Re: [galaxy-dev] Planemo 0.20.0 and xunit

[John Chilton]

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  wrote:
> On Thu, 19 Nov 2015 20:35:42 +
> John Chilton  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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Re: [galaxy-dev] Planemo 0.20.0 and xunit

[Tiago Antao]

On Thu, 19 Nov 2015 20:35:42 +
John Chilton  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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Re: [galaxy-dev] Planemo 0.20.0 and xunit

[John Chilton]

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  wrote:
> On Tue, 17 Nov 2015 14:48:03 +
> John Chilton  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
>
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Re: [galaxy-dev] Planemo 0.20.0 and xunit

[Peter Cock]

On Tue, Nov 17, 2015 at 2:48 PM, John Chilton  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/76721536fa02b73b6cb35d1fb70c9da7f227e9e1

Regards,

Peter
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Re: [galaxy-dev] Planemo 0.20.0 and xunit

[John Chilton]

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  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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