{"push_id":2359771504,"size":18,"distinct_size":6,"ref":"refs/heads/py3_full","head":"19c5f325e4f31d74229142e4424823167bcd248f","before":"416a332be93e93de241f5d2aceadb51ebaac0788","commits":[{"sha":"e594f5f7c407789a667dfcd4908142d5734833dc","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Enhancements to Galaxy profiles and workflow testing.\n\nAdd a new profile database type option \"postgres_docker\". The existing \"postgres\" type option expects a local database to be accessible via the \"psql\" command on Planemo's PATH - probably few people have postgres running directly on their development machine and fewer still have it configured to allow passwordless entry. This newer variant is a much simpler interface - it starts a named container for the official Docker postgres image and uses that to manage the profile. This should make using profiles easier for most developers.\n\nThis new modality does have some shortcomings - it should probably be redone to persist the database somewhere -or- start and stop the same container (currently when the container is stopped the data is gone).\n\nThis also updates the workflow test that encounters Galaxy locks to pickup the environment variable PLANEMO_TEST_WORKFLOW_RUN_PROFILE and PLANEMO_TEST_WORKFLOW_RUN_PROFILE_DATABASE_TYPE and use these to create and use a profile during testing if set as well as setting that variable in Travis to leverage the postgres service already configured for other tests. This more less fixes what I had in mind with #772 but it would be nice to leverage galaxyproject/galaxy#4887 for greater test isolation.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/e594f5f7c407789a667dfcd4908142d5734833dc"},{"sha":"63770ac59ce2ce8ee167bc8bc81d124dbba4ee55","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Merge pull request #773 from jmchilton/profiles_revisited\n\nEnhancements to Galaxy profiles and workflow testing.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/63770ac59ce2ce8ee167bc8bc81d124dbba4ee55"},{"sha":"ccf1efe10f17eb13178d45e1d77b6a5e7bd7c9ea","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Add a native Galaxy workflow (.ga) testing test.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/ccf1efe10f17eb13178d45e1d77b6a5e7bd7c9ea"},{"sha":"919ca7bc33db25009bf2f6a6ca2dc8afe71d159a","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Fix sha1 sum.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/919ca7bc33db25009bf2f6a6ca2dc8afe71d159a"},{"sha":"08c073f0b87a3dce011c77c9cfd38be631c6a543","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Eliminate some dependency resolution on various tests.\n\nHoping this stablizes the tests a bit, I've seen random Conda problems.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/08c073f0b87a3dce011c77c9cfd38be631c6a543"},{"sha":"d5c480b7904fb6208637c94c1b113d663439b995","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Merge pull request #770 from jmchilton/workflow_fixes_2\n\nAdd a native Galaxy workflow (.ga) testing test.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/d5c480b7904fb6208637c94c1b113d663439b995"},{"sha":"7f8c003b63ed09c0fb68e593d04540945f5cd782","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Refactor GalaxyConfig toward unmanages engines (i.e. existing Galaxy instances).","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/7f8c003b63ed09c0fb68e593d04540945f5cd782"},{"sha":"15e2390b45d568e6f540f016e459dc7aeb37dcac","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Planemo command to convert format 2 workflows into .ga workflows.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/15e2390b45d568e6f540f016e459dc7aeb37dcac"},{"sha":"e6f993a3220e2cfa59c9d6d4b84862b7e00f8812","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Merge pull request #771 from jmchilton/wfconvert\n\nPlanemo command to convert format 2 workflows into .ga workflows.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/e6f993a3220e2cfa59c9d6d4b84862b7e00f8812"},{"sha":"1ab9341cb6cab0b8033263483291b06e88e59fd6","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Fix resolving & installing shed repositories from workflows.