Planemo 0.20.0 and xunit
Hi, I have recently upgraded to planemo 0.20.0 and I am getting an error that I cannot resolve: Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown. The output from the tool_test_output.json is empty {} I am using planemo t --install_galaxy I am a bit lost here, can anyone offer a suggestion please? I am afraid this might be too trivial... As a further note, I have this on the log: functional_tests.py: error: no such option: --with-nosehtml Many thanks, Tiago
Thanks for the bug report. Somehow Galaxy isn't installing the development wheels into the transient Galaxy's virtualenv, I've wiped out my planemo caches and I can't reproduce this locally. Can you send me the green log messages at the beginning of the test command as well as the few lines after them (maybe just paste the whole thing into a gist or something). For instance, the most relevant lines for me look like the following: cd /tmp/tmpMLxcOF; git clone --branch 'dev' '/home/john/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/john/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then type virtualenv >/dev/null 2>&1 && virtualenv $GALAXY_VIRTUAL_ENV; else echo "Reusing existing virtualenv $GALAXY_VIRTUAL_ENV"; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} Cloning into 'galaxy-dev'... done. Reusing existing virtualenv /home/john/.planemo/gx_venv Set COMMON_STARTUP_ARGS to --skip-venv --dev-wheels and Testing using galaxy_root /tmp/tmpQZC06H/galaxy-dev Testing tools with command [cd /tmp/tmpQZC06H/galaxy-dev; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --skip-common-startup"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/john/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then type virtualenv >/dev/null 2>&1 && virtualenv $GALAXY_VIRTUAL_ENV; else echo "Reusing existing virtualenv $GALAXY_VIRTUAL_ENV"; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/john/workspace/planemo/project_templates/demo/tool_test_output.html --xunit_report_file /tmp/tmpQZC06H/xunit.xml --structured_data_report_file /home/john/workspace/planemo/project_templates/demo/tool_test_output.json functional.test_toolbox] Set COMMON_STARTUP_ARGS to --skip-venv --skip-common-startup Reusing existing virtualenv /home/john/.planemo/gx_venv -John On Sun, Nov 15, 2015 at 8:51 PM, Tiago Antao <tra@popgen.net> wrote:
Hi,
I have recently upgraded to planemo 0.20.0 and I am getting an error that I cannot resolve:
Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown.
The output from the tool_test_output.json is empty {}
I am using planemo t --install_galaxy
I am a bit lost here, can anyone offer a suggestion please? I am afraid this might be too trivial...
As a further note, I have this on the log: functional_tests.py: error: no such option: --with-nosehtml
Many thanks, Tiago ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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On Tue, Nov 17, 2015 at 2:48 PM, John Chilton <jmchilton@gmail.com> wrote:
Thanks for the bug report. Somehow Galaxy isn't installing the development wheels into the transient Galaxy's virtualenv, I've wiped out my planemo caches and I can't reproduce this locally.
Perhaps unrelated, but I was seeing something similar with https://travis-ci.org/peterjc/pico_galaxy/builds/89678159 failing with: pkg_resources.DistributionNotFound: sqlalchemy-migrate This was despite pip having clearly installed the sqlalchemy-migrate wheel somewhere (presumably not in the right place though). (That was using wheels under the Galaxy dev branch, the same TravisCI setup was working with eggs with the Galaxy master branch) That was using my own virtualenv on top of the system Python. I "fixed" this by adopting the TravisCI provided Python virtualenv (which I'd been meaning to do anyway - my different TravisCI setups had diverged a bit too much), https://travis-ci.org/peterjc/pico_galaxy/builds/91567501 https://github.com/peterjc/pico_galaxy/commit/76721536fa02b73b6cb35d1fb70c9d... Regards, Peter
On Tue, 17 Nov 2015 14:48:03 +0000 John Chilton <jmchilton@gmail.com> wrote:
Thanks for the bug report. Somehow Galaxy isn't installing the development wheels into the transient Galaxy's virtualenv, I've wiped out my planemo caches and I can't reproduce this locally.
From planemo 0.19 to 0.20 I have also found that problem, but I installed many tools on my conda environment to compensate for that (I should have reported that bug also, sorry)
Can you send me the green log messages at the beginning of the test command as well as the few lines after them (maybe just paste the whole thing into a gist or something).
I have put everything on the log on this gist: https://gist.github.com/tiagoantao/488172904527ce854110 Note that my environment is problematic (as in having too much stuff) as I had to pip and conda install quite a few packages due to the virtualenv not being in use. Thanks, Tiago
The latest development release of Galaxy which planemo targets by default requires virtualenv to be available. Can you verify that it is not available on your machine and install it and try again. I will try to have planemo give a clearer error in this case if it is indeed the problem. -John On Tue, Nov 17, 2015 at 8:21 PM, Tiago Antao <tra@popgen.net> wrote:
On Tue, 17 Nov 2015 14:48:03 +0000 John Chilton <jmchilton@gmail.com> wrote:
Thanks for the bug report. Somehow Galaxy isn't installing the development wheels into the transient Galaxy's virtualenv, I've wiped out my planemo caches and I can't reproduce this locally.
From planemo 0.19 to 0.20 I have also found that problem, but I installed many tools on my conda environment to compensate for that (I should have reported that bug also, sorry)
Can you send me the green log messages at the beginning of the test command as well as the few lines after them (maybe just paste the whole thing into a gist or something).
I have put everything on the log on this gist: https://gist.github.com/tiagoantao/488172904527ce854110 Note that my environment is problematic (as in having too much stuff) as I had to pip and conda install quite a few packages due to the virtualenv not being in use.
Thanks, Tiago
On Thu, 19 Nov 2015 20:35:42 +0000 John Chilton <jmchilton@gmail.com> wrote:
The latest development release of Galaxy which planemo targets by default requires virtualenv to be available. Can you verify that it is not available on your machine and install it and try again. I will try to have planemo give a clearer error in this case if it is indeed the problem.
I created a new environment from scratch and installed virtualenv. That did it. Thanks
I'll update planemo to explicitly check for virtualenv before running Galaxy and give a very clear error message in this scenario. I guess I could even make it an explicit dependency of planemo in setup.py/PyPI - I wonder if it would be okay for planemo to mask the OS virtualenv when installing via pip, hmm... -John On Fri, Nov 20, 2015 at 12:58 AM, Tiago Antao <tra@popgen.net> wrote:
On Thu, 19 Nov 2015 20:35:42 +0000 John Chilton <jmchilton@gmail.com> wrote:
The latest development release of Galaxy which planemo targets by default requires virtualenv to be available. Can you verify that it is not available on your machine and install it and try again. I will try to have planemo give a clearer error in this case if it is indeed the problem.
I created a new environment from scratch and installed virtualenv. That did it. Thanks
participants (3)
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John Chilton -
Peter Cock -
Tiago Antao