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Adios2StMan row read/write fixes#2

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rtobar wants to merge 24 commits intomasterfrom
adios2stman-row-readwrite
Open

Adios2StMan row read/write fixes#2
rtobar wants to merge 24 commits intomasterfrom
adios2stman-row-readwrite

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@rtobar rtobar commented Oct 21, 2025

This version of casacore should now fix reads/writes by row. Tested locally like so:

import numpy as np
from casacore.tables import table

t = table("/home/rtobar/test.tab", ack=False)

for start, count in ((0, 2), (1, 3), (40, 1), (3, 100)):
    data = t.getcol("REAL")[start: start + count]
    subdata = t.getcol("REAL", startrow=start, nrow=count)
    diff = data - subdata
    if np.all(diff) == 0.0:
        print("good")
    else:
        print(diff)

And it was all good :)

Summary by Sourcery

Fix row-based read and write operations in the Adios2 storage manager and update the build configuration for ADIOS2 support

Bug Fixes:

  • Correct handling of startrow and nrow parameters for getcol and putcol in Adios2StMan

Build:

  • Update Docker build script to install and configure ADIOS2 dependencies

Tests:

  • Verify row-wise slicing of getcol through manual numpy-based tests

Signed-off-by: Rodrigo Tobar <rtobar@icrar.org>
Signed-off-by: Rodrigo Tobar <rtobar@icrar.org>
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sourcery-ai bot commented Oct 21, 2025

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

This PR refactors the Adios2 storage manager to correctly handle row-based reads and writes by fixing offset and count calculations and updates the Docker build to enable ADIOS2 support.

File-Level Changes

Change Details Files
Fix row‐based read/write logic in Adios2StMan
  • Correct calculation of byte offsets using startrow and nrow
  • Ensure read calls request exactly nrow entries instead of full column
  • Update write method to honor row slicing and adjust buffer sizing
casacore/tables/DataManager/Adios2StMan.cc
casacore/tables/DataManager/Adios2StMan.h
Enable ADIOS2 support in the Docker build
  • Install adios2 development package in the Docker image
  • Set CMake flag WITH_ADIOS2=ON when building casacore
docker/build_casacore.docker

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