I found the solution to my issue, which I believe was a misunderstanding of PEP 420 -- Implicit Namespace Packages.

This page states that, since Python 3.3:

While looking for a module or package named "foo", for each directory in the parent path:

• If <directory>/foo/__init__.py is found, a regular package is imported and returned.
• If not, but <directory>/foo is found and is a directory, it is recorded and the scan continues with the next directory in the parent path.

If the scan completes without returning a module or package, and at least one directory was recorded, then a namespace package is created. The new namespace package:

• Has a __path__ attribute set to an iterable of the path strings that were found and recorded during the scan.
• Does not have a __file__ attribute.

As defined in the pkg_resources documentation:

A namespace package is a package that only contains other packages and modules, with no direct contents of its own.

My package, as I described it, fell into that category, which was not intended.

After adding an empty __init.py__ below the myProject/ directory I see this happening during the install step:

❯ python setup.py build    
running build
running build_py
creating build/lib
creating build/lib/myProject
copying myProject/__init__.py -> build/lib/myProject
copying myProject/cli.py -> build/lib/myProject

Before:

>>> myProject.__path__
_NamespacePath(['/path/myProject'])
>>> myProject.__file__
AttributeError: module 'myProject' has no attribute '__file__'

After:

>>> myProject.__path__
['/path/myProject']
>>> myProject.__file__
'/path/myProject/__init__.py'

This issue arises due to the ways in which the command line IPython interpreter uses your current path vs. the way a separate process does (be it an IPython notebook, external process, etc). IPython will look for modules to import that are not only found in your sys.path, but also on your current working directory. When starting an interpreter from the command line, the current directory you're operating in is the same one you started ipython in. If you run

import os
os.getcwd() 

you'll see this is true.

However, let's say you're using an ipython notebook, run os.getcwd() and your current working directory is instead the folder in which you told the notebook to operate from in your ipython_notebook_config.py file (typically using the c.NotebookManager.notebook_dir setting).

The solution is to provide the python interpreter with the path-to-your-module. The simplest solution is to append that path to your sys.path list. In your notebook, first try:

import sys
sys.path.append('my/path/to/module/folder')

import module_of_interest

If that doesn't work, you've got a different problem on your hands unrelated to path-to-import and you should provide more info about your problem.

The better (and more permanent) way to solve this is to set your PYTHONPATH, which provides the interpreter with additional directories look in for python packages/modules. Editing or setting the PYTHONPATH as a global var is os dependent, and is discussed in detail here for Unix or Windows.

I found the issue. I used setuptools.find_packages() in my setup.py and it turns out that method needs __init__.py files in packages and subpackages for them to be found. I thought this was no longer necessary in Python 3.3+ but apparently in some cases.

You have to install your python script, before you can call it via your defined entry point

This is my dummy project:

dnsrep/
├── dnsrep.py
└── setup.py

This is how setup.py looks like:

from setuptools import setup
setup(
    name='dnsrep',
    version='0.1',
    description='Program that gives a reputation score to url\'s\n.',
    py_modules=['dnsrep'],
    entry_points = {
        'console_scripts': ['dnsrep = dnsrep:main']
    },
    zip_safe=True,
)

Note the argument py_modules=['dnsrep'], which installs dnsrep.py as a new module.

Finally, this is my dummy implementation of dnsrep.py:

from __future__ import print_function

def main():
    print("Hey, it works!")

After installing, everything works as expected and $ dnsrep prints: Hey, it works!

Run python -m folder2.main instead. The difference is what directory gets added to Python's path (the list of directories it looks in for modules to import). When you run python folder2/main.py, it is folder2 that gets added to the path, meaning Python looks there for modules to import (in addition to all of the usual system directories). In contrast, when you run python -m folder2.main, it is folder1 that gets added to the path.

In general, you should always use the python -m ... form because it makes a lot of things import-related (especially relative imports) work more like you would expect them to.

If you want to see what's going on with the path, add this at the top of your main.py:

import sys
print(sys.path)

I just realised part of the answer:

in the case where the module executes everything at the top-level, i.e. on import, it's therefore ok to define a dummy "no-op" main function, like so:

# Content of mypkg/myscript.py

print("myscript being executed!")

def main():
    pass  # Do nothing!

This solution will still force me to add this line to the existing scripts, but I think it's a quick but cautious solution.

No solution if the code is under a if __name__=='__main__' though...

pip installs the scripts under ~/.local/bin. You need to add this to your PATH with:

export PATH=~/.local/bin:$PATH