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Get it working again for newer versions of dependencies #568
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This was referenced Aug 20, 2025
Fix somes invalid imports introduced in the previous commits. Also support numpy v1 and v2 with a fallback import.
This probably changed with some python upgrade.
Since numpy 1.18 creating ragged arrays requires explit opt-in via dtype-object [1]. Let's to that then. [1]: numpy/numpy#14794
ic_electrodes was renamed to icephys_electrodes and the same for add_ic_electrode/create_ic_electrode.
Since pynwb 1.1.0 the unit for stimuli are hardcoded, but supplying a different one gives a warning. So let's just pass in the correct one. [1]: NeurodataWithoutBorders/pynwb#1186 (comment)
The SweepTable was the first icephys table for grouping different patch clamp series together, see NeurodataWithoutBorders/pynwb@21f91920 (Add a SweepTable for icephys data, 2018-11-02) for pynwb 0.6.0. This was superseeded by the icephys metadata tables introduced in pynwb 2.0.0 and finally removed in 3.0.0. While migrating to the icephys metadata tables is on the list [1], we don't want to do this here now. So let's add a nasty hack for injecting a sweep table. [1]: AllenInstitute/IPNWB#47
This is removed in python 3.12. And we can also directly use __version__.
… module This is removed in python 3.12. We can leverage the importlib.resources module introduced in python 3.9 instead.
…ackage This is required for the python 3.14 CI job as not all packages ship wheels.
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This is required for the python 3.14-rc on premise job as not all packages ship wheels.
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This is a collaborative work to decruft ipfx. The goal is to make it usable with newer python/numpy/pynwb versions.
The tests without LIMS pass here locally with python 3.9-3.14rc2, numpy 2.32 and pynwb 3.1.2.
ToDos:
Close #561
Close #567