openPMD / openPMD-api / 3350
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Add functionality to close a file (#746)

* Add IOTask for closing file

* Add API calls for Iteration::close

* Add closeFile to ADIOS2 backend

* remove skipFlush

and other wrongly commited lines

* Add test

* add back skipFlush

* Invalidate file in ADIOS2 after closing

* Remove superfluous ; after function

* Make Iteration::close synchronous by default

Optional parameter `bool flush = true`

* Add closeFile operation to JSON backend

* Remove name parameter from CLOSE_FILE task

* Fix name shadowing

* [wip] close_file for ADIOS1

somehow still fails when creating the second iteration

* Temporary workaround for ADIOS1

* Implement file closing in HDF5

* change erase order

* run a simplified test for ADIOS1

* Split closed into closed and closedByWriter

This enables closing iterations in read-mode, too.
closedByWriter will be mainly useful in streaming mode, which this
commit is preparing

* Fix ADIOS1 test

* cleanup

* Throw if flushing a closed iteration that has been accessed

* Add verifyClosed

* Close files in read mode too

* Test throwing upon accessing an iteration post closing

* Also do sanity-checks in group-based mode

This is currently not necessary, since closing an iteration in
group-based mode is a no-op. It will become relevant in streaming-based
mode, where closing an iteration means discarding its corresponding data
packet.

* Rename m_closed* members of Iteration and update docu

* Unify m_closed(Backend|Frontend) into common enum

* Flush only the closed iteration upon Iteration::close

* Undo unnecessary whitespace changes

* Two small fixes in ADIOS1 IO Handler

1) Remove debugging output
2) Delete buffered attribute writes after performing them

* Prevent throwing in destructor in close_iteration_test

* Do not use boolean attributes

* Revert "Prevent throwing in destructor in close_iteration_test"

This reverts commit 1490db6577b... (continued)

5580 of 6635 relevant lines covered (84.1%)

0.84 hits per line

Jobs
ID Job ID Ran Files Coverage
19 3350.19 (BUILD=~/buildTmp SPACK_ROOT=$HOME/.cache/spack PATH=$PATH:$HOME/.cache/spack/bin BUILD_TYPE=Debug PYBIND11_VERSION=@2.3.0 USE_SHARED=true CXXSPEC="%gcc@7.4.0" USE_MPI=ON USE_PYTHON=ON USE_HDF5=ON USE_ADIOS1=ON USE_ADIOS2=OFF) 0
84.1
 Travis Job 3350.19
Source Files on build 3350
Detailed source file information is not available for this build.