ROLLOUT 0 · h5py/h5py
h5py__h5py-2577
Not solved
479 stotal time
25tool calls
25model calls
5,725tokens generated
210,001prompt tokens read
Test failures/errors recorded in JUnit XML (failures=1, errors=0)
Turn by turn
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System instructions 4,822 characters
You are a principal Python software engineer resolving a repository issue in `/workspace`. Your sole objective is to produce a minimal, root-cause source patch that passes every hidden fail-to-pass and pass-to-pass regression test on the first grading run. ## Critical Environment & Grader Rules 1. **Air-Gapped Sandbox & Available CLI Tools**: No network access. Never run `pip`, `uv`, `conda`, or `git fetch`. Note: `rg` (`ripgrep`) is NOT installed in the container — always use `grep -rn --include="*.py"` for fast exact searches so you never waste a tool call on `command not found`. 2. **Protected Grading Paths**: Before running official verification, the grading harness **strips and reverts all changes** to `tests/`, `test/`, `testing/`, `test_*.py`, `*_test.py`, `conftest.py`, `pyproject.toml`, `setup.cfg`, `pytest.ini`, and `tox.ini`. Every part of your fix MUST reside in non-test production source files. 3. **Untracked File Trap (`git add -N .`)**: `submit_patch` stages ALL untracked files inside `/workspace`! Never leave reproduction or scratch files inside `/workspace` — run reproductions inline via `python3 - <<'PY'` or inside `/tmp/repro.py` in a single `run_command`. 4. **Stdout Truncation Rule**: `run_command` truncates stdout after the first 5,000 characters from the TOP. Always run pytest quietly with short tracebacks: `pytest path/to/test_file.py -k pattern -q --tb=short --no-header` If a test file is large, redirect output to `/tmp/pytest.log` and inspect `tail -n 80 /tmp/pytest.log` so failure tracebacks at the bottom are never cut off. 5. **Strict Pacing Discipline**: `get_status` and `submit_patch` are free and do NOT count toward `max_tool_calls`. Target **16-22 counted tool calls total**, and **begin your first `edit_file` change no later than tool call 15**. Reserve at least 4 calls for verification, `git status --short && git diff`, and submission. ## Execution Protocol ### Phase 1 — Pinpoint Code & Tests Immediately (1-2 tool calls) - The user message already contains `Workspace Layout` — do NOT waste a turn running `ls` on top-level directories. - Run a single compound `run_command` with `grep -rn --include="*.py"` to locate: (a) the exact symbols, error strings, or functions from the problem description, (b) **all parallel or sibling implementations** (for example sync + async variants, `Client` + `AsyncClient`, serializer + deserializer, multiple backends/dialects, base + subclass methods, `__init__.py` / `__all__` exports), and (c) the closest existing unit test files under `tests/`. ### Phase 2 — Deep Read & Spec Anchor (2-5 tool calls) - Use `read_file` with generous `start_line` and `end_line` windows (180-300 lines per call so you read whole modules in fewer calls) on the target function/class, callers, type annotations, and neighboring tests. - Before editing, verify every explicit and implicit requirement from the issue: exact parameter names, defaults, boundary/domain edge cases, exception types/messages, `None` vs empty collection vs falsy (`0`, `False`, `""`) semantics, mutability/copying, and return types. ### Phase 3 — Reproduce Bug in One Call (1 tool call) - Run ONE concise command (`python3 - <<'PY' ... PY` or targeted `pytest ... -q --tb=short --no-header`) via `run_command` to observe the exact pre-fix failure. Do NOT spend multiple tool calls writing separate reproduction scripts. ### Phase 4 — Surgical Implementation Across All Parallel Paths (1-4 tool calls) - Begin editing by tool call 15! Use `edit_file` with 4-6 lines of exact surrounding context copied from `read_file`. - Update ALL parallel codepaths (sync/async, multiple classes/dialects, type hints) consistently so partial fixes do not fail sibling tests. - **2-Strike Edit Rule**: If `edit_file` fails twice on the same block due to whitespace or escaping, do not retry `edit_file` a third time — apply an atomic Python transformation via `run_command` and immediately verify `python3 -m py_compile path/to/file.py`. ### Phase 5 — Edge-Case Verification, Diff Hygiene & Clean Exit (2-4 tool calls) - Run a single compound `run_command` testing both your reproduction + boundary edge cases (`None`, empty input, leading/trailing delimiters, subdomain/prefix boundaries, subclass/async parity) AND the relevant existing `pytest` module(s) with `-q --tb=short --no-header`. - Run `git status --short && git diff` via `run_command`. Confirm: - ZERO untracked (`??`) files in `/workspace` (`rm -f` any untracked workspace files immediately), - ZERO modifications to `tests/` or protected config files (`git checkout -- tests/` if touched), - Minimal, clean diff with valid imports and indentation. - Call `submit_patch` once verification passes, then respond with a brief 2-sentence plain-text summary and make NO further tool calls.
Task prompt 7,613 characters
You are evaluating a software engineering task for repository h5py/h5py.
Problem Statement:
dataset.read_direct fails with ZeroDivisionError when '0 in shape'
Potential regression of #281, or simply related. H5py allows storing of empty arrays where any one of the dimensions can be 0 (e.g., `(0,)`, `(1, 0)`, `(1, 0, 3)`). If this dataset is read using `read_direct`, a `ZeroDivisionError` is thrown.
<details>
<summary>System version details (click to expand)</summary>
* Operating System (e.g. Windows 10, MacOS 10.11, Ubuntu 16.04.2 LTS, CentOS 7)
Arch Linux
* Python version (e.g. 2.7, 3.5)
3.6.0
* Where Python was acquired (e.g. system Python on MacOS or Linux, Anaconda on
Windows)
System repositories
* h5py version (e.g. 2.6)
2.7.0
* HDF5 version (e.g. 1.8.17)
1.10
</details>
Minimal script:
```python
import h5py
import numpy as np
print(h5py.version.info)
shape = (0,) # also try (1, 0, 2) or anything with 0 in it
hfile = h5py.File("/tmp/zerodata.h5", "w")
ds = hfile.create_dataset("ds", data=np.zeros(shape))
print("---------------------------------")
print(ds)
print(hfile["ds"])
print(hfile["ds"][:])
dsread = np.zeros(shape)
hfile["ds"].read_direct(dsread) # division by zero
hfile.close()
```
Output
```
Summary of the h5py configuration
---------------------------------
h5py 2.7.0
HDF5 1.10.0
Python 3.6.0 (default, Jan 16 2017, 12:12:55)
[GCC 6.3.1 20170109]
sys.platform linux
sys.maxsize 9223372036854775807
numpy 1.12.1
---------------------------------
<HDF5 dataset "ds": shape (0,), type "<f8">
<HDF5 dataset "ds": shape (0,), type "<f8">
[]
Traceback (most recent call last):
File "zero.py", line 17, in <module>
hfile["ds"].read_direct(dsread) # division by zero
File "/usr/lib/python3.6/site-packages/h5py/_hl/dataset.py", line 654, in read_direct
for mspace in dest_sel.broadcast(source_sel.mshape):
File "/usr/lib/python3.6/site-packages/h5py/_hl/selections.py", line 303, in broadcast
chunks = tuple(x//y for x, y in zip(count, tshape))
File "/usr/lib/python3.6/site-packages/h5py/_hl/selections.py", line 303, in <genexpr>
chunks = tuple(x//y for x, y in zip(count, tshape))
ZeroDivisionError: integer division or modulo by zero
```
## Task Budget (Session terminates when any budget is exhausted)
- Time allowance: 7.5 minutes
- Tool calls allowance: 30 calls
- Max loop iterations: 40 turns
## Execution Environment Rules
- Single command timeout: 90 seconds (commands exceeding this fail without ending the session)
- Command output limit: 5000 characters
- File view limit: 150 lines per read_file call
- File character limit: 10000 characters per read_file call
- Environment is offline (no network/PyPI access). All repository and test dependencies are ALREADY pre-installed. Do NOT attempt to run pip install or download packages.
## Instructions:
0. All source code is under `/workspace`. Do NOT search outside `/workspace` (e.g. `/usr/`, `/wheels/`, system site-packages). If imports fail, the issue is in the source code under `/workspace`, not in missing system packages.
1. Analyze the problem statement and any provided hints carefully to identify all requested script paths, CLI subcommands, or Python modules.
2. Inspect existing codebase conventions and test files before making edits.
3. Verify your implementation using targeted tests or inline assertions before submitting.
4. Call submit_patch only after your implementation is complete and verified.
5. As your final action, you must return a text-only response reporting your completion to terminate the session.
## Workspace Layout
The repository is located at `/workspace`. Here is the directory tree (up to 3 levels):
```
./LICENSE
./MANIFEST.in
./README.rst
./api_gen.py
./appveyor.yml
./asv.conf.json
./azure-pipelines.yml
./benchmarks
./ci
./ci/appveyor
./ci/appveyor/vs2008_patch
./ci/azure-pipelines-steps.yml
./ci/bundle_hdf5_whl.py
./ci/cibw_before_all_macos.sh
./ci/cibw_before_all_windows.sh
./ci/cibw_test_command.sh
./ci/fix_paths.py
./ci/get_hdf5_if_needed.sh
./ci/get_hdf5_win.py
./ci/triage_build.sh
./ci/upload_coverage.py
./codecov.yml
./dev-install.sh
./docs
./docs_api
./docs_api/Makefile
./docs_api/_static
./docs_api/automod.py
./docs_api/conf.py
./docs_api/h5.rst
./docs_api/h5a.rst
./docs_api/h5ac.rst
./docs_api/h5d.rst
./docs_api/h5ds.rst
./docs_api/h5f.rst
./docs_api/h5fd.rst
./docs_api/h5g.rst
./docs_api/h5i.rst
./docs_api/h5l.rst
./docs_api/h5o.rst
./docs_api/h5p.rst
./docs_api/h5pl.rst
./docs_api/h5r.rst
./docs_api/h5s.rst
./docs_api/h5t.rst
./docs_api/h5z.rst
./docs_api/index.rst
./docs_api/objects.rst
./examples
./github_deploy_key_h5py_h5py.enc
./h5py
./h5py/__init__.py
./h5py/_conv.pxd
./h5py/_conv.pyx
./h5py/_errors.pxd
./h5py/_errors.pyx
./h5py/_hl
./h5py/_hl/__init__.py
./h5py/_hl/attrs.py
./h5py/_hl/base.py
./h5py/_hl/compat.py
./h5py/_hl/dataset.py
./h5py/_hl/datatype.py
./h5py/_hl/dims.py
./h5py/_hl/files.py
./h5py/_hl/filters.py
./h5py/_hl/group.py
./h5py/_hl/selections.py
./h5py/_hl/selections2.py
./h5py/_hl/vds.py
./h5py/_locks.pxi
./h5py/_objects.pxd
./h5py/_objects.pyx
./h5py/_proxy.pxd
./h5py/_proxy.pyx
./h5py/_selector.pyx
./h5py/api_compat.h
./h5py/api_functions.txt
./h5py/api_types_ext.pxd
./h5py/api_types_hdf5.pxd
./h5py/h5.pxd
./h5py/h5.pyx
./h5py/h5a.pxd
./h5py/h5a.pyx
./h5py/h5ac.pxd
./h5py/h5ac.pyx
./h5py/h5d.pxd
./h5py/h5d.pyx
./h5py/h5ds.pxd
./h5py/h5ds.pyx
./h5py/h5f.pxd
./h5py/h5f.pyx
./h5py/h5fd.pxd
./h5py/h5fd.pyx
./h5py/h5g.pxd
./h5py/h5g.pyx
./h5py/h5i.pxd
./h5py/h5i.pyx
./h5py/h5l.pxd
./h5py/h5l.pyx
./h5py/h5o.pxd
./h5py/h5o.pyx
./h5py/h5p.pxd
./h5py/h5p.pyx
./h5py/h5pl.pxd
./h5py/h5pl.pyx
./h5py/h5py_warnings.py
./h5py/h5r.pxd
./h5py/h5r.pyx
./h5py/h5s.pxd
./h5py/h5s.pyx
./h5py/h5t.pxd
./h5py/h5t.pyx
./h5py/h5z.pxd
./h5py/h5z.pyx
./h5py/ipy_completer.py
./h5py/tests
./h5py/tests/__init__.py
./h5py/tests/common.py
./h5py/tests/conftest.py
./h5py/tests/data_files
./h5py/tests/test_attribute_create.py
./h5py/tests/test_attrs.py
./h5py/tests/test_attrs_data.py
./h5py/tests/test_base.py
./h5py/tests/test_big_endian_file.py
./h5py/tests/test_completions.py
./h5py/tests/test_dataset.py
./h5py/tests/test_dataset_getitem.py
./h5py/tests/test_dataset_swmr.py
./h5py/tests/test_datatype.py
./h5py/tests/test_dimension_scales.py
./h5py/tests/test_dims_dimensionproxy.py
./h5py/tests/test_dtype.py
./h5py/tests/test_errors.py
./h5py/tests/test_file.py
./h5py/tests/test_file2.py
./h5py/tests/test_file_alignment.py
./h5py/tests/test_file_image.py
./h5py/tests/test_filters.py
./h5py/tests/test_group.py
./h5py/tests/test_h5.py
./h5py/tests/test_h5d_direct_chunk.py
./h5py/tests/test_h5f.py
./h5py/tests/test_h5o.py
./h5py/tests/test_h5p.py
./h5py/tests/test_h5pl.py
./h5py/tests/test_h5s.py
./h5py/tests/test_h5t.py
./h5py/tests/test_h5z.py
./h5py/tests/test_objects.py
./h5py/tests/test_ros3.py
./h5py/tests/test_selections.py
./h5py/tests/test_slicing.py
./h5py/tests/test_vds
./h5py/utils.pxd
./h5py/utils.pyx
./h5py/version.py
./licenses
./licenses/hdf5.txt
./licenses/license.txt
./licenses/pytables.txt
./licenses/python.txt
./licenses/stdint.txt
./lzf
./lzf/LICENSE.txt
./lzf/README.txt
./lzf/example.c
./lzf/lzf
./lzf/lzf/lzf.h
./lzf/lzf/lzfP.h
./lzf/lzf/lzf_c.c
./lzf/lzf/lzf_d.c
./lzf/lzf_filter.c
./lzf/lzf_filter.h
./news
./news/TEMPLATE.rst
./other
./other/garbage.py
./other/iterate_deadlock.py
./other/unterm-generator.py
./other/vlen_leak.py
./pylintrc
./pyproject.toml
./pytest.ini
./rever.xsh
./setup.py
./setup_build.py
./setup_configure.py
./tox.ini
```
Turn 1at 64 s568 tokens out5,306 prompt tokens
The user is reporting a `ZeroDivisionError` when calling `dataset.read_direct` on a dataset that has at least one dimension equal to 0. The traceback provided in the problem statement points to: `h5py/_hl/dataset.py`, line 654, in `read_direct` `h5py/_hl/selections.py`, line 303, in `broadcast` The exact line causing the error is: `chunks = tuple(x//y for x, y in zip(count, tshape))` It seems `y` (which comes from `tshape`) is 0. Let's start by reproducing this bug.
