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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
MIT License
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Put sample cells and genes in the repo #701

Closed scottgigante-immunai closed 1 year ago

scottgigante-immunai commented 1 year ago

Too many tests are flaking due to pulling cells and genes from URL.

codecov[bot] commented 1 year ago

Codecov Report

Base: 95.05% // Head: 95.05% // No change to project coverage :thumbsup:

Coverage data is based on head (7043369) compared to base (42a5138). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #701 +/- ## ======================================= Coverage 95.05% 95.05% ======================================= Files 153 153 Lines 4062 4062 Branches 206 206 ======================================= Hits 3861 3861 Misses 131 131 Partials 70 70 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `94.95% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/openproblems-bio/openproblems/pull/701?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio) | Coverage Δ | | |---|---|---| | [openproblems/data/sample/sample.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/701/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL2RhdGEvc2FtcGxlL3NhbXBsZS5weQ==) | `100.00% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio)

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LuckyMD commented 1 year ago

I guess tests are still pulling test data from urls though, no? Will that also still be flaky? Although, this solution should then at least cover method only PRs.

scottgigante-immunai commented 1 year ago

That's right -- but pulling from each URL once seems to be less problematic than pulling from a single URL many times, which is what we're doing here with the sample data. Too many requests to the same resource seems to be the major issue here.