3 domain users 4.0K Dec  2 12:11 typing
drwxr-xr-x 3 tjk3 domain users 4.0K Dec  2 12:11 utils

The poetry installation might cause some significant confusion since, e.g., we have both the utils submodule and the utils.py within the same folder...

Tagging @ElishaBayode @Nick-P-Adams for awareness...