TOOL CALL · run_command
{
"command": "python3 - <<'PY'\nimport h5py\nimport numpy as np\nimport os\n\nshape = (0,)\nfilename = \"/tmp/zerodata.h5\"\nif os.path.exists(filename):\n os.remove(filename)\n\nwith h5py.File(filename, \"w\") as hfile:\n ds = hfile.create_dataset(\"ds\", data=np.zeros(shape))\n print(\"---------------------------------\")\n print(ds)\n \n dsread = np.zeros(shape)\n try:\n hfile[\"ds\"].read_direct(dsread)\n print(\"Success!\")\n except ZeroDivisionError as e:\n print(f\"Caught expected ZeroDivisionError: {e}\")\n except Exception as e:\n print(f\"Caught unexpected exception: {type(e).__name__}: {e}\")\n\n# Try other shapes too\nfor shape in [(1, 0), (1, 0, 3)]:\n filename = f\"/tmp/zerodata_{shape}.h5\"\n if os.path.exists(filename):\n os.remove(filename)\n with h5py.File(filename, \"w\") as hfile:\n ds = hfile.create_dataset(\"ds\", data=np.zeros(shape))\n dsread = np.zeros(shape)\n try:\n hfile[\"ds\"].read_direct(dsread)\n print(f\"Success for shape {shape}!\")\n except ZeroDivisionError as e:\n print(f\"Caught expected ZeroDivisionError for shape {shape}: {e}\")\n except Exception as e:\n print(f\"Caught unexpected exception for shape {shape}: {type(e).__name__}: {e}\")\nPY\n"
}Result of run_command 1,569 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "Traceback (most recent call last):\n File \"/workspace/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/workspace/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/workspace/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"details": {
"stdout": "",
"stderr": "Traceback (most recent call last):\n File \"/workspace/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/workspace/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/workspace/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"exit_code": 1
}
}Generated tokens 568 tokens · stopped: STOP
<|channel>thought
The user is reporting a `ZeroDivisionError` when calling `dataset.read_direct` on a dataset that has at least one dimension equal to 0.
The traceback provided in the problem statement points to:
`h5py/_hl/dataset.py`, line 654, in `read_direct`
`h5py/_hl/selections.py`, line 303, in `broadcast`
The exact line causing the error is:
`chunks = tuple(x//y for x, y in zip(count, tshape))`
It seems `y` (which comes from `tshape`) is 0.
Let's start by reproducing this bug.<channel|><|tool_call>call:run_command{command:<|"|>python3 - <<'PY'
import h5py
import numpy as np
import os
shape = (0,)
filename = "/tmp/zerodata.h5"
if os.path.exists(filename):
os.remove(filename)
with h5py.File(filename, "w") as hfile:
ds = hfile.create_dataset("ds", data=np.zeros(shape))
print("---------------------------------")
print(ds)
dsread = np.zeros(shape)
try:
hfile["ds"].read_direct(dsread)
print("Success!")
except ZeroDivisionError as e:
print(f"Caught expected ZeroDivisionError: {e}")
except Exception as e:
print(f"Caught unexpected exception: {type(e).__name__}: {e}")
# Try other shapes too
for shape in [(1, 0), (1, 0, 3)]:
filename = f"/tmp/zerodata_{shape}.h5"
if os.path.exists(filename):
os.remove(filename)
with h5py.File(filename, "w") as hfile:
ds = hfile.create_dataset("ds", data=np.zeros(shape))
dsread = np.zeros(shape)
try:
hfile["ds"].read_direct(dsread)
print(f"Success for shape {shape}!")
except ZeroDivisionError as e:
print(f"Caught expected ZeroDivisionError for shape {shape}: {e}")
except Exception as e:
print(f"Caught unexpected exception for shape {shape}: {type(e).__name__}: {e}")
PY
<|"|>}<tool_call|><|tool_response>
Turn 2at 95 s686 tokens out6,322 prompt tokens
Ah, I forgot that I cannot import the package from inside its installation directory. I need to move to `/tmp` or change `PYTHONPATH`. Actually, the protocol says "Run reproductions inline via `python3 - <<'PY'` or inside `/tmp/repro.py` in a single `run_command`". It seems I need to make sure I'm not in the `h5py` package root if it's in the current directory. I am in `/workspace`, and `h5py` is a subdirectory. `import h5py` should work unless the current directory is added to `sys.path` and it finds the folder `h5py` and thinks it's the package. Wait, the error says: `ImportError: You cannot import h5py from inside the install directory.` This is a check in `h5py/__init__.py`. Let's try running from `/tmp`.
TOOL CALL · run_command
{
"command": "cd /tmp && python3 - <<'PY'\nimport h5py\nimport numpy as np\nimport os\nimport sys\n# Add /workspace to path so it can find the local h5py if needed, \n# but the error message suggests h5py is already installed or available.\n# However, we want to test the code in /workspace.\nsys.path.insert(0, '/workspace')\n\nshape = (0,)\nfilename = \"/tmp/zerodata.h5\"\nif os.path.exists(filename):\n os.remove(filename)\n\nwith h5py.File(filename, \"w\") as hfile:\n ds = hfile.create_dataset(\"ds\", data=np.zeros(shape))\n print(\"---------------------------------\")\n print(ds)\n \n dsread = np.zeros(shape)\n try:\n hfile[\"ds\"].read_direct(dsread)\n print(\"Success!\")\n except ZeroDivisionError as e:\n print(f\"Caught expected ZeroDivisionError: {e}\")\n except Exception as e:\n print(f\"Caught unexpected exception: {type(e).__name__}: {e}\")\n\n# Try other shapes too\nfor shape in [(1, 0), (1, 0, 3)]:\n filename = f\"/tmp/zerodata_{shape}.h5\"\n if os.path.exists(filename):\n os.remove(filename)\n with h5py.File(filename, \"w\") as hfile:\n ds = hfile.create_dataset(\"ds\", data=np.zeros(shape))\n dsread = np.zeros(shape)\n try:\n hfile[\"ds\"].read_direct(dsread)\n print(f\"Success for shape {shape}!\")\n except ZeroDivisionError as e:\n print(f\"Caught expected ZeroDivisionError for shape {shape}: {e}\")\n except Exception as e:\n print(f\"Caught unexpected exception for shape {shape}: {type(e).__name__}: {e}\")\nPY\n"
}Result of run_command 1,539 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "Traceback (most recent call last):\n File \"/h5py/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/h5py/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/h5py/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"details": {
"stdout": "",
"stderr": "Traceback (most recent call last):\n File \"/h5py/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/h5py/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/h5py/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"exit_code": 1
}
}Generated tokens 686 tokens · stopped: STOP
Ah, I forgot that I cannot import the package from inside its installation directory. I need to move to `/tmp` or change `PYTHONPATH`.
Actually, the protocol says "Run reproductions inline via `python3 - <<'PY'` or inside `/tmp/repro.py` in a single `run_command`". It seems I need to make sure I'm not in the `h5py` package root if it's in the current directory. I am in `/workspace`, and `h5py` is a subdirectory. `import h5py` should work unless the current directory is added to `sys.path` and it finds the folder `h5py` and thinks it's the package.
Wait, the error says:
`ImportError: You cannot import h5py from inside the install directory.`
This is a check in `h5py/__init__.py`.
Let's try running from `/tmp`.
<channel|><|tool_call>call:run_command{command:<|"|>cd /tmp && python3 - <<'PY'
import h5py
import numpy as np
import os
import sys
# Add /workspace to path so it can find the local h5py if needed,
# but the error message suggests h5py is already installed or available.
# However, we want to test the code in /workspace.
sys.path.insert(0, '/workspace')
shape = (0,)
filename = "/tmp/zerodata.h5"
if os.path.exists(filename):
os.remove(filename)
with h5py.File(filename, "w") as hfile:
ds = hfile.create_dataset("ds", data=np.zeros(shape))
print("---------------------------------")
print(ds)
dsread = np.zeros(shape)
try:
hfile["ds"].read_direct(dsread)
print("Success!")
except ZeroDivisionError as e:
print(f"Caught expected ZeroDivisionError: {e}")
except Exception as e:
print(f"Caught unexpected exception: {type(e).__name__}: {e}")
# Try other shapes too
for shape in [(1, 0), (1, 0, 3)]:
filename = f"/tmp/zerodata_{shape}.h5"
if os.path.exists(filename):
os.remove(filename)
with h5py.File(filename, "w") as hfile:
ds = hfile.create_dataset("ds", data=np.zeros(shape))
dsread = np.zeros(shape)
try:
hfile["ds"].read_direct(dsread)
print(f"Success for shape {shape}!")
except ZeroDivisionError as e:
print(f"Caught expected ZeroDivisionError for shape {shape}: {e}")
except Exception as e:
print(f"Caught unexpected exception for shape {shape}: {type(e).__name__}: {e}")
PY
<|"|>}<tool_call|><|tool_response>
Turn 3at 110 s215 tokens out7,467 prompt tokens
It seems the environment already has `h5py` installed. I should not be adding `/workspace` to `sys.path` if it's already installed, OR I should be careful about how I'm doing it. Actually, if I want to test the changes I make in `/workspace`, I MUST use the code in `/workspace`. The error `ImportError: You cannot import h5py from inside the install directory` happens because someone put the check in `h5py/__init__.py` to prevent importing from the source tree if it's not installed. Wait, if I am in `/tmp` and I add `/workspace` to `sys.path`, and there is a folder `/workspace/h5py`, then `import h5py` will load from `/workspace/h5py`. Let's check `h5py/__init__.py` to see what that check is.
TOOL CALL · read_file
{
"filepath": "h5py/__init__.py"
}Result of read_file 3,947 characters
{
"status": "ok",
"filepath": "h5py/__init__.py",
"content": "# This file is part of h5py, a Python interface to the HDF5 library.\n#\n# http://www.h5py.org\n#\n# Copyright 2008-2013 Andrew Collette and contributors\n#\n# License: Standard 3-clause BSD; see \"license.txt\" for full license terms\n# and contributor agreement.\n\n\"\"\"\n This is the h5py package, a Python interface to the HDF5\n scientific data format.\n\"\"\"\n\nfrom warnings import warn as _warn\nimport atexit\n\n\n# --- Library setup -----------------------------------------------------------\n\n# When importing from the root of the unpacked tarball or git checkout,\n# Python sees the \"h5py\" source directory and tries to load it, which fails.\n# We tried working around this by using \"package_dir\" but that breaks Cython.\ntry:\n from . import _errors\nexcept ImportError:\n import os.path as _op\n if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\n else:\n raise\n\nfrom . import version\n\nif version.hdf5_version_tuple != version.hdf5_built_version_tuple:\n _warn((\"h5py is running against HDF5 {0} when it was built against {1}, \"\n \"this may cause problems\").format(\n '{0}.{1}.{2}'.format(*version.hdf5_version_tuple),\n '{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple)\n ))\n\n\n_errors.silence_errors()\n\nfrom ._conv import register_converters as _register_converters, \\\n unregister_converters as _unregister_converters\n_register_converters()\natexit.register(_unregister_converters)\n\nfrom .h5z import _register_lzf\n_register_lzf()\n\n\n# --- Public API --------------------------------------------------------------\n\nfrom . import h5a, h5d, h5ds, h5f, h5fd, h5g, h5r, h5s, h5t, h5p, h5z, h5pl\n\nfrom ._hl import filters\nfrom ._hl.base import is_hdf5, HLObject, Empty\nfrom ._hl.files import (\n File,\n register_driver,\n unregister_driver,\n registered_drivers,\n)\nfrom ._hl.group import Group, SoftLink, ExternalLink, HardLink\nfrom ._hl.dataset import Dataset\nfrom ._hl.datatype import Datatype\nfrom ._hl.attrs import AttributeManager\nfrom ._hl.vds import VirtualSource, VirtualLayout\n\nfrom ._selector import MultiBlockSlice\nfrom .h5 import get_config\nfrom .h5r import Reference, RegionReference\nfrom .h5t import (special_dtype, check_dtype,\n vlen_dtype, string_dtype, enum_dtype, ref_dtype, regionref_dtype,\n opaque_dtype,\n check_vlen_dtype, check_string_dtype, check_enum_dtype, check_ref_dtype,\n check_opaque_dtype,\n)\nfrom .h5s import UNLIMITED\n\nfrom .version import version as __version__\n\n\ndef run_tests(args=''):\n \"\"\"Run tests with pytest and returns the exit status as an int.\n \"\"\"\n # Lazy-loading of tests package to avoid strong dependency on test\n # requirements, e.g. pytest\n from .tests import run_tests\n return run_tests(args)\n\n\ndef enable_ipython_completer():\n \"\"\" Call this from an interactive IPython session to enable tab-completion\n of group and attribute names.\n \"\"\"\n import sys\n if 'IPython' in sys.modules:\n ip_running = False\n try:\n from IPython.core.interactiveshell import InteractiveShell\n ip_running = InteractiveShell.initialized()\n except ImportError:\n # support <ipython-0.11\n from IPython import ipapi as _ipapi\n ip_running = _ipapi.get() is not None\n except Exception:\n pass\n if ip_running:\n from . import ipy_completer\n return ipy_completer.load_ipython_extension()\n\n raise RuntimeError('Completer must be enabled in active ipython session')",
"start_line": 1,
"end_line": 115,
"total_lines": 115,
"is_truncated": false
}Generated tokens 215 tokens · stopped: STOP
It seems the environment already has `h5py` installed. I should not be adding `/workspace` to `sys.path` if it's already installed, OR I should be careful about how I'm doing it.
Actually, if I want to test the changes I make in `/workspace`, I MUST use the code in `/workspace`. The error `ImportError: You cannot import h5py from inside the install directory` happens because someone put the check in `h5py/__init__.py` to prevent importing from the source tree if it's not installed.
Wait, if I am in `/tmp` and I add `/workspace` to `sys.path`, and there is a folder `/workspace/h5py`, then `import h5py` will load from `/workspace/h5py`.
Let's check `h5py/__init__.py` to see what that check is.
<channel|><|tool_call>call:read_file{filepath:<|"|>h5py/__init__.py<|"|>}<tool_call|><|tool_response>
Turn 4at 135 s425 tokens out8,886 prompt tokens
The check is:
```python
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):\n raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.")
else:
raise
```
If `setup.py` is in the parent directory of `h5py`, it raises the error.
In `/workspace`, there is `setup.py` and `h5py/`. So if I'm in `/workspace` and `import h5py`, it will find `/workspace/h5py` and trigger this.
The best way to use the installed `h5py` (if it is already installed) is simply to `import h5py` without adding `/workspace` to `sys.path`. But I want to test the code in `/workspace`.
If I want to test the code in `/workspace`, I should probably use a virtualenv or just not have `setup.py` in the parent directory. But I can't move `setup.py`.
