Added inheritance filter to gemini plugin #223
Conversation
|
Finally works!! Please review @brainstorm @guillermo-carrasco @robinandeer |
moonso
force-pushed
the
gemini-inheritance
branch
from
c3ac6d9
to
aa9011e
Compare
| @@ -53,6 +53,12 @@ def gemini_path(request): | |||
| gemini_db = "tests/fixtures/HapMapFew.db" | |||
| return gemini_db | |||
|
|
|||
| @pytest.fixture(scope='function') | |||
There was a problem hiding this comment.
Does this decorator tell you when that "big" GEMINI db is not there?
Would it make sense to be a bit smarter here and pull the S3 file when and if it's not present while running the testsuite? Could save some time for new devs/beginners before they figure it out when reading the docs...
Automation >> Docs
There was a problem hiding this comment.
Sorry I added this then changed my mind but forgot to remove. Thanks for noting!
We should have a dedicated test database as issued in #225
|
Cool stuff Måns! Just went through the PR, seems fine to me except the HapMapMany test/comment I left... It would make sense to have an exception for pulling the data from S3: When tests are running on TravisCI, do not pull those in. Other than that, excellent job! ;) |
|
I have no idea why the tests fails, it's working on my local installation... |
|
@robinandeer would you like to have a last review of this? |
- Add a .coveragec file to control what code is excluded when checking test coverage. Modify this file if there is repeated types of code that should be excluded from coverage testing. - Remove coverage testing when using gemini.gim since it does not work.
|
hmm I don't even get what's the problem exactly, the stacktrace is confusing :-/ |
|
@guillermo-carrasco think that the problem has to do with gemini.gim uses |
|
|
|
How are we standing on this? Doesn't GEMINI do a test for this case or are they not using py.test? I don't like the idea of merging in code that will make tests fail just bc having a "broken master branch" tag in the README is not a good thing for potential collaborators etc. to see @moonso @brainstorm @guillermo-carrasco @henrikstranneheim ?? |
|
I had to deal with GEMINI's "testsuite" in PR arq5x/gemini#719... TL;DR: Not fun. Best chance you guys get is pinging BrentP on this if you are really stuck, IMHO... |
|
Yeah let's bring in BrentP and see what he has to say Otherwise I guess we'll drop that unit test and/or work around it 😕 |
No description provided.