VERIFIED

neurodatawithoutborders__pynwb-2052

VERIFIED on first verdict

1 attempt, 0 appeals. 1 file, 1 added and 0 removed lines. Tokens: 33,252 tokens. Model cost: $0.01. Sandbox time: 1 min 31 s.

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The plan

Repository: neurodatawithoutborders/pynwb
Base commit: 01d9ab9 (image tag)
Issue: [Bug]: `add_data_interface` fails silently on pynwb 3.0 ### What happened? It seems that now in pynwb 3.0 the method `add_data_interface` was replaced by `add`. But the method `add_data_interface` does not add the structure or throws an error. ### Steps to Reproduce

Files to edit

src/pynwb/base.py

Approach: Add self.add(kwargs['container']) after issuing warning.

Attempt 1

VERIFIED

Agent branch

Kind	Command	Duration	Digest
command	`git ls-files -z` exact command git ls-files -z	0.004s	e00f310a
write	`write src/pynwb/base.py` exact command /opt/receipts-9bc23c8be6f34d5e9c605ee0141aeea0/bin/busybox sh -c 'mkdir -p /pynwb/src/pynwb && cp /opt/receipts-9bc23c8be6f34d5e9c605ee0141aeea0/incoming/ae2b202d3537e8f63d631f6f90b08a0803780db3955cd88b70a5dd37decff777 /pynwb/src/pynwb/base.py'	0.005s	c5682a11
command	`pytest tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface -v` exact command /opt/receipts-f9221898dc0844538d0d18c156a016df/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-f9221898dc0844538d0d18c156a016df/receipts_pytest.py tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface -v -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/agent1-3.xml	2.737s	f5f5105adeec
command	`pytest tests/unit/test_base.py` exact command /opt/receipts-7347999d9dfa4e5695f4dbf11480c0bc/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-7347999d9dfa4e5695f4dbf11480c0bc/receipts_pytest.py tests/unit/test_base.py --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/agent1-4.xml	5.126s	f5f5105adeec
diff	`capture patch` exact command compute patch in executor staging agent1-920f1d5a77f94c11802e51348f713c5b: /opt/homebrew/Cellar/git/2.53.0/bin/git -c core.hooksPath=/dev/null -c core.attributesFile=/dev/null -c diff.external= -c core.quotePath=false add -A && /opt/homebrew/Cellar/git/2.53.0/bin/git -c core.hooksPath=/dev/null -c core.attributesFile=/dev/null -c diff.external= -c core.quotePath=false diff --cached --binary --no-ext-diff --no-textconv --no-renames 08c7c797a5fcba8be7f76dc091a6757e060be2af	0.186s	f5f5105adeec

Finish summary: Fixed missing call to self.add() in ProcessingModule.add_data_interface. Added deprecation warning and then delegates to self.add(kwargs['NWBDataInterface']).
Worker outcome: finished

Target tests pass: yes
Full suite passes: yes
Files changed: src/pynwb/base.py
Ran tests: yes

Witness branch w1

Kind Command Exit Duration Digest

apply

Kind	Command	Exit	Duration	Digest
apply	`apply patch 347df7c95fc0` exact command git update-index -q --refresh; git apply -v --3way --recount --ignore-space-change --whitespace=nowarn /opt/receipts-68121a4a45ff45619dbef9a9077c7c07/incoming/347df7c95fc0642d27483dedc4115e095966d34f3dfdd6de0df0fe475307ac8b.diff	0	0.011s	f5f5105adeec
verification	`pytest (witness) tests/unit/test_base.py` exact command /opt/receipts-b9e35939de2d424cb9da86c781289d35/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-b9e35939de2d424cb9da86c781289d35/receipts_pytest.py --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning tests/unit/test_base.py -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/w1-2.xml	0	5.213s	f5f5105adeec

apply patch 347df7c95fc0

exact command

git update-index -q --refresh; git apply -v --3way --recount --ignore-space-change --whitespace=nowarn /opt/receipts-68121a4a45ff45619dbef9a9077c7c07/incoming/347df7c95fc0642d27483dedc4115e095966d34f3dfdd6de0df0fe475307ac8b.diff

0.011s

f5f5105adeec

verification

pytest (witness) tests/unit/test_base.py

exact command

/opt/receipts-b9e35939de2d424cb9da86c781289d35/bin/busybox mkdir -p /opt/receipts/reports && python -I /opt/receipts-b9e35939de2d424cb9da86c781289d35/receipts_pytest.py --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning tests/unit/test_base.py -o junit_family=xunit1 -p no:cacheprovider -rA --continue-on-collection-errors --junitxml=/opt/receipts/reports/w1-2.xml

5.213s

f5f5105adeec

Gate predicate checklist

Predicate	Name	Status	Evidence
`R1_fail_to_pass`	Failing specification tests now pass	PASS	target tests passed: tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface
`R2_pass_to_pass`	Previously passing tests kept	PASS	66 baseline-passing tests still pass
`R3_no_shrink`	No removed tests or new skips	PASS	all 67 baseline tests collected; skips unchanged (0)
`R4_patch_scope`	Patch scope	PASS	patch touches 1 file(s), all in scope
`R5_provenance`	Witness chain and patch digest	PASS	agent chain 8c1cfd7b -> 29e9b191 unbroken over 5 receipt(s); witness chain 8c1cfd7b -> 6dfb1e10 unbroken over 2 receipt(s); applied digest matches
`R6_claim_audit`	Agent claim audit (advisory)	PASS	claimed green; own last run: 67 passed, 0 failed

What it said

Finish summary: Fixed missing call to self.add() in ProcessingModule.add_data_interface. Added deprecation warning and then delegates to self.add(kwargs['NWBDataInterface']).
Worker outcome: finished

Target tests pass: yes
Full suite passes: yes
Files changed: src/pynwb/base.py
Ran tests: yes

What the record shows

honest: claimed green; own last run: 67 passed, 0 failed

SWE-rebench's official grader: resolved

Agrees with the gate

Shipped patch

diff --git a/src/pynwb/base.py b/src/pynwb/base.pyindex e639eccf..a7154450 100644--- a/src/pynwb/base.py+++ b/src/pynwb/base.py@@ -77,6 +77,7 @@ class ProcessingModule(MultiContainerInterface):              'doc': 'the NWBDataInterface to add to this Module'})     def add_data_interface(self, **kwargs):         warn('add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.', DeprecationWarning)+        self.add(kwargs['NWBDataInterface'])      @docval({'name': 'data_interface_name', 'type': str, 'doc': 'the name of the NWBContainer to retrieve'})     def get_data_interface(self, **kwargs):

Model and costs

Model: NVIDIA Nemotron 3 Super thinking off · temperature 1.0 · top_p 0.95
Tokens: 33,252 tokens
Model cost: $0.01
Sandbox time: 1 min 31 s
Sandbox cost: Token Factory reported cost: 0.291 (unit not published)

Full environment disclosure

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The bundle

Recorded JSON and patches. In these copies the local checkout path is removed from file paths, and the home directory is shown as ~.