Wait, if I'm in `/tmp` and I add `/workspace` to `sys.path`, Python will find the `h5py` directory in `/workspace`. Since it's a package, it will try to import it. The `__init__.py` of that package will then check for `../setup.py`, and it will find `/workspace/setup.py`.
The intended way to use `h5py` is to have it installed via `pip install .` which moves it to `site-packages`.
Let's check if `h5py` is already installed and where it is.
TOOL CALL · run_command
{
"command": "python3 -c \"import h5py; print(h5py.__file__)\""
}Result of run_command 1,571 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "Traceback (most recent call last):\n File \"/workspace/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/workspace/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/workspace/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"details": {
"stdout": "",
"stderr": "Traceback (most recent call last):\n File \"/workspace/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/workspace/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/workspace/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"exit_code": 1
}
}Generated tokens 425 tokens · stopped: STOP
The check is:
```python
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):\n raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.")
else:
raise
```
If `setup.py` is in the parent directory of `h5py`, it raises the error.
In `/workspace`, there is `setup.py` and `h5py/`. So if I'm in `/workspace` and `import h5py`, it will find `/workspace/h5py` and trigger this.
The best way to use the installed `h5py` (if it is already installed) is simply to `import h5py` without adding `/workspace` to `sys.path`. But I want to test the code in `/workspace`.
If I want to test the code in `/workspace`, I should probably use a virtualenv or just not have `setup.py` in the parent directory. But I can't move `setup.py`.
Wait, if I'm in `/tmp` and I add `/workspace` to `sys.path`, Python will find the `h5py` directory in `/workspace`. Since it's a package, it will try to import it. The `__init__.py` of that package will then check for `../setup.py`, and it will find `/workspace/setup.py`.
The intended way to use `h5py` is to have it installed via `pip install .` which moves it to `site-packages`.
Let's check if `h5py` is already installed and where it is.
<channel|><|tool_call>call:run_command{command:<|"|>python3 -c "import h5py; print(h5py.__file__)"<|"|>}<tool_call|><|tool_response>
Turn 5at 149 s186 tokens out9,758 prompt tokens
It seems the current working directory is `/workspace`, so `import h5py` is picking up `/workspace/h5py` first. I should `cd` to a directory that is not `/workspace` and does NOT have `/workspace` in the `PYTHONPATH` unless it's the installed version. Wait, the environment instructions say: "No network access. Never run `pip`, `uv`, `conda`, or `git fetch`." and "All repository and test dependencies are ALREADY pre-installed." This means `h5py` should already be installed in `site-packages`. If I `cd /tmp`, `import h5py` should load the installed version.
TOOL CALL · run_command
{
"command": "cd /tmp && python3 -c \"import h5py; print(h5py.__file__)\""
}Result of run_command 1,541 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "Traceback (most recent call last):\n File \"/h5py/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/h5py/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/h5py/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"details": {
"stdout": "",
"stderr": "Traceback (most recent call last):\n File \"/h5py/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/h5py/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/h5py/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"exit_code": 1
}
}Generated tokens 186 tokens · stopped: STOP
It seems the current working directory is `/workspace`, so `import h5py` is picking up `/workspace/h5py` first.
I should `cd` to a directory that is not `/workspace` and does NOT have `/workspace` in the `PYTHONPATH` unless it's the installed version.
Wait, the environment instructions say: "No network access. Never run `pip`, `uv`, `conda`, or `git fetch`." and "All repository and test dependencies are ALREADY pre-installed."
This means `h5py` should already be installed in `site-packages`.
If I `cd /tmp`, `import h5py` should load the installed version.
<channel|><|tool_call>call:run_command{command:<|"|>cd /tmp && python3 -c "import h5py; print(h5py.__file__)"<|"|>}<tool_call|><|tool_response>
Turn 6at 151 s54 tokens out10,403 prompt tokens
Wait, what is `/h5py/h5py/__init__.py`? Let's see what's in `/h5py`.
TOOL CALL · run_command
{
"command": "ls -R /h5py"
}Result of run_command 4,945 characters
{
"status": "ok",
"stdout": "/h5py:\nLICENSE\nMANIFEST.in\nREADME.rst\napi_gen.py\nappveyor.yml\nasv.conf.json\nazure-pipelines.yml\nbenchmarks\nci\ncodecov.yml\ndev-install.sh\ndocs\ndocs_api\nexamples\ngithub_deploy_key_h5py_h5py.enc\nh5py\nlicenses\nlzf\nnews\nother\npylintrc\npyproject.toml\npytest.ini\nrever.xsh\nsetup.py\nsetup_build.py\nsetup_configure.py\ntox.ini\n\n/h5py/benchmarks:\n__init__.py\nbenchmark_slicing.py\nbenchmarks.py\n\n/h5py/ci:\nappveyor\nazure-pipelines-steps.yml\nbundle_hdf5_whl.py\ncibw_before_all_macos.sh\ncibw_before_all_windows.sh\ncibw_test_command.sh\nfix_paths.py\nget_hdf5_if_needed.sh\nget_hdf5_win.py\ntriage_build.sh\nupload_coverage.py\n\n/h5py/ci/appveyor:\nvs2008_patch\n\n/h5py/ci/appveyor/vs2008_patch:\nreadme.txt\nsetup_x64.bat\nsetup_x86.bat\nx64\nx86\n\n/h5py/ci/appveyor/vs2008_patch/x64:\n600dd186-2429-11d7-8bf6-00b0d03daa06.reg\n600dd187-2429-11d7-8bf6-00b0d03daa06.reg\n600dd188-2429-11d7-8bf6-00b0d03daa06.reg\n600dd189-2429-11d7-8bf6-00b0d03daa06.reg\n656d875f-2429-11d7-8bf6-00b0d03daa06.reg\n656d8760-2429-11d7-8bf6-00b0d03daa06.reg\n656d8763-2429-11d7-8bf6-00b0d03daa06.reg\n656d8766-2429-11d7-8bf6-00b0d03daa06.reg\nVC_OBJECTS_PLATFORM_INFO.reg\n\n/h5py/ci/appveyor/vs2008_patch/x86:\n600dd186-2429-11d7-8bf6-00b0d03daa06.reg\n600dd187-2429-11d7-8bf6-00b0d03daa06.reg\n600dd188-2429-11d7-8bf6-00b0d03daa06.reg\n600dd189-2429-11d7-8bf6-00b0d03daa06.reg\n656d875f-2429-11d7-8bf6-00b0d03daa06.reg\n656d8760-2429-11d7-8bf6-00b0d03daa06.reg\n656d8763-2429-11d7-8bf6-00b0d03daa06.reg\n656d8766-2429-11d7-8bf6-00b0d03daa06.reg\nVC_OBJECTS_PLATFORM_INFO.reg\n\n/h5py/docs:\nMakefile\nbuild.rst\nconf.py\nconfig.rst\ncontributing.rst\nfaq.rst\nhigh\nindex.rst\nlicenses.rst\nmpi.rst\nquick.rst\nrefs.rst\nrelated_projects.rst\nrelease_guide.rst\nrequirements-rtd.txt\nspecial.rst\nstrings.rst\nswmr.rst\nvds.rst\nwhatsnew\n\n/h5py/docs/high:\nattr.rst\ndataset.rst\ndims.rst\nfile.rst\ngroup.rst\nlowlevel.rst\n\n/h5py/docs/whatsnew:\n2.0.rst\n2.1.rst\n2.10.rst\n2.2.rst\n2.3.rst\n2.4.rst\n2.5.rst\n2.6.rst\n2.7.1.rst\n2.7.rst\n2.8.rst\n2.9.rst\n3.0.rst\n3.1.rst\n3.10.rst\n3.11.rst\n3.12.rst\n3.13.rst\n3.2.rst\n3.3.rst\n3.4.rst\n3.5.rst\n3.6.rst\n3.7.rst\n3.8.rst\n3.9.rst\nindex.rst\n\n/h5py/docs_api:\nMakefile\n_static\nautomod.py\nconf.py\nh5.rst\nh5a.rst\nh5ac.rst\nh5d.rst\nh5ds.rst\nh5f.rst\nh5fd.rst\nh5g.rst\nh5i.rst\nh5l.rst\nh5o.rst\nh5p.rst\nh5pl.rst\nh5r.rst\nh5s.rst\nh5t.rst\nh5z.rst\nindex.rst\nobjects.rst\n\n/h5py/docs_api/_static:\n\n/h5py/examples:\nbytesio.py\ncollective_io.py\ndataset_concatenation.py\ndual_pco_edge.py\neiger_use_case.py\nexcalibur_detector_modules.py\nmultiblockslice_interleave.py\nmultiprocessing_example.py\npercival_use_case.py\nstore_and_retrieve_units_example.py\nstore_datetimes.py\nswmr_inotify_example.py\nswmr_multiprocess.py\nthreading_example.py\nvds_simple.py\nwrite-direct-compressed.py\n\n/h5py/h5py:\n__init__.py\n_conv.pxd\n_conv.pyx\n_errors.pxd\n_errors.pyx\n_hl\n_locks.pxi\n_objects.pxd\n_objects.pyx\n_proxy.pxd\n_proxy.pyx\n_selector.pyx\napi_compat.h\napi_functions.txt\napi_types_ext.pxd\napi_types_hdf5.pxd\nh5.pxd\nh5.pyx\nh5a.pxd\nh5a.pyx\nh5ac.pxd\nh5ac.pyx\nh5d.pxd\nh5d.pyx\nh5ds.pxd\nh5ds.pyx\nh5f.pxd\nh5f.pyx\nh5fd.pxd\nh5fd.pyx\nh5g.pxd\nh5g.pyx\nh5i.pxd\nh5i.pyx\nh5l.pxd\nh5l.pyx\nh5o.pxd\nh5o.pyx\nh5p.pxd\nh5p.pyx\nh5pl.pxd\nh5pl.pyx\nh5py_warnings.py\nh5r.pxd\nh5r.pyx\nh5s.pxd\nh5s.pyx\nh5t.pxd\nh5t.pyx\nh5z.pxd\nh5z.pyx\nipy_completer.py\ntests\nutils.pxd\nutils.pyx\nversion.py\n\n/h5py/h5py/_hl:\n__init__.py\nattrs.py\nbase.py\ncompat.py\ndataset.py\ndatatype.py\ndims.py\nfiles.py\nfilters.py\ngroup.py\nselections.py\nselections2.py\nvds.py\n\n/h5py/h5py/tests:\n__init__.py\ncommon.py\nconftest.py\ndata_files\ntest_attribute_create.py\ntest_attrs.py\ntest_attrs_data.py\ntest_base.py\ntest_big_endian_file.py\ntest_completions.py\ntest_dataset.py\ntest_dataset_getitem.py\ntest_dataset_swmr.py\ntest_datatype.py\ntest_dimension_scales.py\ntest_dims_dimensionproxy.py\ntest_dtype.py\ntest_errors.py\ntest_file.py\ntest_file2.py\ntest_file_alignment.py\ntest_file_image.py\ntest_filters.py\ntest_group.py\ntest_h5.py\ntest_h5d_direct_chunk.py\ntest_h5f.py\ntest_h5o.py\ntest_h5p.py\ntest_h5pl.py\ntest_h5s.py\ntest_h5t.py\ntest_h5z.py\ntest_objects.py\ntest_ros3.py\ntest_selections.py\ntest_slicing.py\ntest_vds\n\n/h5py/h5py/tests/data_files:\n__init__.py\nvlen_string_dset.h5\nvlen_string_dset_utc.h5\nvlen_string_s390x.h5\n\n/h5py/h5py/tests/test_vds:\n__init__.py\ntest_highlevel_vds.py\ntest_lowlevel_vds.py\ntest_virtual_source.py\n\n/h5py/licenses:\nhdf5.txt\nlicense.txt\npytables.txt\npython.txt\nstdint.txt\n\n/h5py/lzf:\nLICENSE.txt\nREADME.txt\nexample.c\nlzf\nlzf_filter.c\nlzf_filter.h\n\n/h5py/lzf/lzf:\nlzf.h\nlzfP.h\nlzf_c.c\nlzf_d.c\n\n/h5py/news:\nTEMPLATE.rst\n\n/h5py/other:\ngarbage.py\niterate_deadlock.py\nunterm-generator.py\nvlen_leak.py\n",
"stderr": "",
"exit_code": 0
}Generated tokens 54 tokens · stopped: STOP
Wait, what is `/h5py/h5py/__init__.py`?
Let's see what's in `/h5py`.<channel|><|tool_call>call:run_command{command:<|"|>ls -R /h5py<|"|>}<tool_call|><|tool_response>
Turn 7at 160 s139 tokens out13,274 prompt tokens
It seems the library is installed in `/h5py/h5py`. This is very confusing. Wait, the workspace layout says: ``` ./h5py ./h5py/__init__.py ... ``` But `ls -R /h5py` shows: ``` /h5py: ... h5py ... /h5py/h5py: __init__.py ... ``` And `/workspace` is where I am. Let's see what's in `/workspace`.
TOOL CALL · run_command
{
"command": "ls -F /workspace"
}Result of run_command 410 characters
{
"status": "ok",
"stdout": "LICENSE\nMANIFEST.in\nREADME.rst\napi_gen.py\nappveyor.yml\nasv.conf.json\nazure-pipelines.yml\nbenchmarks/\nci/\ncodecov.yml\ndev-install.sh*\ndocs/\ndocs_api/\nexamples/\ngithub_deploy_key_h5py_h5py.enc\nh5py/\nlicenses/\nlzf/\nnews/\nother/\npylintrc\npyproject.toml\npytest.ini\nrever.xsh\nsetup.py*\nsetup_build.py\nsetup_configure.py\ntox.ini\n",
"stderr": "",
"exit_code": 0
}Generated tokens 139 tokens · stopped: STOP
It seems the library is installed in `/h5py/h5py`. This is very confusing.
Wait, the workspace layout says:
```
./h5py
./h5py/__init__.py
...
```
But `ls -R /h5py` shows:
```
/h5py:
...
h5py
...
/h5py/h5py:
__init__.py
...
```
And `/workspace` is where I am. Let's see what's in `/workspace`.
<channel|><|tool_call>call:run_command{command:<|"|>ls -F /workspace<|"|>}<tool_call|><|tool_response>
Turn 8at 167 s91 tokens out13,601 prompt tokens
Okay, so `/workspace` has the source code. And `/h5py` is another directory that also looks like the source code. Wait, if I run `python3`, where is it looking for packages? Let's check `sys.path`.
TOOL CALL · run_command
{
"command": "python3 -c \"import sys; print('\\n'.join(sys.path))\""
}Result of run_command 199 characters
{
"status": "ok",
"stdout": "\n/usr/local/lib/python310.zip\n/usr/local/lib/python3.10\n/usr/local/lib/python3.10/lib-dynload\n/usr/local/lib/python3.10/site-packages\n",
"stderr": "",
"exit_code": 0
}Generated tokens 91 tokens · stopped: STOP
Okay, so `/workspace` has the source code.
And `/h5py` is another directory that also looks like the source code.
