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Workflow tests caching #62

Merged
merged 43 commits into from
Jan 11, 2024
Merged

Workflow tests caching #62

merged 43 commits into from
Jan 11, 2024

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sfmig
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@sfmig sfmig commented Dec 20, 2023 •
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Fixes issue #34

  • removed code smell from if case in parametrised test
  • added mocking home directory in tests
  • data caching: the data is only downloaded once from GIN (in the config_GIN_dict fixture), then copied across for the rest of the test by mocking the pooch.retrieve function.
  • smoketest for entry point

Rebase after #64 is squash-merged

Caching right now relies on the pooch.retrieve() function, which won't download the data if it already exists, and filename and hash match. We could instead / further reduce testing time in CI using Github's cache action

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codecov bot commented Dec 20, 2023 •
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Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (017f005) 80.88% compared to head (9c8dfaf) 82.75%.

Files Patch % Lines
tests/cellfinder_core/conftest.py 97.91% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #62      +/-   ##
==========================================
+ Coverage   80.88%   82.75%   +1.87%     
==========================================
  Files          27       27              
  Lines        1522     1577      +55     
==========================================
+ Hits         1231     1305      +74     
+ Misses        291      272      -19

☔ View full report in Codecov by Sentry.
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@sfmig sfmig linked an issue Dec 22, 2023 that may be closed by this pull request
Cellfinder workflow tests further improvements + caching #34
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@sfmig sfmig mentioned this pull request Dec 22, 2023
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@sfmig sfmig changed the title Workflow tests improvements Workflow tests caching Jan 9, 2024
@sfmig
bring back default_input_config_cellfinder fixture
d2dfb2f
@sfmig
finalise adding local config as parameter in test_read_cellfinder_config
2651d46
@sfmig
add local config to remaining unit tests
39043ee
@sfmig
add local config and GIN config to test main
8418ef0
@sfmig
monkeypatched home in integration tests (only works in main)
167d78e
@sfmig
skip tests that use subprocess for now
1f141da
@sfmig
monkeypatch pooch.retrieve when forcing download
35824df
@sfmig
make config local fixture copy downloaded GIN data (rather than re-do…
a4d1e39 
…wnload again)
@sfmig
fix output dir definition
0c59ba9
@sfmig
docstrings and remove merge artifact
e3b3900
@sfmig
fill in docstrings
f6f2978
@sfmig
add GIN default location as a fixture
6bc68fb
@sfmig
remove commented out GIN default location
5cdbbeb
@sfmig
remove tests for running script (monkeypatched home function not pass…
a3e5370 
…ed to subprocess, and all subsequent steps already tested)
@sfmig
replace entry point test for smoketest
c4c998d
@sfmig
fixes from rebase
f84be90
@sfmig sfmig marked this pull request as ready for review January 10, 2024 19:24
@sfmig sfmig mentioned this pull request Jan 10, 2024
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alessandrofelder
alessandrofelder approved these changes Jan 11, 2024
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Thanks - this looks good to me.

I do think caching on GH actions is worth it, as the idea is for the CI tests to run fast (when on small data) and we expect quite a bit of activity on this repo in the immediate future - so it will make our lives easier and more in-flow!

It might also be worth mocking Path.home only on local repos, and not on CI, so we run CI tests closer to a real-life scenario.

I'd suggest doing this in a separate PR tackling #65 though, as this is already a reduction in CI time.

@alessandrofelder alessandrofelder merged commit ffee651 into main Jan 11, 2024
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@alessandrofelder alessandrofelder deleted the smg/workflow-tests-caching branch January 11, 2024 11:41
@adamltyson
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I do think caching on GH actions is worth it, as the idea is for the CI tests to run fast (when on small data) and we expect quite a bit of activity on this repo in the immediate future - so it will make our lives easier and more in-flow!

We cache data in some of the other repos and it works very well.

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Cellfinder workflow tests further improvements + caching
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@sfmig @adamltyson @alessandrofelder