Fix import of removed scanpy _get_obs_rep/_set_obs_rep - #1050
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scanpy 1.13.0a1 removed the private helpers scanpy.get._get_obs_rep and scanpy.get._set_obs_rep, breaking `import pertpy`. These helpers only resolved X vs a named layer, which AnnData now handles directly, so replace them with direct adata.X / adata.layers access. Fixes #1049 Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1050 +/- ##
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Coverage 78.76% 78.77%
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Files 51 51
Lines 7167 7170 +3
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+ Hits 5645 5648 +3
Misses 1522 1522
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The pooch migration (#980) dropped the retry-with-backoff loop that the previous _download had, leaving max_retries/retry_delay as dead params. Transient failures such as 'Connection reset by peer' (URLError, an OSError subclass) or a requests ConnectionError therefore aborted the download immediately, causing flaky test failures on CI. Reinstate the retry loop around pooch.retrieve, retrying on OSError and requests.exceptions.RequestException with a delay between attempts, and add unit tests covering the retry, exhaustion, and non-transient paths. Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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Description
scanpy 1.13.0a1 removed the private helpers
scanpy.get._get_obs_repandscanpy.get._set_obs_rep, which brokeimport pertpywith:These helpers only resolved
Xvs a named layer, which AnnData handles directly (andplot_heatmapin the same file already did inline).This replaces the imports with direct
adata.X/adata.layers[...]access.Fixes #1049
Testing
tests/preprocessing/test_grna_assignment.pypasses (23 passed).