Wait, if I run `python3`, where is it looking for packages?
Let's check `sys.path`.
<channel|><|tool_call>call:run_command{command:<|"|>python3 -c "import sys; print('\n'.join(sys.path))"<|"|>}<tool_call|><|tool_response>
Turn 9at 176 s118 tokens out13,797 prompt tokens
The `sys.path` does not include `/workspace` or `/h5py`. So when I do `import h5py` from `/workspace`, Python finds `/workspace/h5py` because the current directory is usually in `sys.path` as `''` or the current path. Wait, let's check `sys.path` again with `import sys; print(sys.path)`.
TOOL CALL · run_command
{
"command": "python3 -c \"import sys; print(sys.path)\""
}Result of run_command 211 characters
{
"status": "ok",
"stdout": "['', '/usr/local/lib/python310.zip', '/usr/local/lib/python3.10', '/usr/local/lib/python3.10/lib-dynload', '/usr/local/lib/python3.10/site-packages']\n",
"stderr": "",
"exit_code": 0
}Generated tokens 118 tokens · stopped: STOP
The `sys.path` does not include `/workspace` or `/h5py`.
So when I do `import h5py` from `/workspace`, Python finds `/workspace/h5py` because the current directory is usually in `sys.path` as `''` or the current path.
Wait, let's check `sys.path` again with `import sys; print(sys.path)`.
<channel|><|tool_call>call:run_command{command:<|"|>python3 -c "import sys; print(sys.path)"<|"|>}<tool_call|><|tool_response>
Turn 10at 187 s146 tokens out14,019 prompt tokens
Yes, `''` is at the beginning. That means the current directory is searched first. If I want to use the *installed* version of `h5py`, I should move to a directory where no directory named `h5py` exists. `/tmp` is good. But wait, if I am in `/tmp`, and I `import h5py`, it should look into `/usr/local/lib/python3.10/site-packages`. Is `h5py` installed there?
TOOL CALL · run_command
{
"command": "ls /usr/local/lib/python3.10/site-packages/h5py"
}Result of run_command 313 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "ls: cannot access '/usr/local/lib/python3.10/site-packages/h5py': No such file or directory\n",
"details": {
"stdout": "",
"stderr": "ls: cannot access '/usr/local/lib/python3.10/site-packages/h5py': No such file or directory\n",
"exit_code": 2
}
}Generated tokens 146 tokens · stopped: STOP
Yes, `''` is at the beginning. That means the current directory is searched first.
If I want to use the *installed* version of `h5py`, I should move to a directory where no directory named `h5py` exists. `/tmp` is good.
But wait, if I am in `/tmp`, and I `import h5py`, it should look into `/usr/local/lib/python3.10/site-packages`.
Is `h5py` installed there?
<channel|><|tool_call>call:run_command{command:<|"|>ls /usr/local/lib/python3.10/site-packages/h5py<|"|>}<tool_call|><|tool_response>
Turn 11at 193 s105 tokens out14,286 prompt tokens
So `h5py` is NOT installed in `site-packages`. Then where was it coming from when I did `cd /tmp && python3 -c "import h5py; print(h5py.__file__)"`? It said `/h5py/h5py/__init__.py`. Wait, is `/h5py` in the `PYTHONPATH` environment variable?
TOOL CALL · run_command
{
"command": "env | grep PYTHONPATH"
}Result of run_command 127 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "",
"details": {
"stdout": "",
"stderr": "",
"exit_code": 1
}
}Generated tokens 105 tokens · stopped: STOP
So `h5py` is NOT installed in `site-packages`.
Then where was it coming from when I did `cd /tmp && python3 -c "import h5py; print(h5py.__file__)"`?
It said `/h5py/h5py/__init__.py`.
Wait, is `/h5py` in the `PYTHONPATH` environment variable?
<channel|><|tool_call>call:run_command{command:<|"|>env | grep PYTHONPATH<|"|>}<tool_call|><|tool_response>
Turn 12at 202 s118 tokens out14,446 prompt tokens
No `PYTHONPATH`.
Wait, look at the error again:
`Traceback (most recent call last):`
`File "/h5py/h5py/__init__.py", line 25, in <module>`
`from . import _errors`
How did it find `/h5py/h5py/__init__.py`?
Maybe `/h5py` is a symbolic link to `/workspace`?
TOOL CALL · run_command
{
"command": "ls -ld /h5py"
}Result of run_command 120 characters
{
"status": "ok",
"stdout": "lrwxrwxrwx 1 root root 10 Nov 14 03:16 /h5py -> /workspace\n",
"stderr": "",
"exit_code": 0
}Generated tokens 118 tokens · stopped: STOP
No `PYTHONPATH`.
Wait, look at the error again:
`Traceback (most recent call last):`
`File "/h5py/h5py/__init__.py", line 25, in <module>`
`from . import _errors`
How did it find `/h5py/h5py/__init__.py`?
Maybe `/h5py` is a symbolic link to `/workspace`?
<channel|><|tool_call>call:run_command{command:<|"|>ls -ld /h5py<|"|>}<tool_call|><|tool_response>
Turn 13at 287 s209 tokens out2,986 prompt tokens
Ah! `/h5py` is a symlink to `/workspace`.
Since `/h5py` is likely in the `sys.path` by default in this environment (or something similar), it's always trying to import from the source.
The logic in `h5py/__init__.py` is:
```python
if 'setup.py' in os.listdir(os.path.dirname(os.getcwd())):
raise ImportError("You cannot import h5py from inside the install directory")
```
Wait, no, it was:
```python
if 'setup.py' in os.listdir(os.path.dirname(os.path.abspath(__file__))):
```
Let me check `h5py/__init__.py` again to see exactly what's there.
TOOL CALL · read_file
{
"end_line": 50,
"filepath": "h5py/__init__.py",
"start_line": 1
}Result of read_file 1,835 characters
{
"status": "ok",
"filepath": "h5py/__init__.py",
"content": "# This file is part of h5py, a Python interface to the HDF5 library.\n#\n# http://www.h5py.org\n#\n# Copyright 2008-2013 Andrew Collette and contributors\n#\n# License: Standard 3-clause BSD; see \"license.txt\" for full license terms\n# and contributor agreement.\n\n\"\"\"\n This is the h5py package, a Python interface to the HDF5\n scientific data format.\n\"\"\"\n\nfrom warnings import warn as _warn\nimport atexit\n\n\n# --- Library setup -----------------------------------------------------------\n\n# When importing from the root of the unpacked tarball or git checkout,\n# Python sees the \"h5py\" source directory and tries to load it, which fails.\n# We tried working around this by using \"package_dir\" but that breaks Cython.\ntry:\n from . import _errors\nexcept ImportError:\n import os.path as _op\n if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\n else:\n raise\n\nfrom . import version\n\nif version.hdf5_version_tuple != version.hdf5_built_version_tuple:\n _warn((\"h5py is running against HDF5 {0} when it was built against {1}, \"\n \"this may cause problems\").format(\n '{0}.{1}.{2}'.format(*version.hdf5_version_tuple),\n '{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple)\n ))\n\n\n_errors.silence_errors()\n\nfrom ._conv import register_converters as _register_converters, \\\n unregister_converters as _unregister_converters\n_register_converters()\natexit.register(_unregister_converters)\n\nfrom .h5z import _register_lzf",
"start_line": 1,
"end_line": 50,
"total_lines": 115,
"is_truncated": false
}Generated tokens 209 tokens · stopped: STOP
Ah! `/h5py` is a symlink to `/workspace`.
Since `/h5py` is likely in the `sys.path` by default in this environment (or something similar), it's always trying to import from the source.
The logic in `h5py/__init__.py` is:
```python
if 'setup.py' in os.listdir(os.path.dirname(os.getcwd())):
raise ImportError("You cannot import h5py from inside the install directory")
```
Wait, no, it was:
```python
if 'setup.py' in os.listdir(os.path.dirname(os.path.abspath(__file__))):
```
Let me check `h5py/__init__.py` again to see exactly what's there.<channel|><|tool_call>call:read_file{filepath:<|"|>h5py/__init__.py<|"|>,start_line:1,end_line:50}<tool_call|><|tool_response>
Turn 14at 315 s391 tokens out3,768 prompt tokens
The code is:
```python
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):\n raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.")
else:
raise
```
`_op.dirname(__file__)` is `/workspace/h5py`.
`_op.join(..., '..', 'setup.py')` is `/workspace/setup.py`.
Since `/workspace/setup.py` exists, it raises the `ImportError`.
Wait, `from . import _errors` is being called. If `_errors` is a compiled module (which it usually is in `h5py`), and it hasn't been compiled yet in `/workspace/h5py`, it will raise `ImportError`.
To fix this for reproduction, I should either:
1. Build `h5py` in the workspace.
2. Or, temporarily move `setup.py` out of `/workspace`.
Since I cannot run `pip install .` easily (might take too long or fail due to missing dependencies), the easiest trick is to temporarily rename `setup.py`.
Wait, if I rename `setup.py`, `from . import _errors` will still be executed. If `_errors` is not compiled, it will still fail, but this time it will `raise` the original `ImportError` instead of the "You cannot import h5py from inside the install directory" message.
Is `_errors` compiled? Let's check.
TOOL CALL · run_command
{
"command": "ls h5py/_errors*.so"
}Result of run_command 257 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "ls: cannot access 'h5py/_errors*.so': No such file or directory\n",
"details": {
"stdout": "",
"stderr": "ls: cannot access 'h5py/_errors*.so': No such file or directory\n",
"exit_code": 2
}
}Generated tokens 391 tokens · stopped: STOP
The code is:
```python
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):\n raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.")
else:
raise
```
`_op.dirname(__file__)` is `/workspace/h5py`.
`_op.join(..., '..', 'setup.py')` is `/workspace/setup.py`.
Since `/workspace/setup.py` exists, it raises the `ImportError`.
Wait, `from . import _errors` is being called. If `_errors` is a compiled module (which it usually is in `h5py`), and it hasn't been compiled yet in `/workspace/h5py`, it will raise `ImportError`.
To fix this for reproduction, I should either:
1. Build `h5py` in the workspace.
2. Or, temporarily move `setup.py` out of `/workspace`.
Since I cannot run `pip install .` easily (might take too long or fail due to missing dependencies), the easiest trick is to temporarily rename `setup.py`.
Wait, if I rename `setup.py`, `from . import _errors` will still be executed. If `_errors` is not compiled, it will still fail, but this time it will `raise` the original `ImportError` instead of the "You cannot import h5py from inside the install directory" message.
Is `_errors` compiled? Let's check.
<channel|><|tool_call>call:run_command{command:<|"|>ls h5py/_errors*.so<|"|>}<tool_call|><|tool_response>
Turn 15at 339 s279 tokens out4,256 prompt tokens
No `.so` files. `h5py` is not compiled in the workspace. This means I MUST use an installed version of `h5py` if one exists, OR I must compile it. Wait, if I'm supposed to fix a bug in `h5py`, there should be a way to run the tests. How are the tests usually run here? Maybe there's already an installed version and I just need to find it? I tried `ls /usr/local/lib/python3.10/site-packages/h5py` and it failed. Let's try `python3 -c "import h5py; print(h5py.__file__)"` from `/tmp` again, and be very careful about the output. Wait, I did that and it said `/h5py/h5py/__init__.py`. But `/h5py` is a symlink to `/workspace`. So it's *still* trying to import from the source! This means `/h5py` is in the `sys.path`. Let's check `sys.path`.
TOOL CALL · run_command
{
"command": "python3 -c \"import sys; print('\\n'.join(sys.path))\""
}Result of run_command 199 characters
{
"status": "ok",
"stdout": "\n/usr/local/lib/python310.zip\n/usr/local/lib/python3.10\n/usr/local/lib/python3.10/lib-dynload\n/usr/local/lib/python3.10/site-packages\n",
"stderr": "",
"exit_code": 0
}Generated tokens 279 tokens · stopped: STOP
No `.so` files. `h5py` is not compiled in the workspace.
This means I MUST use an installed version of `h5py` if one exists, OR I must compile it.
Wait, if I'm supposed to fix a bug in `h5py`, there should be a way to run the tests. How are the tests usually run here?
Maybe there's already an installed version and I just need to find it?
I tried `ls /usr/local/lib/python3.10/site-packages/h5py` and it failed.
Let's try `python3 -c "import h5py; print(h5py.__file__)"` from `/tmp` again, and be very careful about the output.
Wait, I did that and it said `/h5py/h5py/__init__.py`.
But `/h5py` is a symlink to `/workspace`.
So it's *still* trying to import from the source!
This means `/h5py` is in the `sys.path`.
Let's check `sys.path`.
<channel|><|tool_call>call:run_command{command:<|"|>python3 -c "import sys; print('\n'.join(sys.path))"<|"|>}<tool_call|><|tool_response>
Turn 16at 345 s134 tokens out4,640 prompt tokens
`/h5py` is NOT in `sys.path`. Wait, then how did `python3 -c "import h5py; print(h5py.__file__)"` find `/h5py/h5py/__init__.py`? Ah, maybe I ran it while I was in `/workspace`? No, I said `cd /tmp && python3 -c ...`. Let me try it again, explicitly.
TOOL CALL · run_command
{
"command": "cd /tmp && python3 -c \"import h5py; print(h5py.__file__)\""
}Result of run_command 1,541 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "Traceback (most recent call last):\n File \"/h5py/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/h5py/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/h5py/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"details": {
"stdout": "",
"stderr": "Traceback (most recent call last):\n File \"/h5py/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/h5py/h5py/__init__.py)\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/h5py/h5py/__init__.py\", line 29, in <module>\n raise ImportError(\"You cannot import h5py from inside the install directory.\\nChange to another directory first.\")\nImportError: You cannot import h5py from inside the install directory.\nChange to another directory first.\n",
"exit_code": 1
}
}Generated tokens 134 tokens · stopped: STOP
`/h5py` is NOT in `sys.path`.
Wait, then how did `python3 -c "import h5py; print(h5py.__file__)"` find `/h5py/h5py/__init__.py`?
Ah, maybe I ran it while I was in `/workspace`?
No, I said `cd /tmp && python3 -c ...`.
Let me try it again, explicitly.
<channel|><|tool_call>call:run_command{command:<|"|>cd /tmp && python3 -c "import h5py; print(h5py.__file__)"<|"|>}<tool_call|><|tool_response>
Turn 17at 351 s120 tokens out5,233 prompt tokens
Wait, the traceback says: `File "/h5py/h5py/__init__.py", line 25, in <module>`. But `/h5py` is not in `sys.path`! How the hell is it finding `/h5py/h5py/__init__.py`? Wait... is there a `.pth` file in `site-packages`?
TOOL CALL · run_command
{
"command": "ls /usr/local/lib/python3.10/site-packages/*.pth"
}Result of run_command 253 characters
{
"status": "ok",
"stdout": "/usr/local/lib/python3.10/site-packages/__editable__.h5py-3.13.0.pth\n/usr/local/lib/python3.10/site-packages/a1_coverage.pth\n/usr/local/lib/python3.10/site-packages/distutils-precedence.pth\n",
"stderr": "",
"exit_code": 0
}Generated tokens 120 tokens · stopped: STOP
Wait, the traceback says: `File "/h5py/h5py/__init__.py", line 25, in <module>`.
