Get it working again for newer versions of dependencies#582

Merged

t-b merged 28 commits intomasterfrom

science-staging-v2

Sep 5, 2025

Commits on Aug 26, 2025

Move JSON handling code into package to remove dependency on AllenSDK

gouwens
authored and
t-b
committed
Move deprecation handling into package from AllenSDK

gouwens
authored and
t-b
committed
Change package version in x_to_nwb to check IPFX, not AllenSDK

gouwens
authored and
t-b
committed
Move LIMS credential managment into IPFX from AllenSDK

gouwens
authored and
t-b
committed
Change json_utilities imports in tests

gouwens
authored and
t-b
committed
Remove SDK as option for data source in scripts

gouwens
authored and
t-b
committed
Remove dependency on allensdk Manifest.safe_mkdir

gouwens
authored and
t-b
committed
Remove allensdk as dependency

gouwens
authored and
t-b
committed
Bump version

gouwens
authored and
t-b
committed
Relax pynwb version dependency

gouwens
authored and
t-b
committed
tests: Get them working again
t-b
committed
lims_queries.py/able_to_connect_to_lims: Catch KeyError as well
t-b
committed
run_feature_collection/extract_features: Fix numpy exception
t-b
committed
treewide: Adapt to new pynwb 3.0 API
t-b
committed
tests: Use correct units for stimulus
t-b
committed
treewide: Allow to inject a SweepTable
t-b
committed
requirements.txt: Don't require a fixed pynwb version
t-b
committed
.github/workflows/github-actions-ci.yml: Don't install allensdk anymore
t-b
committed
.github/workflows/github-actions-ci.yml: Split steps for better readability
t-b
committed
.github/workflows/github-actions-ci.yml: Extend python test range
t-b
committed
ipfx/x_to_nwb/conversion_utils.py: Avoid using the pkg_resources module
t-b
committed
tests/test_mies_nwb_pipeline_output.py: Avoid using the pkg_resources module
t-b
committed
.github/workflows/github-actions-ci.yml: Install libhdf5-dev debian package
t-b
committed
setup.py: Adapt supported python versions
t-b
committed
.github/workflows: Test on-premise also with more python versions
t-b
committed
docker/Dockerfile: Install libhdf5-dev as well
t-b
committed

Commits on Aug 27, 2025

ipfx/lims_queries.py: Fix racy dictionary querying
t-b
committed
.github/workflows/nightly-onprem.yml: Remove branch logic
t-b
committed

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Get it working again for newer versions of dependencies#582

Get it working again for newer versions of dependencies#582
t-b merged 28 commits intomasterfrom
science-staging-v2

Commits on Aug 26, 2025

Move JSON handling code into package to remove dependency on AllenSDK

Move deprecation handling into package from AllenSDK

Change package version in x_to_nwb to check IPFX, not AllenSDK

Move LIMS credential managment into IPFX from AllenSDK

Change json_utilities imports in tests

Remove SDK as option for data source in scripts

Remove dependency on allensdk Manifest.safe_mkdir

Remove allensdk as dependency

Bump version

Relax pynwb version dependency

tests: Get them working again

lims_queries.py/able_to_connect_to_lims: Catch KeyError as well

run_feature_collection/extract_features: Fix numpy exception

treewide: Adapt to new pynwb 3.0 API

tests: Use correct units for stimulus

treewide: Allow to inject a SweepTable

requirements.txt: Don't require a fixed pynwb version

.github/workflows/github-actions-ci.yml: Don't install allensdk anymore

.github/workflows/github-actions-ci.yml: Split steps for better readability

.github/workflows/github-actions-ci.yml: Extend python test range

ipfx/x_to_nwb/conversion_utils.py: Avoid using the pkg_resources module

tests/test_mies_nwb_pipeline_output.py: Avoid using the pkg_resources module

.github/workflows/github-actions-ci.yml: Install libhdf5-dev debian package

setup.py: Adapt supported python versions

.github/workflows: Test on-premise also with more python versions

docker/Dockerfile: Install libhdf5-dev as well

Commits on Aug 27, 2025

ipfx/lims_queries.py: Fix racy dictionary querying

.github/workflows/nightly-onprem.yml: Remove branch logic