Cannot run test cases: ModuleNotFoundError

[robmoss]

Hi @m-d-grunnill

I cannot run the test cases because they contain import statements that refer to src.metacast, and while src/ is a directory it isn't a valid Python module:

$ python3 tests/test_event_que.py 
Traceback (most recent call last):
  File "/home/.../MetaCast/tests/test_event_que.py", line 9, in <module>
    from src.metacast import MetaCaster
ModuleNotFoundError: No module named 'src'

If I replace src.metacast with metacast, I can run all of the test cases in a virtual environment where I have installed MetaCast, and they all succeed.

Creating a virtual environment (e.g., in ./venv) and installing MetaCast is relatively straightforward, and the following could be saved as a shell script (e.g., run_tests.sh):

$ python3 -m venv ./venv
$ . venv/bin/activate
$ pip install .
$ for test_file in tests/test_*.py; do python3 "${test_file}"; done
....
----------------------------------------------------------------------
Ran 4 tests in 0.553s

OK
.
----------------------------------------------------------------------
Ran 1 test in 0.000s

OK
                                                                                              .
----------------------------------------------------------------------                         
Ran 1 test in 0.960s

OK
........
----------------------------------------------------------------------
Ran 8 tests in 0.259s

OK

NOTE: In the rest of this comment, I provide a suggestion about how to automate the test cases. I do not expect you to implement this kind of automation as a necessary step in the JOSS review process. This is just a suggestion for your consideration, entirely independent of my comments for the JOSS review.

Alternatively, you could consider using an automation tool. For example, I use nox for running test cases, building and publishing online documentation, running code checks, etc. To run the MetaCast test cases with nox, you can create a file called noxfile.py with the following content:

import nox
import pathlib

@nox.session(reuse_venv=True)
def tests(session):
    """Run test cases."""
    session.install('.')
    test_dir = pathlib.Path('tests')
    for test_file in test_dir.glob('test_*.py'):
        session.run('python3', test_file)

If you install nox, you can then run it from the root of the repository to run the test cases:

$ nox
nox > Running session tests
nox > Creating virtual environment (virtualenv) using python3 in .nox/tests
nox > python -m pip install .
nox > python3 tests/test_event_que.py
....
----------------------------------------------------------------------
Ran 4 tests in 0.610s

OK
nox > python3 tests/test_metacaster.py
........
----------------------------------------------------------------------
Ran 8 tests in 0.263s

OK
nox > python3 tests/test_lhs_and_prcc.py
                                                                                              .
----------------------------------------------------------------------                         
Ran 1 test in 1.014s

OK
nox > python3 tests/test_infection_seeding.py
.
----------------------------------------------------------------------
Ran 1 test in 0.000s

OK
nox > Session tests was successful.

You could then add a GitHub workflow that installs Python, then installs and runs nox.

[m-d-grunnill]

Thanks for these suggestions. The nox file with github workflow ha been incorporated too.

[robmoss]

Oh, nice use of a matrix to run the tests against different Python versions!