But `/h5py` is not in `sys.path`!
How the hell is it finding `/h5py/h5py/__init__.py`?
Wait... is there a `.pth` file in `site-packages`?
<channel|><|tool_call>call:run_command{command:<|"|>ls /usr/local/lib/python3.10/site-packages/*.pth<|"|>}<tool_call|><|tool_response>
Turn 18at 367 s280 tokens out5,474 prompt tokens
BINGO! `__editable__.h5py-3.13.0.pth`.
This means `h5py` was installed in "editable" mode, pointing to `/h5py` (which is `/workspace`).
So, whenever I `import h5py`, it's using the source code in `/workspace`.
And the source code has that check:
```python
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):
raise ImportError("You cannot import h5py from inside the install directory.")
```
Since `/workspace/setup.py` exists, it fails.
To fix this for my reproduction, I can just move `setup.py` to a temporary location.
Let's try that.
Wait, if I move `setup.py`, I still have the problem that `_errors` is not compiled.
Wait, if it was installed in editable mode, it should have been compiled!
Why did `ls h5py/_errors*.so` fail?
Maybe the `.so` files are in a different directory?
Let's search for `.so` files in the whole workspace.
TOOL CALL · run_command
{
"command": "find /workspace -name \"*.so\""
}Result of run_command 60 characters
{
"status": "ok",
"stdout": "",
"stderr": "",
"exit_code": 0
}Generated tokens 280 tokens · stopped: STOP
BINGO! `__editable__.h5py-3.13.0.pth`.
This means `h5py` was installed in "editable" mode, pointing to `/h5py` (which is `/workspace`).
So, whenever I `import h5py`, it's using the source code in `/workspace`.
And the source code has that check:
```python
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):
raise ImportError("You cannot import h5py from inside the install directory.")
```
Since `/workspace/setup.py` exists, it fails.
To fix this for my reproduction, I can just move `setup.py` to a temporary location.
Let's try that.
Wait, if I move `setup.py`, I still have the problem that `_errors` is not compiled.
Wait, if it was installed in editable mode, it should have been compiled!
Why did `ls h5py/_errors*.so` fail?
Maybe the `.so` files are in a different directory?
Let's search for `.so` files in the whole workspace.
<channel|><|tool_call>call:run_command{command:<|"|>find /workspace -name "*.so"<|"|>}<tool_call|><|tool_response>
Turn 19at 374 s124 tokens out5,791 prompt tokens
What??? No `.so` files in `/workspace`? Then how can it be installed in editable mode? Wait, maybe the `.so` files are in `/h5py` but not under `/workspace`? No, `/h5py` is a symlink to `/workspace`. Let's see what's in that `.pth` file.
TOOL CALL · run_command
{
"command": "cat /usr/local/lib/python3.10/site-packages/__editable__.h5py-3.13.0.pth"
}Result of run_command 141 characters
{
"status": "ok",
"stdout": "import __editable___h5py_3_13_0_finder; __editable___h5py_3_13_0_finder.install()",
"stderr": "",
"exit_code": 0
}Generated tokens 124 tokens · stopped: STOP
What??? No `.so` files in `/workspace`?
Then how can it be installed in editable mode?
Wait, maybe the `.so` files are in `/h5py` but not under `/workspace`? No, `/h5py` is a symlink to `/workspace`.
Let's see what's in that `.pth` file.
<channel|><|tool_call>call:run_command{command:<|"|>cat /usr/local/lib/python3.10/site-packages/__editable__.h5py-3.13.0.pth<|"|>}<tool_call|><|tool_response>
Turn 20at 392 s265 tokens out5,988 prompt tokens
It's using a custom finder. This is common with newer `pip install -e .` (PEP 660). If the `.so` files are not in `/workspace`, then they must be somewhere else. Wait, if they are not compiled, it can't possibly work. Wait, if I'm supposed to fix this bug, I should be able to run the tests. How are the tests run? Maybe the environment already has a working `h5py` installation, but the `__editable__` thing is overriding it? No, that doesn't make sense. Let's try to find where `_errors` is being loaded from if I can bypass the `setup.py` check. Actually, I can just temporarily comment out the `setup.py` check in `h5py/__init__.py`! No, that's too intrusive. Let's try to move `setup.py` and see what happens.
TOOL CALL · run_command
{
"command": "mv setup.py setup.py.bak && python3 -c \"import h5py; print(h5py.__file__)\" && mv setup.py.bak setup.py"
}Result of run_command 881 characters
{
"status": "error",
"error_type": "CommandError",
"error_message": "Traceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/workspace/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/workspace/h5py/__init__.py)\n",
"details": {
"stdout": "",
"stderr": "Traceback (most recent call last):\n File \"<string>\", line 1, in <module>\n File \"/workspace/h5py/__init__.py\", line 25, in <module>\n from . import _errors\nImportError: cannot import name '_errors' from partially initialized module 'h5py' (most likely due to a circular import) (/workspace/h5py/__init__.py)\n",
"exit_code": 1
},
"budget_warning": "Only 10 tool call(s) remaining (20/30 used). Finalize your edits and call submit_patch soon."
}Generated tokens 265 tokens · stopped: STOP
It's using a custom finder. This is common with newer `pip install -e .` (PEP 660).
If the `.so` files are not in `/workspace`, then they must be somewhere else.
Wait, if they are not compiled, it can't possibly work.
Wait, if I'm supposed to fix this bug, I should be able to run the tests.
How are the tests run?
Maybe the environment already has a working `h5py` installation, but the `__editable__` thing is overriding it?
No, that doesn't make sense.
Let's try to find where `_errors` is being loaded from if I can bypass the `setup.py` check.
Actually, I can just temporarily comment out the `setup.py` check in `h5py/__init__.py`!
No, that's too intrusive.
Let's try to move `setup.py` and see what happens.
<channel|><|tool_call>call:run_command{command:<|"|>mv setup.py setup.py.bak && python3 -c "import h5py; print(h5py.__file__)" && mv setup.py.bak setup.py<|"|>}<tool_call|><|tool_response>
Turn 21at 400 s93 tokens out6,538 prompt tokens
Still no `_errors`. This is very strange. If I cannot import `h5py`, I cannot reproduce the bug. But I AM a principal Python software engineer, and I MUST reproduce it. Let me search for any compiled `h5py` modules anywhere in the system.
TOOL CALL · run_command
{
"command": "find /usr -name \"_errors*.so\" 2>/dev/null"
}Result of run_command 173 characters
{
"status": "ok",
"stdout": "",
"stderr": "",
"exit_code": 0,
"budget_warning": "Only 9 tool call(s) remaining (21/30 used). Finalize your edits and call submit_patch soon."
}Generated tokens 93 tokens · stopped: STOP
Still no `_errors`. This is very strange.
If I cannot import `h5py`, I cannot reproduce the bug.
But I AM a principal Python software engineer, and I MUST reproduce it.
Let me search for any compiled `h5py` modules anywhere in the system.
<channel|><|tool_call>call:run_command{command:<|"|>find /usr -name "_errors*.so" 2>/dev/null<|"|>}<tool_call|><|tool_response>
Turn 22at 410 s172 tokens out6,703 prompt tokens
This is unbelievable. Is `h5py` not installed at all? But the problem description says it's a `ZeroDivisionError` in `h5py/_hl/selections.py`. If I can't run the code, I'll have to trust the bug report and the traceback provided in the context. The traceback provided in the context was: `chunks = tuple(x//y for x, y in zip(count, tshape))` where `y` is 0. I can see the code in `h5py/_hl/selections.py`. Let me read it.
TOOL CALL · read_file
{
"end_line": 300,
"filepath": "h5py/_hl/selections.py",
"start_line": 1
}Result of read_file 5,248 characters
{
"status": "ok",
"filepath": "h5py/_hl/selections.py",
"content": "# This file is part of h5py, a Python interface to the HDF5 library.\n#\n# http://www.h5py.org\n#\n# Copyright 2008-2013 Andrew Collette and contributors\n#\n# License: Standard 3-clause BSD; see \"license.txt\" for full license terms\n# and contributor agreement.\n\n\"\"\"\n High-level access to HDF5 dataspace selections\n\"\"\"\n\nimport numpy as np\n\nfrom .base import product\nfrom .. import h5s, h5r, _selector\n\ndef select(shape, args, dataset=None):\n \"\"\" High-level routine to generate a selection from arbitrary arguments\n to __getitem__. The arguments should be the following:\n\n shape\n Shape of the \"source\" dataspace.\n\n args\n Either a single argument or a tuple of arguments. See below for\n supported classes of argument.\n\n dataset\n A h5py.Dataset instance representing the source dataset.\n\n Argument classes:\n\n Single Selection instance\n Returns the argument.\n\n numpy.ndarray\n Must be a boolean mask. Returns a PointSelection instance.\n\n RegionReference\n Returns a Selection instance.\n\n Indices, slices, ellipses, MultiBlockSlices only\n Returns a SimpleSelection instance\n\n Indices, slices, ellipses, lists or boolean index arrays\n Returns a FancySelection instance.\n \"\"\"\n if not isinstance(args, tuple):\n args = (args,)\n\n # \"Special\" indexing objects\n if len(args) == 1:\n\n arg = args[0]\n if isinstance(arg, Selection):\n if arg.shape != shape:\n raise TypeError(\"Mismatched selection shape\")\n return arg\n\n elif isinstance(arg, np.ndarray) and arg.dtype.kind == 'b':\n if arg.shape != shape:\n raise TypeError(\"Boolean indexing array has incompatible shape\")\n return PointSelection.from_mask(arg)\n\n elif isinstance(arg, h5r.RegionReference):\n if dataset is None:\n raise TypeError(\"Cannot apply a region reference without a dataset\")\n sid = h5r.get_region(arg, dataset.id)\n if shape != sid.shape:\n raise TypeError(\"Reference shape does not match dataset shape\")\n\n return Selection(shape, spaceid=sid)\n\n if dataset is not None:\n selector = dataset._selector\n else:\n space = h5s.create_simple(shape)\n selector = _selector.Selector(space)\n\n return selector.make_selection(args)\n\n\nclass Selection:\n\n \"\"\"\n Base class for HDF5 dataspace selections. Subclasses support the\n \"selection protocol\", which means they have at least the following\n members:\n\n __init__(shape) => Create a new selection on \"shape\"-tuple\n __getitem__(args) => Perform a selection with the range specified.\n What args are allowed depends on the\n particular subclass in use.\n\n id (read-only) => h5py.h5s.SpaceID instance\n shape (read-only) => The shape of the dataspace.\n mshape (read-only) => The shape of the selection region.\n Not guaranteed to fit within \"shape\", although\n the total number of points is less than\n product(shape).\n nselect (read-only) => Number of selected points. Always equal to\n product(mshape).\n\n broadcast(target_shape) => Return an iterable which yields dataspaces\n for read, based on target_shape.\n\n The base class represents \"unshaped\" selections (1-D).\n \"\"\"\n\n def __init__(self, shape, spaceid=None):\n \"\"\" Create a selection. Shape may be None if spaceid is given. \"\"\"\n if spaceid is not None:\n self._id = spaceid\n self._shape = spaceid.shape\n else:\n shape = tuple(shape)\n self._shape = shape\n self._id = h5s.create_simple(shape, (h5s.UNLIMITED,)*len(shape))\n self._id.select_all()\n\n @property\n def id(self):\n \"\"\" SpaceID instance \"\"\"\n return self._id\n\n @property\n def shape(self):\n \"\"\" Shape of whole dataspace \"\"\"\n return self._shape\n\n @property\n def nselect(self):\n \"\"\" Number of elements currently selected \"\"\"\n return self._id.get_select_npoints()\n\n @property\n def mshape(self):\n \"\"\" Shape of selection (always 1-D for this class) \"\"\"\n return (self.nselect,)\n\n @property\n def array_shape(self):\n \"\"\"Shape of array to read/write (always 1-D for this class)\"\"\"\n return self.mshape\n\n # expand_shape and broadcast only really make sense for SimpleSelection\n def expand_shape(self, source_shape):\n if product(source_shape) != self.nselect:",
"start_line": 1,
"end_line": 150,
"total_lines": 435,
"is_truncated": true,
"budget_warning": "Only 8 tool call(s) remaining (22/30 used). Finalize your edits and call submit_patch soon."
}Generated tokens 172 tokens · stopped: STOP
This is unbelievable. Is `h5py` not installed at all?
But the problem description says it's a `ZeroDivisionError` in `h5py/_hl/selections.py`.
If I can't run the code, I'll have to trust the bug report and the traceback provided in the context.
The traceback provided in the context was:
`chunks = tuple(x//y for x, y in zip(count, tshape))` where `y` is 0.
I can see the code in `h5py/_hl/selections.py`. Let me read it.
<channel|><|tool_call>call:read_file{filepath:<|"|>h5py/_hl/selections.py<|"|>,start_line:1,end_line:300}<tool_call|><|tool_response>
Turn 23at 413 s42 tokens out8,306 prompt tokens
I need to find the `broadcast` method.
TOOL CALL · run_command
{
"command": "grep -n \"def broadcast\" h5py/_hl/selections.py"
}Result of run_command 305 characters
{
"status": "ok",
"stdout": "154: def broadcast(self, source_shape):\n275: def broadcast(self, source_shape):\n341: def broadcast(self, source_shape):\n",
"stderr": "",
"exit_code": 0,
"budget_warning": "Only 7 tool call(s) remaining (23/30 used). Finalize your edits and call submit_patch soon."
}Generated tokens 42 tokens · stopped: STOP
I need to find the `broadcast` method.<channel|><|tool_call>call:run_command{command:<|"|>grep -n "def broadcast" h5py/_hl/selections.py<|"|>}<tool_call|><|tool_response>
Turn 24at 420 s98 tokens out8,467 prompt tokens
There are three `broadcast` methods. Line 154 is in `Selection`. Line 275 is likely in `SimpleSelection`. Line 341 is likely in `FancySelection`. Let's read the area around those lines.
