test suite generates untracked files

tkonopka commented 1 year ago

Describe the bug

Running make test creates untracked files in the repository root, which is unexpected.

.coverage
data.pickle
test_hap1.vcf
test_hap2.vcf
test_ref.fasta

Logging

NA

Environment (if you do not have a GPU, write No GPU):

Installation method: from github source
OS: Ubuntu 20.04
medaka version: 1.6.1
GPU model: No GPU
Nvidia driver version: 10.1

Additional context

Would it be alright to include .coverage in .gitignore?

As far as I can tell, the other files are not needed to run the test suite, and it would be strange if they were needed elsewhere. Would it be alright to remove these?

I can prepare a PR with these changes if you agree.

cjw85 commented 1 year ago

@mwykes Would be good to track from which tests these are coming and make sure they are being written to a proper tempdir.

cjw85 commented 10 months ago

I have fixed this on our development branch.

nanoporetech / medaka

test suite generates untracked files #378