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Redo testing.#1024

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jmchilton merged 4 commits intogalaxyproject:masterfrom
jmchilton:rework_ci
Jul 22, 2020
Merged

Redo testing.#1024
jmchilton merged 4 commits intogalaxyproject:masterfrom
jmchilton:rework_ci

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@jmchilton jmchilton commented Jul 17, 2020

Fix #945 .

Redo testing.

  • Use pytest.
  • Rework tox to add more bells and whistles (more docs for this in the drop Python 2 branch)
  • Slice and dice the tests in different ways to hopefully make it clearer what is failing in the future.
  • Add a bunch of tests back to Travis - different combinations of Pythons, Galaxy versions, and tests than Github actions though.
  • Skip more client building when not needed - slows down the tests a lot it seems.
  • More debugging in various places - in tests and in app.
  • Fix options in shed_serve.
  • Various gunicorn fixes.
  • Rework some testing framework to use concurrent.futures.

Also change directory for gx_venv because it doesn't default to Python 2 anymore.

@jmchilton jmchilton force-pushed the rework_ci branch 4 times, most recently from 4aa68c2 to f5f0a6d Compare July 17, 2020 23:44
@jmchilton jmchilton force-pushed the rework_ci branch 9 times, most recently from 5d707e3 to cb606ed Compare July 20, 2020 04:03
@jmchilton jmchilton changed the title [WIP] Rework CLI to use pytest. [WIP] Rework CI to use pytest. Jul 20, 2020
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At very least progress - I wonder if this is toolshed problems or gunicorn not having request lengths that are long enough 😅

galaxy.tool_shed.galaxy_install.install_manager INFO 2020-07-20 20:48:09,245 Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/devteam/fastqc' at 21:e7b2202befea
[2020-07-20 20:48:37 +0000] [5249] [CRITICAL] WORKER TIMEOUT (pid:5250)

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The gap there is exactly the default so probably not a toolshed problem.

@jmchilton jmchilton changed the title [WIP] Rework CI to use pytest. [WIP] Redo testing. Jul 21, 2020
@jmchilton jmchilton mentioned this pull request Jul 21, 2020
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Thanks @jmchilton

shell(["ps", "ax"])
exists = os.path.exists(self.pid_file)
print("Killing pid file [%s]" % self.pid_file)
print("pid_file exists? [%s]" % exists)
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I think this should be removed before merging.

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It is all hidden behind the verbose flag though?

except Exception:
if ctx.verbose:
io.shell(['ls', config.galaxy_root])
print("Failed to install tool repositories, Galaxy log:")
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remove?

@jmchilton jmchilton force-pushed the rework_ci branch 7 times, most recently from 17b8490 to c148855 Compare July 22, 2020 02:40
- Use pytest.
- Rework tox to add more bells and whistles.
- Skip more client building when not needed - slows down the tests a lot it seems.
- More debugging in various places - in tests and in app.
- Fix options in shed_serve.
- Various gunicorn fixes.
- Rework some testing framework to use concurrent.futures.
@jmchilton jmchilton changed the title [WIP] Redo testing. Redo testing. Jul 22, 2020
@jmchilton jmchilton merged commit e34ac7b into galaxyproject:master Jul 22, 2020
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Replace nose with pytest

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