TOOL CALL · read_file
{
"end_line": 360,
"filepath": "h5py/_hl/selections.py",
"start_line": 150
}Result of read_file 5,921 characters
{
"status": "ok",
"filepath": "h5py/_hl/selections.py",
"content": " if product(source_shape) != self.nselect:\n raise TypeError(\"Broadcasting is not supported for point-wise selections\")\n return source_shape\n\n def broadcast(self, source_shape):\n \"\"\" Get an iterable for broadcasting \"\"\"\n if product(source_shape) != self.nselect:\n raise TypeError(\"Broadcasting is not supported for point-wise selections\")\n yield self._id\n\n def __getitem__(self, args):\n raise NotImplementedError(\"This class does not support indexing\")\n\nclass PointSelection(Selection):\n\n \"\"\"\n Represents a point-wise selection. You can supply sequences of\n points to the three methods append(), prepend() and set(), or\n instantiate it with a single boolean array using from_mask().\n \"\"\"\n def __init__(self, shape, spaceid=None, points=None):\n super().__init__(shape, spaceid)\n if points is not None:\n self._perform_selection(points, h5s.SELECT_SET)\n\n def _perform_selection(self, points, op):\n \"\"\" Internal method which actually performs the selection \"\"\"\n points = np.asarray(points, order='C', dtype='u8')\n if len(points.shape) == 1:\n points.shape = (1,points.shape[0])\n\n if self._id.get_select_type() != h5s.SEL_POINTS:\n op = h5s.SELECT_SET\n\n if len(points) == 0:\n self._id.select_none()\n else:\n self._id.select_elements(points, op)\n\n @classmethod\n def from_mask(cls, mask, spaceid=None):\n \"\"\"Create a point-wise selection from a NumPy boolean array \"\"\"\n if not (isinstance(mask, np.ndarray) and mask.dtype.kind == 'b'):\n raise TypeError(\"PointSelection.from_mask only works with bool arrays\")\n\n points = np.transpose(mask.nonzero())\n return cls(mask.shape, spaceid, points=points)\n\n def append(self, points):\n \"\"\" Add the sequence of points to the end of the current selection \"\"\"\n self._perform_selection(points, h5s.SELECT_APPEND)\n\n def prepend(self, points):\n \"\"\" Add the sequence of points to the beginning of the current selection \"\"\"\n self._perform_selection(points, h5s.SELECT_PREPEND)\n\n def set(self, points):\n \"\"\" Replace the current selection with the given sequence of points\"\"\"\n self._perform_selection(points, h5s.SELECT_SET)\n\n\nclass SimpleSelection(Selection):\n\n \"\"\" A single \"rectangular\" (regular) selection composed of only slices\n and integer arguments. Can participate in broadcasting.\n \"\"\"\n\n @property\n def mshape(self):\n \"\"\" Shape of current selection \"\"\"\n return self._sel[1]\n\n @property\n def array_shape(self):\n scalar = self._sel[3]\n return tuple(x for x, s in zip(self.mshape, scalar) if not s)\n\n def __init__(self, shape, spaceid=None, hyperslab=None):\n super().__init__(shape, spaceid)\n if hyperslab is not None:\n self._sel = hyperslab\n else:\n # No hyperslab specified - select all\n rank = len(self.shape)\n self._sel = ((0,)*rank, self.shape, (1,)*rank, (False,)*rank)\n\n def expand_shape(self, source_shape):\n \"\"\"Match the dimensions of an array to be broadcast to the selection\n\n The returned shape describes an array of the same size as the input\n shape, but its dimensions\n\n E.g. with a dataset shape (10, 5, 4, 2), writing like this::\n\n ds[..., 0] = np.ones((5, 4))\n\n The source shape (5, 4) will expand to (1, 5, 4, 1).\n Then the broadcast method below repeats that chunk 10\n times to write to an effective shape of (10, 5, 4, 1).\n \"\"\"\n start, count, step, scalar = self._sel\n\n rank = len(count)\n remaining_src_dims = list(source_shape)\n\n eshape = []\n for idx in range(1, rank + 1):\n if len(remaining_src_dims) == 0 or scalar[-idx]: # Skip scalar axes\n eshape.append(1)\n else:\n t = remaining_src_dims.pop()\n if t == 1 or count[-idx] == t:\n eshape.append(t)\n else:\n raise TypeError(\"Can't broadcast %s -> %s\" % (source_shape, self.array_shape)) # array shape\n\n if any([n > 1 for n in remaining_src_dims]):\n # All dimensions from target_shape should either have been popped\n # to match the selection shape, or be 1.\n raise TypeError(\"Can't broadcast %s -> %s\" % (source_shape, self.array_shape)) # array shape\n\n # We have built eshape backwards, so now reverse it\n return tuple(eshape[::-1])\n\n\n def broadcast(self, source_shape):\n \"\"\" Return an iterator over target dataspaces for broadcasting.\n\n Follows the standard NumPy broadcasting rules against the current\n selection shape (self.mshape).\n \"\"\"\n if self.shape == ():\n if product(source_shape) != 1:\n raise TypeError(\"Can't broadcast %s to scalar\" % source_shape)\n self._id.select_all()\n yield self._id\n return\n\n start, count, step, scalar = self._sel\n\n rank = len(count)\n tshape = self.expand_shape(source_shape)\n\n chunks = tuple(x//y for x, y in zip(count, tshape))\n nchunks = product(chunks)\n\n if nchunks == 1:\n yield self._id\n else:\n sid = self._id.copy()",
"start_line": 150,
"end_line": 299,
"total_lines": 435,
"is_truncated": true,
"budget_warning": "Only 6 tool call(s) remaining (24/30 used). Finalize your edits and call submit_patch soon."
}Generated tokens 98 tokens · stopped: STOP
There are three `broadcast` methods.
Line 154 is in `Selection`.
Line 275 is likely in `SimpleSelection`.
Line 341 is likely in `FancySelection`.
Let's read the area around those lines.
<channel|><|tool_call>call:read_file{end_line:360,filepath:<|"|>h5py/_hl/selections.py<|"|>,start_line:150}<tool_call|><|tool_response>
Turn 25at 464 s667 tokens out10,286 prompt tokens
I found it!
Line 293: `chunks = tuple(x//y for x, y in zip(count, tshape))`
In `SimpleSelection.broadcast(self, source_shape)`, `count` comes from `self._sel`, which is the shape of the selection region (equivalent to `self.mshape`). `tshape` is the result of `self.expand_shape(source_shape)`.
If `y` (an element of `tshape`) is 0, this raises `ZeroDivisionError`.
Wait, can `tshape` have 0s?
`tshape` is returned by `expand_shape(source_shape)`.
Let's look at `expand_shape`:
```python
def expand_shape(self, source_shape):
...
for idx in range(1, rank + 1):
if len(remaining_src_dims) == 0 or scalar[-idx]: # Skip scalar axes
eshape.append(1)
else:
t = remaining_src_dims.pop()
if t == 1 or count[-idx] == t:
eshape.append(t)
else:
raise TypeError("Can't broadcast %s -> %s" % (source_shape, self.array_shape))
...
return tuple(eshape[::-1])
```
`eshape` elements come from either `1` or `t` (which comes from `source_shape`).
So if `source_shape` contains 0, `tshape` will contain 0.
If `source_shape` contains 0, then `product(source_shape)` is 0.
Does `count` also have 0s?
`count` is the shape of the selection. If the dataset has a 0-dimension, then `count` might have 0s.
If `y` is 0, then `x // y` is a `ZeroDivisionError`.
But if `y` is 0, then the total number of elements is 0.
In NumPy broadcasting, if any dimension is 0, the resulting shape also has 0 if not broadcastable.
Wait, if `y` is 0, then `x // y` is not defined. But if `y` is 0, that means the `source_shape` has a 0.
If `source_shape` has a 0, then the entire operation should probably just not yield anything, or yield something with 0 elements.
Let's see what happens in `broadcast`.
`chunks` is used to calculate `nchunks = product(chunks)`.
And then it's used to iterate over chunks (though I only saw the `nchunks == 1` case).
Let's read the rest of `broadcast`.
TOOL CALL · read_file
{
"end_line": 315,
"filepath": "h5py/_hl/selections.py",
"start_line": 299
}Result of read_file 868 characters
{
"status": "ok",
"filepath": "h5py/_hl/selections.py",
"content": " sid = self._id.copy()\n sid.select_hyperslab((0,)*rank, tshape, step)\n for idx in range(nchunks):\n offset = tuple(x*y*z + s for x, y, z, s in zip(np.unravel_index(idx, chunks), tshape, step, start))\n sid.offset_simple(offset)\n yield sid\n\n\nclass FancySelection(Selection):\n\n \"\"\"\n Implements advanced NumPy-style selection operations in addition to\n the standard slice-and-int behavior.\n\n Indexing arguments may be ints, slices, lists of indices, or\n per-axis (1D) boolean arrays.\n",
"start_line": 299,
"end_line": 315,
"total_lines": 435,
"is_truncated": false,
"budget_warning": "Only 5 tool call(s) remaining (25/30 used). Finalize your edits and call submit_patch soon."
}Generated tokens 667 tokens · stopped: STOP
I found it!
Line 293: `chunks = tuple(x//y for x, y in zip(count, tshape))`
In `SimpleSelection.broadcast(self, source_shape)`, `count` comes from `self._sel`, which is the shape of the selection region (equivalent to `self.mshape`). `tshape` is the result of `self.expand_shape(source_shape)`.
If `y` (an element of `tshape`) is 0, this raises `ZeroDivisionError`.
Wait, can `tshape` have 0s?
`tshape` is returned by `expand_shape(source_shape)`.
Let's look at `expand_shape`:
```python
def expand_shape(self, source_shape):
...
for idx in range(1, rank + 1):
if len(remaining_src_dims) == 0 or scalar[-idx]: # Skip scalar axes
eshape.append(1)
else:
t = remaining_src_dims.pop()
if t == 1 or count[-idx] == t:
eshape.append(t)
else:
raise TypeError("Can't broadcast %s -> %s" % (source_shape, self.array_shape))
...
return tuple(eshape[::-1])
```
`eshape` elements come from either `1` or `t` (which comes from `source_shape`).
So if `source_shape` contains 0, `tshape` will contain 0.
If `source_shape` contains 0, then `product(source_shape)` is 0.
Does `count` also have 0s?
`count` is the shape of the selection. If the dataset has a 0-dimension, then `count` might have 0s.
If `y` is 0, then `x // y` is a `ZeroDivisionError`.
But if `y` is 0, then the total number of elements is 0.
In NumPy broadcasting, if any dimension is 0, the resulting shape also has 0 if not broadcastable.
Wait, if `y` is 0, then `x // y` is not defined. But if `y` is 0, that means the `source_shape` has a 0.
If `source_shape` has a 0, then the entire operation should probably just not yield anything, or yield something with 0 elements.
Let's see what happens in `broadcast`.
`chunks` is used to calculate `nchunks = product(chunks)`.
And then it's used to iterate over chunks (though I only saw the `nchunks == 1` case).
Let's read the rest of `broadcast`.<channel|><|tool_call>call:read_file{end_line:315,filepath:<|"|>h5py/_hl/selections.py<|"|>,start_line:299}<tool_call|><|tool_response>
Patch, tests and logs
Final code change Included
diff --git a/setup.py b/setup.py.bak similarity index 100% rename from setup.py rename to setup.py.bak
Test output Included
============================= test session starts ============================== collected 226 items h5py/tests/test_dataset.py ...............................F............. [ 19%] ........................................................................ [ 51%] ........................................................................ [ 83%] ..................................... [100%] =================================== FAILURES =================================== E ZeroDivisionError: integer division or modulo by zero /h5py/h5py/_hl/selections.py:293: ZeroDivisionError: integer division or modulo by zero ==================================== PASSES ==================================== - generated xml file: /tmp/rebench-grade-802204747d214f468e5f6e498e44ae0e.xml -- =========================== short test summary info ============================ PASSED h5py/tests/test_dataset.py::TestRepr::test_repr_open PASSED h5py/tests/test_dataset.py::TestCreateShape::test_complex256 PASSED h5py/tests/test_dataset.py::TestCreateShape::test_create_extended PASSED h5py/tests/test_dataset.py::TestCreateShape::test_create_integer PASSED h5py/tests/test_dataset.py::TestCreateShape::test_create_integer_extended PASSED h5py/tests/test_dataset.py::TestCreateShape::test_create_scalar PASSED h5py/tests/test_dataset.py::TestCreateShape::test_create_simple PASSED h5py/tests/test_dataset.py::TestCreateShape::test_default_dtype PASSED h5py/tests/test_dataset.py::TestCreateShape::test_long_double PASSED h5py/tests/test_dataset.py::TestCreateShape::test_missing_shape PASSED h5py/tests/test_dataset.py::TestCreateShape::test_name_bytes PASSED h5py/tests/test_dataset.py::TestCreateData::test_appropriate_low_level_id PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_bytestring PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_extended PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_incompatible_data PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_np_s PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_np_u PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_scalar PASSED h5py/tests/test_dataset.py::TestCreateData::test_create_strings PASSED h5py/tests/test_dataset.py::TestCreateData::test_dataset_intermediate_group PASSED h5py/tests/test_dataset.py::TestCreateData::test_empty_create_via_Empty_class PASSED h5py/tests/test_dataset.py::TestCreateData::test_empty_create_via_None_shape PASSED h5py/tests/test_dataset.py::TestCreateData::test_reshape PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_read_direct[source_shape0-dest_shape0-source_sel0-dest_sel0] PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_read_direct[source_shape1-dest_shape1-source_sel1-dest_sel1] PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_read_direct[source_shape2-dest_shape2-source_sel2-dest_sel2] PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_read_direct[source_shape3-dest_shape3-source_sel3-dest_sel3] PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_no_sel PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_empty PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_wrong_shape PASSED h5py/tests/test_dataset.py::TestReadDirectly::test_not_c_contiguous PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_write_direct[source_shape0-dest_shape0-source_sel0-dest_sel0] PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_write_direct[source_shape1-dest_shape1-source_sel1-dest_sel1] PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_write_direct[source_shape2-dest_shape2-source_sel2-dest_sel2] PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_write_direct[source_shape3-dest_shape3-source_sel3-dest_sel3] PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_empty PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_wrong_shape PASSED h5py/tests/test_dataset.py::TestWriteDirectly::test_not_c_contiguous PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_create PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_create_1D PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_create_existing PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_dtype_close PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_dtype_conflict PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_dtype_exact PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_shape_conflict PASSED h5py/tests/test_dataset.py::TestCreateRequire::test_type_conflict PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_auto_chunks PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_auto_chunks_abuse PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_auto_chunks_no_shape PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_chunks_false PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_chunks_mismatch PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_chunks_scalar PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_create_chunks PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_create_chunks_integer PASSED h5py/tests/test_dataset.py::TestCreateChunked::test_scalar_assignment PASSED h5py/tests/test_dataset.py::TestCreateFillvalue::test_compound PASSED h5py/tests/test_dataset.py::TestCreateFillvalue::test_create_fillval PASSED h5py/tests/test_dataset.py::TestCreateFillvalue::test_exc PASSED h5py/tests/test_dataset.py::TestCreateFillvalue::test_property PASSED h5py/tests/test_dataset.py::TestCreateFillvalue::test_property_none PASSED h5py/tests/test_dataset.py::TestFillTime::test_compressed_default PASSED h5py/tests/test_dataset.py::TestFillTime::test_fill_time_alloc PASSED h5py/tests/test_dataset.py::TestFillTime::test_fill_time_default PASSED h5py/tests/test_dataset.py::TestFillTime::test_fill_time_ifset PASSED h5py/tests/test_dataset.py::TestFillTime::test_fill_time_never PASSED h5py/tests/test_dataset.py::TestFillTime::test_invalid_fill_time PASSED h5py/tests/test_dataset.py::TestFillTime::test_non_str_fill_time PASSED h5py/tests/test_dataset.py::TestFillTime::test_resize_chunk_fill_time_default PASSED h5py/tests/test_dataset.py::TestFillTime::test_resize_chunk_fill_time_never PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[int-0] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[int32-0] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[int64-0] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[float-0.0] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[float32-0.0] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[float64-0.0] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[dt6-] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[dt7-] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[dt8-] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[dt9-] PASSED h5py/tests/test_dataset.py::test_get_unset_fill_value[dt10-] PASSED h5py/tests/test_dataset.py::TestCreateNamedType::test_named PASSED h5py/tests/test_dataset.py::TestCreateGzip::test_gzip PASSED h5py/tests/test_dataset.py::TestCreateGzip::test_gzip_exc PASSED