8:51 p.m.
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
2:48 p.m.
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(a)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
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2:56 p.m.
On Tue, Nov 17, 2015 at 2:48 PM, John Chilton <jmchilton(a)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/76721536fa02b73b6cb35d1fb70...
Regards,
Peter
8:21 p.m.
On Tue, 17 Nov 2015 14:48:03 +0000
John Chilton <jmchilton(a)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
8:35 p.m.
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(a)popgen.net> wrote:
On Tue, 17 Nov 2015 14:48:03 +0000
John Chilton <jmchilton(a)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
12:58 a.m.
On Thu, 19 Nov 2015 20:35:42 +0000
John Chilton <jmchilton(a)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
2:47 p.m.
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(a)popgen.net> wrote:
On Thu, 19 Nov 2015 20:35:42 +0000
John Chilton <jmchilton(a)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
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galaxy-dev@lists.galaxyproject.org
6 comments
3 participants
participants (3)
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John Chilton -
Peter Cock -
Tiago Antao