Add pytest, enable coverage testing, fix key issue#105
Add pytest, enable coverage testing, fix key issue#105mvdbeek merged 28 commits intogalaxyproject:masterfrom
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This issue should have been fixed
| from bioblend.toolshed import ToolShedInstance | ||
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| def valid_keys(): |
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You could also just do
VALID_KEYS = [...]
I think that is a common practice for constants
| "tool_panel_shed_url", | ||
| "install_repository_dependencies", | ||
| "install_resolver_dependencies", | ||
| "install_tool_dependencies" |
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tool_shed_url is also valid, right ? I think I saw that in one of the failing tests
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This is a typo/mistake indeed. It should be tool_shed_url. Thanks for pointing this out!
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| #!/usr/bin/env python | |||
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| from ephemeris.shed_tools_methods import * | |||
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I think we should avoid * imports as a rule, makes it easier to follow what's being tested.
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I have created a new codacy page: https://app.codacy.com/project/galaxyproject/ephemeris/dashboard |
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Okay I am done. Made sure the docker container is a fixture so it is automatically deleted after the tests are done. |
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| result = result.json() | ||
| if options.verbose: | ||
| if verbose: |
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Another direction for the future: the verbose handling should happen via the logging facility. I.e you'd only see INFO and DEBUG levels if you increase verbosity. Which would be nice because it removes the conditional handling here.
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| # It needs to work well with dev. Alternatively we can pin this to 'master' or another stable branch. | ||
| # Preferably a branch that updates with each stable release | ||
| GALAXY_IMAGE = "bgruening/galaxy-stable:dev" |
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That's fine for now, but we can also parameterize the start_container fixture to control which image to start.
Or the simpler variant of controlling it with an ENV var GALAXY_IMAGE = os.environ.get("EPHEMERIS_GALAXY_DOCKER_IMAGE, "bgruening/galaxy-stable:dev")
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Hi. I set out to fix #82 . Then I figured this would be much easier to test using pytest. So I set up pytest as well. Since we use tox, I followed the set of recommendations here:
https://docs.pytest.org/en/latest/goodpractices.html
Also that lead me here:
https://blog.ionelmc.ro/2014/05/25/python-packaging/#the-structure
That is why we now have a
src/folder.I needed to adapt setup.py for that as well. But it should still work.
I also took the opportunity to enable the code to integrate the coverage results with codacy. But I need @jmchilton to integrate that fully. Alternatively I could set up a galaxyproject organization on codacy, but I am not going to do so without explicit permission from a galaxy core member,and certainly not without bypassing John. That is just not a nice thing to do, given he has set up codacy already on his personal codacy page.
I removed some redundant code from the testing files as well. But with me not being involved from the beginning of this project, this might lead to errors later. So reviews are quite welcome.
@erasche, could you check if this fixes #82? @jmchilton could you have a look as well, given that you release the ephemeris package and I had to change setup.py?
This also adresses #71 and #80 .
Best regards,
Ruben