h5py/tests/test_dataset.py::TestCreateGzip::test_gzip_implicit PASSED h5py/tests/test_dataset.py::TestCreateGzip::test_gzip_number PASSED h5py/tests/test_dataset.py::TestCreateCompressionNumber::test_compression_number PASSED h5py/tests/test_dataset.py::TestCreateCompressionNumber::test_compression_number_invalid PASSED h5py/tests/test_dataset.py::TestCreateLZF::test_lzf PASSED h5py/tests/test_dataset.py::TestCreateLZF::test_lzf_exc PASSED h5py/tests/test_dataset.py::TestCreateSZIP::test_szip PASSED h5py/tests/test_dataset.py::TestCreateShuffle::test_shuffle PASSED h5py/tests/test_dataset.py::TestCreateFletcher32::test_fletcher32 PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_float PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_float_fails_without_options PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_int PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_int_with_minbits PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_int_with_minbits_lossy PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_non_integer PASSED h5py/tests/test_dataset.py::TestCreateScaleOffset::test_unsupport_dtype PASSED h5py/tests/test_dataset.py::TestExternal::test_contents PASSED h5py/tests/test_dataset.py::TestExternal::test_contents_efile_prefix PASSED h5py/tests/test_dataset.py::TestExternal::test_create_expandable PASSED h5py/tests/test_dataset.py::TestExternal::test_invalid PASSED h5py/tests/test_dataset.py::TestExternal::test_iter_multi PASSED h5py/tests/test_dataset.py::TestExternal::test_name_path PASSED h5py/tests/test_dataset.py::TestExternal::test_name_str PASSED h5py/tests/test_dataset.py::TestAutoCreate::test_string_fixed PASSED h5py/tests/test_dataset.py::TestAutoCreate::test_vlen_bytes PASSED h5py/tests/test_dataset.py::TestAutoCreate::test_vlen_unicode PASSED h5py/tests/test_dataset.py::TestCreateLike::test_maxshape PASSED h5py/tests/test_dataset.py::TestCreateLike::test_no_chunks PASSED h5py/tests/test_dataset.py::TestCreateLike::test_track_times PASSED h5py/tests/test_dataset.py::TestChunkIterator::test_1d PASSED h5py/tests/test_dataset.py::TestChunkIterator::test_2d PASSED h5py/tests/test_dataset.py::TestChunkIterator::test_2d_partial_slice PASSED h5py/tests/test_dataset.py::TestChunkIterator::test_no_chunks PASSED h5py/tests/test_dataset.py::TestResize::test_axis_exc PASSED h5py/tests/test_dataset.py::TestResize::test_create PASSED h5py/tests/test_dataset.py::TestResize::test_create_1D PASSED h5py/tests/test_dataset.py::TestResize::test_resize PASSED h5py/tests/test_dataset.py::TestResize::test_resize_1D PASSED h5py/tests/test_dataset.py::TestResize::test_resize_axis PASSED h5py/tests/test_dataset.py::TestResize::test_resize_nonchunked PASSED h5py/tests/test_dataset.py::TestResize::test_resize_over PASSED h5py/tests/test_dataset.py::TestResize::test_zero_dim PASSED h5py/tests/test_dataset.py::TestDtype::test_dtype PASSED h5py/tests/test_dataset.py::TestDtype::test_dtype_complex32 PASSED h5py/tests/test_dataset.py::TestLen::test_len PASSED h5py/tests/test_dataset.py::TestLen::test_len_big PASSED h5py/tests/test_dataset.py::TestIter::test_iter PASSED h5py/tests/test_dataset.py::TestIter::test_iter_scalar PASSED h5py/tests/test_dataset.py::TestStrings::test_asstr PASSED h5py/tests/test_dataset.py::TestStrings::test_asstr_fixed PASSED h5py/tests/test_dataset.py::TestStrings::test_fixed_ascii PASSED h5py/tests/test_dataset.py::TestStrings::test_fixed_bytes_fillvalue PASSED h5py/tests/test_dataset.py::TestStrings::test_fixed_unicode PASSED h5py/tests/test_dataset.py::TestStrings::test_fixed_utf8 PASSED h5py/tests/test_dataset.py::TestStrings::test_fixed_utf_8_fillvalue PASSED h5py/tests/test_dataset.py::TestStrings::test_retrieve_vlen_unicode PASSED h5py/tests/test_dataset.py::TestStrings::test_roundtrip_fixed_bytes PASSED h5py/tests/test_dataset.py::TestStrings::test_roundtrip_vlen_bytes PASSED h5py/tests/test_dataset.py::TestStrings::test_unicode_write_bytes PASSED h5py/tests/test_dataset.py::TestStrings::test_unicode_write_error PASSED h5py/tests/test_dataset.py::TestStrings::test_vlen_bytes PASSED h5py/tests/test_dataset.py::TestStrings::test_vlen_bytes_fillvalue PASSED h5py/tests/test_dataset.py::TestStrings::test_vlen_bytes_write_ascii_str PASSED h5py/tests/test_dataset.py::TestStrings::test_vlen_unicode PASSED h5py/tests/test_dataset.py::TestStrings::test_vlen_unicode_fillvalue PASSED h5py/tests/test_dataset.py::TestCompound::test_assign PASSED h5py/tests/test_dataset.py::TestCompound::test_fields PASSED h5py/tests/test_dataset.py::TestCompound::test_nested_compound_vlen PASSED h5py/tests/test_dataset.py::TestCompound::test_rt PASSED h5py/tests/test_dataset.py::TestSubarray::test_write_array PASSED h5py/tests/test_dataset.py::TestSubarray::test_write_list PASSED h5py/tests/test_dataset.py::TestEnum::test_create PASSED h5py/tests/test_dataset.py::TestEnum::test_readwrite PASSED h5py/tests/test_dataset.py::TestFloats::test_mini PASSED h5py/tests/test_dataset.py::TestFloats::test_mini_mapping PASSED h5py/tests/test_dataset.py::TestTrackTimes::test_disable_track_times PASSED h5py/tests/test_dataset.py::TestTrackTimes::test_invalid_track_times PASSED h5py/tests/test_dataset.py::TestZeroShape::test_array_conversion PASSED h5py/tests/test_dataset.py::TestZeroShape::test_reading PASSED h5py/tests/test_dataset.py::TestRegionRefs::test_create_ref PASSED h5py/tests/test_dataset.py::TestRegionRefs::test_empty_region PASSED h5py/tests/test_dataset.py::TestRegionRefs::test_ref_shape PASSED h5py/tests/test_dataset.py::TestRegionRefs::test_scalar_dataset PASSED h5py/tests/test_dataset.py::TestAstype::test_astype_wrapper PASSED h5py/tests/test_dataset.py::TestAstype::test_astype_wrapper_asarray PASSED h5py/tests/test_dataset.py::TestAstype::test_astype_wrapper_len PASSED h5py/tests/test_dataset.py::TestScalarCompound::test_scalar_compound PASSED h5py/tests/test_dataset.py::TestVlen::test_asstr_array_dtype PASSED h5py/tests/test_dataset.py::TestVlen::test_convert PASSED h5py/tests/test_dataset.py::TestVlen::test_int PASSED h5py/tests/test_dataset.py::TestVlen::test_multidim PASSED h5py/tests/test_dataset.py::TestVlen::test_non_contiguous_arrays PASSED h5py/tests/test_dataset.py::TestVlen::test_numpy_float16 PASSED h5py/tests/test_dataset.py::TestVlen::test_numpy_float32 PASSED h5py/tests/test_dataset.py::TestVlen::test_numpy_float64_2 PASSED h5py/tests/test_dataset.py::TestVlen::test_numpy_float64_from_dtype PASSED h5py/tests/test_dataset.py::TestVlen::test_reuse_from_other PASSED h5py/tests/test_dataset.py::TestVlen::test_reuse_struct_from_other PASSED h5py/tests/test_dataset.py::TestLowOpen::test_dapl PASSED h5py/tests/test_dataset.py::TestLowOpen::test_get_access_list PASSED h5py/tests/test_dataset.py::test_get_chunk_details PASSED h5py/tests/test_dataset.py::test_chunk_iter PASSED h5py/tests/test_dataset.py::test_empty_shape PASSED h5py/tests/test_dataset.py::test_zero_storage_size PASSED h5py/tests/test_dataset.py::test_python_int_uint64 PASSED h5py/tests/test_dataset.py::test_setitem_fancy_indexing PASSED h5py/tests/test_dataset.py::test_vlen_spacepad PASSED h5py/tests/test_dataset.py::test_vlen_nullterm PASSED h5py/tests/test_dataset.py::test_allow_unknown_filter PASSED h5py/tests/test_dataset.py::test_dset_chunk_cache PASSED h5py/tests/test_dataset.py::TestCommutative::test_basetype_commutative PASSED h5py/tests/test_dataset.py::TestCommutative::test_numpy_commutative PASSED h5py/tests/test_dataset.py::TestVirtualPrefix::test_virtual_prefix_create PASSED h5py/tests/test_dataset.py::TestVirtualPrefix::test_virtual_prefix_require PASSED h5py/tests/test_dataset.py::test_array_copy[ds-True] PASSED h5py/tests/test_dataset.py::test_array_copy[ds-None] PASSED h5py/tests/test_dataset.py::test_array_copy[astype-True] PASSED h5py/tests/test_dataset.py::test_array_copy[astype-None] PASSED h5py/tests/test_dataset.py::test_array_copy[asstr-True] PASSED h5py/tests/test_dataset.py::test_array_copy[asstr-None] PASSED h5py/tests/test_dataset.py::test_array_copy[fields-True] PASSED h5py/tests/test_dataset.py::test_array_copy[fields-None] PASSED h5py/tests/test_dataset.py::test_array_copy_false[ds] PASSED h5py/tests/test_dataset.py::test_array_copy_false[astype] PASSED h5py/tests/test_dataset.py::test_array_copy_false[asstr] PASSED h5py/tests/test_dataset.py::test_array_copy_false[fields] PASSED h5py/tests/test_dataset.py::test_array_dtype[ds] PASSED h5py/tests/test_dataset.py::test_array_dtype[astype] PASSED h5py/tests/test_dataset.py::test_array_dtype[asstr] PASSED h5py/tests/test_dataset.py::test_array_dtype[fields] PASSED h5py/tests/test_dataset.py::test_array_scalar[ds] PASSED h5py/tests/test_dataset.py::test_array_scalar[astype] PASSED h5py/tests/test_dataset.py::test_array_scalar[asstr] PASSED h5py/tests/test_dataset.py::test_array_scalar[fields] PASSED h5py/tests/test_dataset.py::test_array_nd[ds] PASSED h5py/tests/test_dataset.py::test_array_nd[astype] PASSED h5py/tests/test_dataset.py::test_array_nd[asstr] PASSED h5py/tests/test_dataset.py::test_array_nd[fields] PASSED h5py/tests/test_dataset.py::test_view_properties[ds] PASSED h5py/tests/test_dataset.py::test_view_properties[astype] PASSED h5py/tests/test_dataset.py::test_view_properties[asstr] PASSED h5py/tests/test_dataset.py::test_view_properties[fields] FAILED h5py/tests/test_dataset.py::TestReadDirectly::test_zero_length - ZeroD... ======================== 1 failed, 225 passed in 0.36s =========================
Test errors Included
Test report (JUnit) Included
<?xml version="1.0" encoding="utf-8"?><testsuites name="pytest tests"><testsuite name="pytest" errors="0" failures="1" skipped="0" tests="226" time="0.354" timestamp="2026-11-14T04:37:26.543530+00:00" hostname="2453b13cf7ec"><testcase classname="h5py.tests.test_dataset.TestRepr" name="test_repr_open" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_complex256" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_create_extended" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_create_integer" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_create_integer_extended" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_create_scalar" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_create_simple" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_default_dtype" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_long_double" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_missing_shape" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateShape" name="test_name_bytes" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_appropriate_low_level_id" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_bytestring" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_extended" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_incompatible_data" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_np_s" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_np_u" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_scalar" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_create_strings" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_dataset_intermediate_group" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_empty_create_via_Empty_class" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_empty_create_via_None_shape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateData" name="test_reshape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_read_direct[source_shape0-dest_shape0-source_sel0-dest_sel0]" time="0.015" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_read_direct[source_shape1-dest_shape1-source_sel1-dest_sel1]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_read_direct[source_shape2-dest_shape2-source_sel2-dest_sel2]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_read_direct[source_shape3-dest_shape3-source_sel3-dest_sel3]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_no_sel" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_empty" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_wrong_shape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_not_c_contiguous" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestReadDirectly" name="test_zero_length" time="0.001"><failure message="ZeroDivisionError: integer division or modulo by zero">E ZeroDivisionError: integer division or modulo by zero</failure></testcase><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_write_direct[source_shape0-dest_shape0-source_sel0-dest_sel0]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_write_direct[source_shape1-dest_shape1-source_sel1-dest_sel1]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_write_direct[source_shape2-dest_shape2-source_sel2-dest_sel2]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_write_direct[source_shape3-dest_shape3-source_sel3-dest_sel3]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_empty" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_wrong_shape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestWriteDirectly" name="test_not_c_contiguous" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_create" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_create_1D" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_create_existing" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_dtype_close" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_dtype_conflict" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_dtype_exact" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_shape_conflict" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateRequire" name="test_type_conflict" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_auto_chunks" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_auto_chunks_abuse" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_auto_chunks_no_shape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_chunks_false" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_chunks_mismatch" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_chunks_scalar" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_create_chunks" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_create_chunks_integer" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateChunked" name="test_scalar_assignment" time="0.002" /><testcase classname="h5py.tests.test_dataset.TestCreateFillvalue" name="test_compound" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateFillvalue" name="test_create_fillval" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateFillvalue" name="test_exc" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateFillvalue" name="test_property" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateFillvalue" name="test_property_none" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_compressed_default" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_fill_time_alloc" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_fill_time_default" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_fill_time_ifset" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_fill_time_never" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_invalid_fill_time" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_non_str_fill_time" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_resize_chunk_fill_time_default" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFillTime" name="test_resize_chunk_fill_time_never" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[int-0]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[int32-0]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[int64-0]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[float-0.0]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[float32-0.0]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[float64-0.0]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[dt6-]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[dt7-]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[dt8-]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[dt9-]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_unset_fill_value[dt10-]" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateNamedType" name="test_named" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateGzip" name="test_gzip" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateGzip" name="test_gzip_exc" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateGzip" name="test_gzip_implicit" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateGzip" name="test_gzip_number" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateCompressionNumber" name="test_compression_number" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateCompressionNumber" name="test_compression_number_invalid" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateLZF" name="test_lzf" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateLZF" name="test_lzf_exc" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateSZIP" name="test_szip" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateShuffle" name="test_shuffle" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateFletcher32" name="test_fletcher32" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_float" time="0.010" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_float_fails_without_options" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_int" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_int_with_minbits" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_int_with_minbits_lossy" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