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| bash -c 'if [ "$TRAVIS" = "true" ] ; then python-codacy-coverage -r coverage.xml; fi' | ||
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| # This is only the case when the pull request is run from the ephemeris repo. So this is checked. | ||
| bash -c 'if [ "$TRAVIS" = "true" ] && [ "$TRAVIS_REPO_SLUG" = "galaxyproject/ephemeris" ] ; then python-codacy-coverage -r coverage.xml; fi' |
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I think this belongs in the deploy stage of the travis.yml. We shouldn't adapt our testing to travis, we should adapt travis to our testing. Same with the sed command.
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👍 will change this.
Also there is some problems with codacy coverage still... Working on it.
EDIT: By the way:
I can only get the envsitepackagesdir inside tox. So I have to run sed inside tox unfortunately.
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| import pytest | ||
| import yaml | ||
| from docker_for_galaxy import start_container |
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You can add # noqa: F401 at the end of this line and drop lines 17 and 18
from docker_for_galaxy import start_container # noqa: F401
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need the two spaces before the comment as usual, github formatting strips this here
| bash | ||
| commands = | ||
| pytest --cov={envsitepackagesdir}/ephemeris --cov-report xml {[tox]test_dir} | ||
| pytest -v --cov={envsitepackagesdir}/ephemeris --cov-report xml {[tox]test_dir} |
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wouldn't this work ?
pytest -v --cov src --cov-report xml
it does work locally for me, and I think you won't have to sed the xml file
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Does it work in a tox environment? Because when I tried that in a tox environment it did not work.
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it seems to:
$ tox -e py36-pytest
GLOB sdist-make: /Users/mvandenb/src/ephemeris/setup.py
py36-pytest create: /Users/mvandenb/src/ephemeris/.tox/py36-pytest
py36-pytest installdeps: -rrequirements.txt, pytest, pytest-cov, coverage, codacy-coverage, docker
py36-pytest inst: /Users/mvandenb/src/ephemeris/.tox/dist/ephemeris-0.9.1.dev0.zip
py36-pytest installed: atomicwrites==1.1.5,attrs==18.1.0,bioblend==0.11.0,boto==2.49.0,certifi==2018.8.13,chardet==3.0.4,codacy-coverage==1.3.11,coverage==4.5.1,docker==3.5.0,docker-pycreds==0.3.0,docutils==0.14,ephemeris==0.9.1.dev0,galaxy-lib==18.5.13,idna==2.7,Jinja2==2.10,MarkupSafe==1.0,more-itertools==4.3.0,packaging==17.1,pluggy==0.7.1,py==1.5.4,pyparsing==2.2.0,pytest==3.7.2,pytest-cov==2.5.1,PyYAML==3.13,requests==2.19.1,requests-toolbelt==0.8.0,six==1.11.0,urllib3==1.23,websocket-client==0.51.0
py36-pytest runtests: PYTHONHASHSEED='1055593875'
py36-pytest runtests: commands[0] | pytest -v --cov=ephemeris --cov-report xml
========================================================================== test session starts ===========================================================================
platform darwin -- Python 3.6.5, pytest-3.7.2, py-1.5.4, pluggy-0.7.1 -- /Users/mvandenb/src/ephemeris/.tox/py36-pytest/bin/python3.6
cachedir: .pytest_cache
rootdir: /Users/mvandenb/src/ephemeris, inifile:
plugins: cov-2.5.1
collected 7 items
tests/test_run_data_managers.py::TestRunDataManagers::test_install_data_managers PASSED [ 14%]
tests/test_run_data_managers.py::TestRunDataManagers::test_run_data_managers
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I take that back:
ERROR: Failed to generate report: No data to report.
ERROR: InvocationError for command '/Users/mvandenb/src/ephemeris/.tox/py36-pytest/bin/pytest -v --cov=ephemeris --cov-report xml' (exited with code 4)
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@mvdbeek are all issues solved satisfactorily? |
2 participants
Added the code to log a stderr when a data manager job is failing.
I also ported run-data-managers to the new pytest framework. So this extra logging stuff is also tested.
This should fix #107 .
After a lot of trail and error due to various issues, codacy and coverage should work on this branch.