neurodatawithoutborders__pynwb-1669

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

{
  "datasets": [
    "opd_e4b_cispo_v5",
    "opd_e4b_pure_v6a",
    "opd_e4b_pure_v6b",
    "opd_e4b_pure_v7",
    "opd_e4b_pure_v7b"
  ],
  "examples": 30,
  "instance_id": "neurodatawithoutborders__pynwb-1669",
  "problem_statement": "[Bug]: Error on parsing nwb_version attribute\n### What happened?\n\nI'm in the process of updating our CI pipeline to validate the IPNWB/MIES generated NWB.\r\npynwb is updated from 2.1.0 to 2.3.1.\r\n\r\nThe file passes validation.\r\n\r\nSee also https://github.com/AllenInstitute/MIES/pull/1650.\r\n\r\nNow the problem is that the file can not be opened anymore because `/nwb_version` has an unexpected HDF5 format. This was not an issue with 2.1.0. a1f472b1 (Check nwb_version on read (#1612), 2022-12-18) seems to be culprit.\r\n\r\n```\r\nHDF5 \"E:\\projekte\\mies-igor\\HardwareBasic_1-V2.nwb\" {\r\nATTRIBUTE \"nwb_version\" {\r\n   DATATYPE  H5T_STRING {\r\n      STRSIZE 5;\r\n      STRPAD H5T_STR_NULLPAD;\r\n      CSET H5T_CSET_UTF8;\r\n      CTYPE H5T_C_S1;\r\n   }\r\n   DATASPACE  SCALAR\r\n   DATA {\r\n   (0): \"2.2.4\"\r\n   }\r\n}\r\n}\r\n```\n\n### Steps to Reproduce\n\n```python\nimport pynwb\r\n\r\nio = pynwb.NWBHDF5IO(\"HardwareBasic_1-V2.nwb\", 'r', load_namespaces=True)\r\nnwbfile = io.read()\n```\n\n\n### Traceback\n\n```python\nC:\\users\\thomas\\Anaconda3\\lib\\site-packages\\hdmf\\spec\\namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.1.3 because version 1.5.1 is already loaded.\r\n  warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\r\nC:\\users\\thomas\\Anaconda3\\lib\\site-packages\\hdmf\\spec\\namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.2.4 because version 2.6.0-alpha is already loaded.\r\n  warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\r\nTraceback (most recent call last):\r\n  File \"read.py\", line 4, in <module>\r\n    nwbfile = io.read()\r\n  File \"C:\\users\\thomas\\Anaconda3\\lib\\site-packages\\hdmf\\utils.py\", line 645, in func_call\r\n    return func(args[0], **pargs)\r\n  File \"C:\\users\\thomas\\Anaconda3\\lib\\site-packages\\pynwb\\__init__.py\", line 280, in read\r\n    file_version_str, file_version = self.nwb_version\r\n  File \"C:\\users\\thomas\\Anaconda3\\lib\\site-packages\\pynwb\\__init__.py\", line 262, in nwb_version\r\n    nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\r\nTypeError: a bytes-like object is required, not 'str'\n```\n\n\n### Operating System\n\nWindows\n\n### Python Executable\n\nConda\n\n### Python Version\n\n3.8\n\n### Package Versions\n\n[HardwareBasic_1-V2.zip](https://github.com/NeurodataWithoutBorders/pynwb/files/10996295/HardwareBasic_1-V2.zip)\r\n\r\n[environment_for_issue.txt](https://github.com/NeurodataWithoutBorders/pynwb/files/10996306/environment_for_issue.txt)\n\n### Code of Conduct\n\n- [X] I agree to follow this project's [Code of Conduct](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/.github/CODE_OF_CONDUCT.rst)\n- [X] Have you checked the [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?\n- [X] Have you ensured this bug was not already [reported](https://github.com/NeurodataWithoutBorders/pynwb/issues)?",
  "repo": "NeurodataWithoutBorders/pynwb",
  "source": "v2/experiments/train_data/opd_e4b_cispo_v5/verified_rft_messages.jsonl",
  "source_sha256": "a43610ad0dfb6ace95375cfae09000f41afc0338cc925af870a4ade7a9b20c4c"
}

{
  "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"
    }
  ]
}