FAIRmat-NFDI / pynxtools / 23194260232

82%

Build Type

push

github

Committed by web-flow

Commit Message

An append mode for already existing hdf5 files (#146)

* A quick append mode for already existing hdf5 files

* Deactivate append-functionality-specific tests need fixture

* revert definitions to those from master

* manual moving over content related to the append mode from the cenem, feature testing branch, configured the default such that when in append mode we always skip the verification currently, standalone validate on the HDF5 file should be used instead on these files

* attempt to hardening against attempts to recreate existent hdf5 nodes that would cause h5py to throw and thus may leave the resulting hdf5 file in a dangling state

* suggestion from lukaspie

* docs skeleton for the append mode

* note on skip-verify

* reactivate tests for append mode

* constrain logic in the writer

* fix test skeleton, cleanup remains

* Test and proper hardening

* clear tests, only caplog capture remains

* Deactivate tests for py3.10 given conflict with molid, see nomad-FAIR issue #2545

* remove spurious whitespace changes

* reactivate mypy precommit, fix wrong block indentation in writer

* include working with caplog

* remove whitespace

* whitespace precommit config

* docs

* add flag append_mode, complete documentation, add tests accordingly

* add flag append_mode, complete documentation, add tests accordingly

* Fixes for compression observed necessary during NXapm runthrough from the AHoD2026, reactivating python 3.10

* reviewer comments

* edit test to reflect that version handling has now been added

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Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>

Run Details

103 of 126 new or added lines in 5 files covered. (81.75%)

2 existing lines in 1 file now uncovered.

5823 of 7117 relevant lines covered (81.82%)

0.82 hits per line