More tests for align.py

[groutr]

Description of proposed changes

Increase test coverage for align.py.

This PR also adds an __init__.py to the tests directory so that the augur doesn't have to be installed to run the tests. This may, or may not, be desired. Open to feedback.

Related issue(s)

Related to #476

[elebow]

I'm not sure it's necessary to have a __init__.py in tests/, regardless of whether augur is available in the path.

I don't have augur in my path (or installed on my system at all), and the tests run correctly through pytest. Installing augur with pip doesn't seem to affect that.

[elebow]

It should be safe to assume that the current working directory during test execution is the root of the project, so test fixtures can be referred to by simple strings like "test/data/align/test_aligned_sequences.fasta".

[groutr]

Ok. I like that better.

[groutr]

@elebow I'm going to write it off as a quirk in my original dev environment. I created a new one and can't seem to reproduce the issue I was having.
(see comment below)

Reverting the __init__.py commit.

[groutr]

@elebow That comment was premature. Removing __init__.py triggered the issue I was having. Without it, pytest fails with an import error for augur.

~/projects/augur align_tests*
(augur-dev) ❯ pytest tests/
========================================================================= test session starts =========================================================================
platform linux -- Python 3.7.6, pytest-5.4.1, py-1.8.1, pluggy-0.12.0
rootdir: /home/grout/projects/augur
plugins: cov-2.8.1
collected 16 items / 1 error / 15 selected                                                                                                                            

=============================================================================== ERRORS ================================================================================
________________________________________________________________ ERROR collecting tests/test_align.py _________________________________________________________________
ImportError while importing test module '/home/grout/projects/augur/tests/test_align.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_align.py:8: in <module>
    from augur import align
E   ModuleNotFoundError: No module named 'augur'

[elebow]

@groutr See https://docs.pytest.org/en/latest/usage.html#calling-pytest-through-python-m-pytest. Pytest behaves differently depending on whether it is invoked as pytest or python -m pytest—The second one automatically adds the current directory to the path.

I personally prefer to use a helper script, like run_tests.sh.

[groutr]

@elebow, oops, I didn't see the run_tests.sh. Force of habit had me calling pytests directly.

[huddlej]

Thank you, @groutr! These tests look good to me.

Would you mind rebasing these 5 commits into a single commit with a clear description of the tests you've added? That will make the final merge cleaner on our end.

[groutr]

@huddlej, I'll do this first thing Monday morning.