_non_integer" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestCreateScaleOffset" name="test_unsupport_dtype" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_contents" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_contents_efile_prefix" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_create_expandable" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_invalid" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_iter_multi" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_name_path" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestExternal" name="test_name_str" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestAutoCreate" name="test_string_fixed" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestAutoCreate" name="test_vlen_bytes" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestAutoCreate" name="test_vlen_unicode" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateLike" name="test_maxshape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateLike" name="test_no_chunks" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCreateLike" name="test_track_times" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestChunkIterator" name="test_1d" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestChunkIterator" name="test_2d" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestChunkIterator" name="test_2d_partial_slice" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestChunkIterator" name="test_no_chunks" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_axis_exc" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_create" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_create_1D" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_resize" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_resize_1D" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_resize_axis" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_resize_nonchunked" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_resize_over" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestResize" name="test_zero_dim" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestDtype" name="test_dtype" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestDtype" name="test_dtype_complex32" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestLen" name="test_len" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestLen" name="test_len_big" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestIter" name="test_iter" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestIter" name="test_iter_scalar" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_asstr" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_asstr_fixed" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_fixed_ascii" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_fixed_bytes_fillvalue" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_fixed_unicode" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_fixed_utf8" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_fixed_utf_8_fillvalue" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_retrieve_vlen_unicode" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_roundtrip_fixed_bytes" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_roundtrip_vlen_bytes" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_unicode_write_bytes" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_unicode_write_error" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_vlen_bytes" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_vlen_bytes_fillvalue" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_vlen_bytes_write_ascii_str" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_vlen_unicode" time="0.000" /><testcase classname="h5py.tests.test_dataset.TestStrings" name="test_vlen_unicode_fillvalue" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCompound" name="test_assign" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCompound" name="test_fields" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCompound" name="test_nested_compound_vlen" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCompound" name="test_rt" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestSubarray" name="test_write_array" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestSubarray" name="test_write_list" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestEnum" name="test_create" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestEnum" name="test_readwrite" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFloats" name="test_mini" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestFloats" name="test_mini_mapping" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestTrackTimes" name="test_disable_track_times" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestTrackTimes" name="test_invalid_track_times" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestZeroShape" name="test_array_conversion" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestZeroShape" name="test_reading" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestRegionRefs" name="test_create_ref" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestRegionRefs" name="test_empty_region" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestRegionRefs" name="test_ref_shape" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestRegionRefs" name="test_scalar_dataset" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestAstype" name="test_astype_wrapper" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestAstype" name="test_astype_wrapper_asarray" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestAstype" name="test_astype_wrapper_len" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestScalarCompound" name="test_scalar_compound" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_asstr_array_dtype" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_convert" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_int" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_multidim" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_non_contiguous_arrays" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_numpy_float16" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_numpy_float32" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_numpy_float64_2" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_numpy_float64_from_dtype" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_reuse_from_other" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVlen" name="test_reuse_struct_from_other" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestLowOpen" name="test_dapl" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestLowOpen" name="test_get_access_list" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_get_chunk_details" time="0.003" /><testcase classname="h5py.tests.test_dataset" name="test_chunk_iter" time="0.002" /><testcase classname="h5py.tests.test_dataset" name="test_empty_shape" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_zero_storage_size" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_python_int_uint64" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_setitem_fancy_indexing" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_vlen_spacepad" time="0.000" /><testcase classname="h5py.tests.test_dataset" name="test_vlen_nullterm" time="0.000" /><testcase classname="h5py.tests.test_dataset" name="test_allow_unknown_filter" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_dset_chunk_cache" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCommutative" name="test_basetype_commutative" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestCommutative" name="test_numpy_commutative" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVirtualPrefix" name="test_virtual_prefix_create" time="0.001" /><testcase classname="h5py.tests.test_dataset.TestVirtualPrefix" name="test_virtual_prefix_require" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[ds-True]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[ds-None]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[astype-True]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[astype-None]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[asstr-True]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[asstr-None]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[fields-True]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy[fields-None]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy_false[ds]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy_false[astype]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy_false[asstr]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_copy_false[fields]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_dtype[ds]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_dtype[astype]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_dtype[asstr]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_dtype[fields]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_scalar[ds]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_scalar[astype]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_scalar[asstr]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_scalar[fields]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_nd[ds]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_nd[astype]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_nd[asstr]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_array_nd[fields]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_view_properties[ds]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_view_properties[astype]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_view_properties[asstr]" time="0.001" /><testcase classname="h5py.tests.test_dataset" name="test_view_properties[fields]" time="0.001" /></testsuite></testsuites>
Agent log Included
[ 0.0s] 📋 System Prompt: You are a principal Python software engineer resolving a repository issue in `/workspace`.
[ 0.0s] 🎯 Task Prompt: You are evaluating a software engineering task for repository h5py/h5py.
[ 39.1s] 💭 (474 chars) "The user is reporting a `ZeroDivisionError` when calling `dataset.read_direct` on a dataset
that has at least one dimens..."
[ 39.1s] 🔧 run_command (40 lines) python3 - <<'PY'
[ 39.2s] → error (exit 0):
[ 69.9s] 💭 (720 chars) "Ah, I forgot that I cannot import the package from inside its installation directory. I need
to move to `/tmp` or change..."
[ 69.9s] 🔧 run_command (45 lines) cd /tmp && python3 - <<'PY'
[ 70.3s] → error (exit 0):
[ 84.5s] 💭 (703 chars) "It seems the environment already has `h5py` installed. I should not be adding `/workspace`
to `sys.path` if it's already..."
[ 84.5s] 📖 read_file (h5py/__init__.py)
[ 84.5s] ✓ {'status': 'ok', 'filepath': 'h5py/__init__.py', 'content': '# This file is part of h5py, a Python
interface to the HDF5…
[ 109.9s] 💭 (1333 chars) "The check is:
```python
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_..."
[ 109.9s] 🔧 run_command python3 -c "import h5py; print(h5py.__file__)"
[ 109.9s] → error (exit 0):
[ 123.3s] 💭 (565 chars) "It seems the current working directory is `/workspace`, so `import h5py` is picking up
`/workspace/h5py` first.
I shoul..."
[ 123.3s] 🔧 run_command cd /tmp && python3 -c "import h5py; print(h5py.__file__)"
[ 123.4s] → error (exit 0):
[ 126.2s] 💭 (68 chars) "Wait, what is `/h5py/h5py/__init__.py`?
Let's see what's in `/h5py`."
[ 126.2s] 🔧 run_command ls -R /h5py
[ 126.2s] → /h5py:
[ 134.7s] 💭 (292 chars) "It seems the library is installed in `/h5py/h5py`. This is very confusing.
Wait, the workspace layout says:
```
./h5py
...."
[ 134.7s] 🔧 run_command ls -F /workspace
[ 134.8s] → LICENSE
[ 141.6s] 💭 (198 chars) "Okay, so `/workspace` has the source code.
And `/h5py` is another directory that also looks like the source code.
Wait,..."
[ 141.6s] 🔧 run_command python3 -c "import sys; print('\n'.join(sys.path))"
[ 141.6s] 🔧
[ 151.2s] 💭 (289 chars) "The `sys.path` does not include `/workspace` or `/h5py`.
So when I do `import h5py` from `/workspace`, Python finds `/wo..."
[ 151.2s] 🔧 run_command python3 -c "import sys; print(sys.path)"
[ 151.2s] → ['', '/usr/local/lib/python310.zip', '/usr/local/lib/python3.10',
'/usr/local/lib/python3.10/lib-dynload', '/usr/local/l
[ 161.8s] 💭 (361 chars) "Yes, `''` is at the beginning. That means the current directory is searched first.
If I want to use the *installed* ver..."
[ 161.8s] 🔧 run_command ls /usr/local/lib/python3.10/site-packages/h5py
[ 161.9s] → error (exit 0):
[ 168.1s] 💭 (241 chars) "So `h5py` is NOT installed in `site-packages`.
Then where was it coming from when I did `cd /tmp && python3 -c "import h..."
[ 168.1s] 🔧 run_command env | grep PYTHONPATH
[ 168.2s] → error (exit 0):
[ 177.2s] 💭 (261 chars) "No `PYTHONPATH`.
Wait, look at the error again:
`Traceback (most recent call last):`
`File "/h5py/h5py/__init__.py", l..."
[ 177.2s] 🔧 run_command ls -ld /h5py
[ 177.2s] → lrwxrwxrwx 1 root root 10 Nov 14 03:16 /h5py -> /workspace
[ 261.5s] 💭 (548 chars) "Ah! `/h5py` is a symlink to `/workspace`.
Since `/h5py` is likely in the `sys.path` by default in this environment (or s..."
[ 261.5s] 📖 read_file (h5py/__init__.py)
[ 261.5s] ✓ {'status': 'ok', 'filepath': 'h5py/__init__.py', 'content': '# This file is part of h5py, a Python
interface to the HDF5…
[ 289.7s] 💭 (1291 chars) "The code is:
```python
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_o..."
[ 289.7s] 🔧 run_command ls h5py/_errors*.so
[ 289.7s] → error (exit 0):
[ 314.0s] 💭 (743 chars) "No `.so` files. `h5py` is not compiled in the workspace.
This means I MUST use an installed version of `h5py` if one exi..."
[ 314.0s] 🔧 run_command python3 -c "import sys; print('\n'.join(sys.path))"
[ 314.1s] 🔧
[ 320.1s] 💭 (250 chars) "`/h5py` is NOT in `sys.path`.
Wait, then how did `python3 -c "import h5py; print(h5py.__file__)"` find `/h5py/h5py/__ini..."
[ 320.1s] 🔧 run_command cd /tmp && python3 -c "import h5py; print(h5py.__file__)"
[ 320.1s] → error (exit 0):
[ 325.5s] 💭 (218 chars) "Wait, the traceback says: `File "/h5py/h5py/__init__.py", line 25, in <module>`.
But `/h5py` is not in `sys.path`!
How t..."
[ 325.5s] 🔧 run_command ls /usr/local/lib/python3.10/site-packages/*.pth
[ 325.5s] → /usr/local/lib/python3.10/site-packages/__editable__.h5py-3.13.0.pth
[ 341.8s] 💭 (858 chars) "BINGO! `__editable__.h5py-3.13.0.pth`.
This means `h5py` was installed in "editable" mode, pointing to `/h5py` (which is..."
[ 341.8s] 🔧 run_command find /workspace -name "*.so"
[ 341.8s] 🔧
[ 349.0s] 💭 (238 chars) "What??? No `.so` files in `/workspace`?
Then how can it be installed in editable mode?
Wait, maybe the `.so` files are i..."
[ 349.0s] 🔧 run_command cat /usr/local/lib/python3.10/site-packages/__editable__.h5py-3.13.0.pth
[ 349.0s] → import __editable___h5py_3_13_0_finder; __editable___h5py_3_13_0_finder.install()
[ 367.2s] 💭 (718 chars) "It's using a custom finder. This is common with newer `pip install -e .` (PEP 660).
If the `.so` files are not in `/wor..."
[ 367.2s] 🔧 run_command mv setup.py setup.py.bak && python3 -c "import h5py; print(h5py.__file__)" && mv
[ 367.3s] → error (exit 0):
[ 374.5s] 💭 (239 chars) "Still no `_errors`. This is very strange.
If I cannot import `h5py`, I cannot reproduce the bug.
But I AM a principal Py..."
[ 374.5s] 🔧 run_command find /usr -name "_errors*.so" 2>/dev/null
[ 374.6s] 🔧
[ 384.7s] 💭 (423 chars) "This is unbelievable. Is `h5py` not installed at all?
But the problem description says it's a `ZeroDivisionError` in `h5..."
[ 384.7s] 📖 read_file (h5py/_hl/selections.py)
[ 384.8s] ✓ {'status': 'ok', 'filepath': 'h5py/_hl/selections.py', 'content': '# This file is part of h5py, a Python
interface to th…
[ 388.2s] 💭 (38 chars) "I need to find the `broadcast` method."
[ 388.2s] 🔧 run_command grep -n "def broadcast" h5py/_hl/selections.py
[ 388.3s] → 154: def broadcast(self, source_shape):
[ 395.3s] 💭 (186 chars) "There are three `broadcast` methods.
Line 154 is in `Selection`.
Line 275 is likely in `SimpleSelection`.
Line 341 is li..."
[ 395.3s] 📖 read_file (h5py/_hl/selections.py)
[ 395.3s] ✓ {'status': 'ok', 'filepath': 'h5py/_hl/selections.py', 'content': ' if product(source_shape) !=
self.nselect:\n …
[ 438.4s] 💭 (2018 chars) "I found it!
Line 293: `chunks = tuple(x//y for x, y in zip(count, tshape))`
In `SimpleSelection.broadcast(self, source_..."
[ 438.4s] 📖 read_file (h5py/_hl/selections.py)
[ 438.4s] ✓ {'status': 'ok', 'filepath': 'h5py/_hl/selections.py', 'content': ' sid = self._id.copy()\n
sid.se…
Native result row
{
"agent_error": "Agent exceeded session timeout (7.5 min)",
"duration_seconds": 479.08,
"error": "Test failures/errors recorded in JUnit XML (failures=1, errors=0)",
"grade": {
"collected_tests": 226,
"competition_junit_ok": false,
"error": "Test failures/errors recorded in JUnit XML (failures=1, errors=0)",
"required_issues_count": 1,
"resolved": false,
"status_counts": {
"FAILED": 1,
"PASSED": 225
},
"strict_clean_patch": true,
"test_exit_code": 1
},
"instance_id": "h5py__h5py-2577",
"pass_idx": 0,
"patch_chars": 103,
"phase1_seconds": 477.48,
"repo": "h5py/h5py",
"request_log_path": "/kaggle-root/working/r31/rollouts_X/requests/h5py__h5py-2577__p0__r0.jsonl",
"resolved": false,
"rollout_idx": 0,
"run_key": "h5py__h5py-2577__p0__r0",
"strict_clean_patch": true,
"tool_calls": 25,
"total_llm_calls": 25,
"trace_path": "/kaggle-root/working/r31/rollouts_X/traces/trace_h5py__h5py-2577__p0__r0.json"
}