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broadinstitute / viral-ngs

Viral genomics analysis pipelines
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problem with pytest.ini #315

Closed sbecuwe closed 8 years ago

sbecuwe commented 8 years ago

I'm trying to install viral-ngs 1.4.2, downloaded from the releases web page, following the instructions on readthedocs, but it seems there's a problem with the default pytest.ini. I'm using pytest 2.9.1.

$ py.test -v test/unit/test_tools.py
usage: py.test [options] [file_or_dir] [file_or_dir] [...]
py.test: error: unrecognized arguments: -n --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov reports --cov taxon_filter --cov tools --cov util test/unit/test_tools.py
  inifile: /dev/shm/viral-ngs-1.4.2/pytest.ini
  rootdir: /dev/shm/viral-ngs-1.4.2

Thanks for your feedback!

dpark01 commented 8 years ago

Hi, we just ran into this issue internally as well. For now, the fix is to pip install -r requirements-tests.txt as well. Beyond that though, @tomkinsc is working on a cleaner install process more generally.

dpark01 commented 8 years ago

Let me know if the above suggestion addresses your installation needs.

310 should obviate this