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Handle FieldPerps in Datafile::varAdded() and Datafile::varPtr() (next) #2095

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merged 11 commits into from
Sep 30, 2020

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johnomotani
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Fix from #2093 into next.

@johnomotani
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Added a test of attributes in test-io and test-io_hdf5. See #2102 (comment).

I don't think we actually test the legacy netcdf interface, but if we do the tests will fail. It might not be a bad thing to fail and warn any users who are using legacy netcdf that there might be odd issues if they try to read netCDF4 files? We'd need to check in the test if it is using legacy netcdf in that case...

* next: (31 commits)
  Make sure test-restart-io sets exit code correctly on failure
  Don't read/write FieldPerps in guard cells
  Use last boundary point for global y-index in restart IO test
  Better fix for reading/writing FieldPerp index
  Rename *local -> *global argument in mesh index routines
  Remove deprecated YLOCAL() in examples/laplace-petsc3d
  Fix case-sensitivity of __contains__()
  __eq__() comparison operator for BoutOptions()
  Use no boundary form of global index conversion in FieldPerp I/O
  Use more consistent global index when writing/reading `FieldPerp`s
  Add Mesh::getLocal{X,Y,Z}Index{NoBoundaries} methods
  install python3-h5py on travis@fedora
  Remove unnecessary hardcoding of dump_format in test-invpar
  CMake: Add missing requirement on PETSc for AMG test
  Require netCDF for some tests
  Use global mesh/dump in test-io_hdf5
  Some tidying up to test-restarting
  Enable HDF5 in all Travis jobs
  Enable some HDF5-specific tests in default test set
  Fix bug in DataFormat::writeFieldAttributes with FieldPerp
  ...
@ZedThree
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I merged next in locally, and test-io still fails -- but I think that's because we've now changed the behaviour. test-io.grd.nc is read in, and fperp doesn't have a yindex_global. Previously it got 0, and now it gets 2. The benchmark file still contains 0 though, so we just need to update that.

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@ZedThree your update looks good to me 👍

ZedThree
ZedThree previously approved these changes Sep 28, 2020
@ZedThree ZedThree merged commit e1fcc06 into next Sep 30, 2020
@ZedThree ZedThree deleted the fieldperp-io-fix-next branch September 30, 2020 13:28
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2 participants