hdmf-dev__hdmf-683

Snapshot captured 2026-11-12T17:06:59.476467+00:00 · Autoresearch-Arena/gemma-4-developer-agent

{
  "datasets": [
    "opd_e4b_pure_v6a",
    "opd_e4b_pure_v6b"
  ],
  "examples": 4,
  "instance_id": "hdmf-dev__hdmf-683",
  "problem_statement": "Adding child to parent container does not always mark parent as modified \n## Description\r\n\r\nIf a child container already has a parent and that child is added to a new container (so a link will be made in the ObjectMapper), then currently, the new container is not marked as modified. This is relevant when exporting. Adding a link to an existing object would not mark the file as modified, so it would not get rebuilt.\r\n\r\n## Steps to Reproduce\r\n\r\n```python\r\nchild_obj1 = Container('test child 1')\r\nobj1 = ContainerWithChild()\r\nobj1.set_modified(False)  # set to False so that we can test that it is set to True next\r\nobj1.field1 = child_obj1\r\nself.assertTrue(obj1.modified)\r\nself.assertIs(obj1.field1, child_obj1)\r\n\r\nobj3 = ContainerWithChild()\r\nobj3.set_modified(False)  # set to False so that we can test that it is set to True next\r\nobj3.field1 = child_obj1  # child_obj1 already has a parent\r\nself.assertTrue(obj3.modified)\r\nself.assertIs(obj3.field1, child_obj1)\r\n```\r\n```python\r\nobj1 = Container('obj1')\r\nobj2 = Container('obj2')\r\nobj1.parent = obj2\r\nfoo = Foo()   # Foo is a MultiContainerInterface\r\nfoo.set_modified(False)  # set to False so that we can test whether add_container makes it True\r\nfoo.add_container(obj1)\r\nself.assertTrue(foo.modified)  # fails\r\n\r\n\r\n```\r\n## Environment\r\n\r\n<!--Please describe your environment according to the following bullet points.-->\r\n\r\n    Python Executable: Conda\r\n    Python Version: Python 3.9\r\n    Operating System: Windows\r\n    HDMF Version: dev\r\n\r\n## Checklist\r\n\r\n- [x] Have you ensured the bug was not already [reported](https://github.com/hdmf-dev/hdmf/issues) ?\r\n- [x] Have you included a brief and descriptive title?\r\n- [x] Have you included a clear description of the problem you are trying to solve?\r\n- [x] Have you included a minimal code snippet that reproduces the issue you are encountering?\r\n- [x] Have you checked our [Contributing](https://github.com/hdmf-dev/hdmf/blob/dev/docs/CONTRIBUTING.rst) document?",
  "repo": "hdmf-dev/hdmf",
  "source": "v2/experiments/train_data/opd_e4b_pure_v6a/verified_rft_messages.jsonl",
  "source_sha256": "f045b7ca5b3883a1e2eaee81e1c02a4a1b53dd7b7b36e98bacb2ba5823a15148"
}

{
  "captured_at": "2026-11-12T17:06:59.476467+00:00",
  "membership": "archived training",
  "membership_evidence": "Task issues extracted from preserved verified_rft_messages training examples. This is not a verified current RL wave manifest.",
  "name": "Preserved post-training task archive",
  "source": "Autoresearch-Arena/gemma-4-developer-agent",
  "source_revision": "016496de222aaafca0d4ee4c18efc63ba616f76e",
  "sources": [
    {
      "path": "v2/experiments/train_data/opd_e4b_cispo_v5/verified_rft_messages.jsonl",
      "sha256": "a43610ad0dfb6ace95375cfae09000f41afc0338cc925af870a4ade7a9b20c4c"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_hybrid_v3/verified_rft_messages.jsonl",
      "sha256": "bd326303eb127e8e5e08f03daf97bb88d79d19709d59f3f93f348bc56686a8df"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_onpolicy_v3/verified_rft_messages.jsonl",
      "sha256": "960c680e797e823a0d3a22f4b1d5ef60a72971373d703b877340b0c9126aaf68"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_pure_v6a/verified_rft_messages.jsonl",
      "sha256": "f045b7ca5b3883a1e2eaee81e1c02a4a1b53dd7b7b36e98bacb2ba5823a15148"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_pure_v6b/verified_rft_messages.jsonl",
      "sha256": "0f62460a9706eea5e1605255896f191ab00cb5706c5f1f2e1c293e9a718218dc"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_pure_v7/verified_rft_messages.jsonl",
      "sha256": "e37f7bd675322f3f81500b73559d60d5f602ca0537bf19f5cb06332c728c7b72"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_pure_v7b/verified_rft_messages.jsonl",
      "sha256": "b864bdc8695183433eef6e31cb8d33fad44ba3aded2170c1ade4ad5b2944ce23"
    },
    {
      "path": "v2/experiments/train_data/opd_e4b_self_audit_v4/verified_rft_messages.jsonl",
      "sha256": "0026023745afb8f3dc1c176dc7f7171157b4ad5a66656b524af218e8e19ceee6"
    },
    {
      "path": "v2/experiments/train_data/rft_e4b_aligned_v2/verified_rft_messages.jsonl",
      "sha256": "92a4515fee9d152b0d4c510ee3ce4caaaffe2003ba7584469f8027f174aab18c"
    },
    {
      "path": "v2/experiments/train_data/rft_v1/verified_rft_messages.jsonl",
      "sha256": "a42453ccd7ac7680b0a03865e8e7080bc8bf74c8d9d193b440c441ed46f8512b"
    },
    {
      "path": "v2/experiments/train_data/rft_v2/verified_rft_messages.jsonl",
      "sha256": "18f4b3bd7e651f83c6acab479c9475e3fa50dc652a384f309e97146983ac85ba"
    }
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}