\n\nUsed by run/serve/test of workflows.\n\n- Update for modern ephemeris usage.\n- Update to work with .ga files an not just explicit tool: sections in format 2 workflows.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/1ab9341cb6cab0b8033263483291b06e88e59fd6"},{"sha":"c0d1e8d06a2c4b396f5c45d423880149fe1fa318","author":{"name":"Björn Grüning","email":"0e992fbc137cfbe2bbe7f34a4a9cce8a620c105e@gruenings.eu"},"message":"fix linting","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/c0d1e8d06a2c4b396f5c45d423880149fe1fa318"},{"sha":"99d5847466210e90248b761bbf36634fa53f0551","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Merge pull request #776 from jmchilton/fix_workflow_to_shed_installs\n\nFix resolving & installing shed repositories from workflows.","distinct":false,"url":"https://api.github.com/repos/jmchilton/planemo/commits/99d5847466210e90248b761bbf36634fa53f0551"},{"sha":"a523389641b552f335db557e9517edbb1beec4a2","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Enable full Python 3 test suite.","distinct":true,"url":"https://api.github.com/repos/jmchilton/planemo/commits/a523389641b552f335db557e9517edbb1beec4a2"},{"sha":"cc99a08003616c8c6f1cec991636e56fb939a1e8","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Python 3 testing debug - STRIP THIS OUT BEFORE MERGE.","distinct":true,"url":"https://api.github.com/repos/jmchilton/planemo/commits/cc99a08003616c8c6f1cec991636e56fb939a1e8"},{"sha":"068946891813e56d7f58e086a2376d3f7d48a046","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@earlham.ac.uk"},"message":"Python3: unicodify filehash\n\nFix the following test:\n```\n$ nosetests tests/test_dependency_script.py\n..F.....\n======================================================================\nFAIL: test_good_examples (tests.test_dependency_script.DependencyScriptTestCase)\n----------------------------------------------------------------------\nTraceback (most recent call last):\n  File \"/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_dependency_script.py\", line 79, in test_good_examples\n    self._check_exit_code(ds_cmd, 0)\n  File \"/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_utils.py\", line 100, in _check_exit_code\n    raise AssertionError(message)\n...\n-------------------- >> begin captured stdout << ---------------------\nCommand list output is [Downloading http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz to '/tmp/tmp8mq79eb0/download_cache/samtools-0.1.16-linux-i386.tgz'\nVerifying checksum for samtools-0.1.16-linux-i386.tgz\nError processing /usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/data/repos/package_1/tool_dependencies.xml - Checksum failure for /tmp/tmp8mq79eb0/download_cache/samtools-0.1.16-linux-i386.tgz, got b'7090bd62142df0ed3a2b4000292fc0edc917e773d0269c2f3f5b0d36b7888c22' but wanted '7090bd62142df0ed3a2b4000292fc0edc917e773d0269c2f3f5b0d36b7888c22'\n...\n```","distinct":true,"url":"https://api.github.com/repos/jmchilton/planemo/commits/068946891813e56d7f58e086a2376d3f7d48a046"},{"sha":"158024f78ab4cfbd1c0d78e7288b13b289c33ccd","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@earlham.ac.uk"},"message":"Small Python3 fix","distinct":true,"url":"https://api.github.com/repos/jmchilton/planemo/commits/158024f78ab4cfbd1c0d78e7288b13b289c33ccd"},{"sha":"3b8d163c8fd1aae12930d4903ec69b73a98f9ac6","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@earlham.ac.uk"},"message":"Move logging after dir has been created","distinct":true,"url":"https://api.github.com/repos/jmchilton/planemo/commits/3b8d163c8fd1aae12930d4903ec69b73a98f9ac6"},{"sha":"19c5f325e4f31d74229142e4424823167bcd248f","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@earlham.ac.uk"},"message":"Python3: fix downloading of latest SQLite database","distinct":true,"url":"https://api.github.com/repos/jmchilton/planemo/commits/19c5f325e4f31d74229142e4424823167bcd248f"}]}
{"actor":{"display_login":"nsoranzo"}}