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openbraininstitute / libsonata
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add-docstrings

add-learning-engine

cleanup

cleanup-config-tests

fix-build

gnuinstalldirs

jplanas/cond-modif-sonata-ext

jplanas/copyright-update

katta/bluebrain2openbraininstitute

katta/comp_sets_2

katta/compartment_set_input

katta/install_dev

master

refs/tags/v0.1.30

refs/tags/v0.1.31

remove-file-locks

rev-hdf5

scikit-build-core

test-format

update-catch2

update-clang-format

update-coverage

update-docstrings

update-hdf5-v1.14.6

update-highfive

update-pybind11

v0.1.32

v0.1.33

v0.1.34

weji/build_sdist

weji/duplicate_keys

weji/electric_fields

weji/seclamp

weji/seclamp_more

Committed 02 Apr 2026 09:01AM UTC coverage: 93.163% (-0.004%) from 93.167%

Build # 23892759807

Build Type

Pull #38

github

Committed by

mgeplf

Commit Message

Don't use HDF5's default locking behavior when opening files read only

* HDF5 uses file locks to implement a `Single Writer, Multiple Reader` model
* We expect the SONATA HDF5 files to always be finished reading, so we
  don't benefit from this, and on some files systems, there are a finite
  amount of locks (plus it's a pessimizing default)
* we don't want to rely on `HDF5_USE_FILE_LOCKING` to be set
* see more info: https://support.hdfgroup.org/documentation/hdf5/latest/_file_lock.html
* Note: this requires that any other files opened with the HDF5 library
  be opened with the same flags.  Thus, if `h5py` is used to open the file
  concurrently with `libsonata`, there may be failures if the locking
  flags aren't set the same we are using `use_file_locking=True` and
  `ignore_when_disabled=True`

Pull Request Pull Request #38: Don't use HDF5's default locking behavior when opening files read only

Coverage Stats

17 of 18 new or added lines in 4 files covered. (94.44%)

2480 of 2662 relevant lines covered (93.16%)

51.41 hits per line

Relevant lines Covered

2662 RELEVANT LINES 2480 COVERED LINES

51.41 HITS PER LINE

Source Files on master

Recent builds

Builds	Branch	Commit	Type	Ran	Committer	Via	Coverage
23892759807	remove-file-locks	Don't use HDF5's default locking behavior when opening files read only * HDF5 uses file locks to implement a `Single Writer, Multiple Reader` model * We expect the SONATA HDF5 files to always be finished reading, so we don't benefit from this, ...	Pull #38	02 Apr 2026 09:03AM UTC	mgeplf	github	93.16
23850488226	remove-file-locks	Don't use HDF5's default locking behavior when opening files read only * HDF5 uses file locks to implement a `Single Writer, Multiple Reader` model * We expect the SONATA HDF5 files to always be finished reading, so we don't benefit from this, ...	Pull #38	01 Apr 2026 01:22PM UTC	mgeplf	github	93.16
23850470934	remove-file-locks	Don't use HDF5's default locking behavior when opening files read only * HDF5 uses file locks to implement a `Single Writer, Multiple Reader` model * We expect the SONATA HDF5 files to always be finished reading, so we don't benefit from this, ...	push	01 Apr 2026 01:16PM UTC	mgeplf	github	93.16
23850061638	remove-file-locks	Don't use HDF5's default locking behavior when opening files read only * HDF5 uses file locks to implement a `Single Writer, Multiple Reader` model * We expect the SONATA HDF5 files to always be finished reading, so we don't benefit from this, ...	Pull #38	01 Apr 2026 01:06PM UTC	mgeplf	github	93.16
23847216577	remove-file-locks	HDF5 uses file locks to implement a Single Writer, multiple reader model * we do not benefit from this, so turn off locking	push	01 Apr 2026 11:54AM UTC	mgeplf	github	93.16
23639753236	master	SEClamp: Check the sum of duration_levels (#36)	push	27 Mar 2026 09:29AM UTC	web-flow	github	93.17
23638115760	weji/seclamp_more	check non-negative duration in inputs	Pull #36	27 Mar 2026 08:41AM UTC	WeinaJi	github	93.17
23638051316	master	Replace python setup.py sdist with python -m build --sdist (#37) vcs_versioning becomes the dependency of setuptools_scm 10.0.3. To solve the transitive dependency problem, we replace the legacy python setup.py sdist with the modern build python ...	push	27 Mar 2026 08:39AM UTC	web-flow	github	93.15
23607026228	weji/build_sdist	replace python setup.py sdist with python -m build --sdist	push	26 Mar 2026 04:56PM UTC	WeinaJi	github	93.15
23602189016	weji/seclamp_more	check non-negative duration in inputs	Pull #36	26 Mar 2026 03:18PM UTC	WeinaJi	github	93.17

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