Recursively git ignore .log files

[dandye]

Description of proposed changes

Recursively git ignore all *.log files (update: those created by bash run_tests.sh now cleaned up since #703)

Although #703 cleans up the .log files created by unit tests, this approach future proofs (assuming future .log files aren't desired in src tree).

Related issue(s)

Fixes #700

Testing

Steps taken to test the proposed changes:

Execute run_tests.sh:

(nextstrain)  ddye@cornix  ~/Projects/nextstrain/augur   git_ignore_run_tests_logs  bash run_tests.sh
Running unit tests and doctests with pytest
================================================================================================= test session starts ==================================================================================================
platform darwin -- Python 3.9.2, pytest-5.4.3, py-1.10.0, pluggy-0.13.1 -- /usr/local/opt/[email protected]/bin/python3.9
cachedir: .pytest_cache
rootdir: /Users/ddye/Projects/nextstrain/augur, inifile: pytest.python3.ini, testpaths: augur/, tests/
plugins: mock-2.0.0, cov-2.8.1
collected 241 items

augur/align.py::augur.align.strip_non_reference PASSED
...

Verify the .log files no longer dirty git:

(nextstrain)  ✘ ddye@cornix  ~/Projects/nextstrain/augur   git_ignore_run_tests_logs  git status
On branch git_ignore_run_tests_logs
Untracked files:
  (use "git add <file>..." to include in what will be committed)
	alignment.fasta.to_align.fasta

nothing added to commit but untracked files present (use "git add" to track)

[huddlej]

Thank you for taking the time to prepare and submit this PR, @dandye! Ignoring *.log files seems like a good idea generally, but I've opted for a solution in #703 that removes the log files after they get created. This way we avoid the unnecessary files completely instead of ignoring them.

If you'd like to revise this PR to ignore all log files, we could definitely merge that.

If you're interested in contributing more to Augur, check out the other open issues and leave a comment on any issue(s) you'd like to tackle.

[dandye]

Thank you for taking the time to prepare and submit this PR, @dandye! Ignoring *.log files seems like a good idea generally, but I've opted for a solution in #703 that removes the log files after they get created. This way we avoid the unnecessary files completely instead of ignoring them.

If you'd like to revise this PR to ignore all log files, we could definitely merge that.

If you're interested in contributing more to Augur, check out the other open issues and leave a comment on any issue(s) you'd like to tackle.

Thank you for the nice welcome message!

At your suggestion, I've pushed an update to recursively git ignore all log files, which I believe obviates the .gitignore entry for "slurm logs" (which I've deleted).

[huddlej]

Great! Thanks, @dandye!