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Add base methods for iterator serialization #924
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CodyCBakerPhD
commented
Jul 30, 2023
CodyCBakerPhD
commented
Jul 30, 2023
CodyCBakerPhD
commented
Jul 30, 2023
oruebel
reviewed
Jul 31, 2023
rly
reviewed
Aug 4, 2023
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## dev #924 +/- ##
==========================================
+ Coverage 88.33% 88.34% +0.01%
==========================================
Files 45 45
Lines 9284 9292 +8
Branches 2651 2653 +2
==========================================
+ Hits 8201 8209 +8
Misses 765 765
Partials 318 318
☔ View full report in Codecov by Sentry. |
CodyCBakerPhD
changed the title
Add 'number_of_jobs' to top-level io.write() for Zarr parallel support
Add base methods for iterator serialization
Aug 4, 2023
rly
reviewed
Aug 4, 2023
rly
approved these changes
Aug 8, 2023
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Motivation
Zarr supports efficient parallelization, and a sister PR (hdmf-dev/hdmf-zarr#111) adds this capability but requires the argument
number_of_jobs
to be propagated from a top level of theHDMFIO.write
due to the super call at this lineIt also has a subtle condition in that our iterators (which in this role primarily define how to access data from a source) must be pickleable, so I've defined methods related to that for the
GenericDataChunkIterator
(which for several reasons should be the only type of iterator allowed for usage in parallelization)An example in practice can be found downstream: catalystneuro/neuroconv#536
Checklist
ruff
from the source directory.