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Update to pynwb 3.0 #2338

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t-b opened this issue Jan 29, 2025 · 0 comments
Open
3 tasks

Update to pynwb 3.0 #2338

t-b opened this issue Jan 29, 2025 · 0 comments
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CodeQuality enhancement New feature or request

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@t-b
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t-b commented Jan 29, 2025

rc1 is out, tested today works, see 1!

  • Switch to 3.0.0 final
  • Wait for new dandi version which supports it
  • Apply script adaptations
git diff .
diff --git a/tools/nwb-read-tests/nwbv2-read-test.py b/tools/nwb-read-tests/nwbv2-read-test.py
index 65d915020..6a389683b 100755
--- a/tools/nwb-read-tests/nwbv2-read-test.py
+++ b/tools/nwb-read-tests/nwbv2-read-test.py
@@ -25,7 +25,7 @@ def checkFile(path):
         return 1

     # 1.) pynwb Validation
-    comp = run(["python", "-m", "pynwb.validate", path],
+    comp = run(["pynwb-validate", path],
                stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=120)

     if comp.returncode != 0:
@@ -49,7 +49,7 @@ def checkFile(path):
         nwbfile = io.read()

         print(f"nwbfile: {nwbfile}")
-        print(f"ic_electrodes: {nwbfile.ic_electrodes}")
+        print(f"icephys_electrodes: {nwbfile.icephys_electrodes}")
         print(f"sweep_table: {nwbfile.sweep_table}")
         print(f"lab_meta_data: {nwbfile.lab_meta_data}")
         print(f"acquisition: {nwbfile.acquisition}")
@t-b t-b added CodeQuality enhancement New feature or request labels Jan 29, 2025
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