feat: sanitise attributes for HDF5#80
Open
LDeakin wants to merge 4 commits into
Open
Conversation
There was a problem hiding this comment.
Pull request overview
This PR improves NetCDF/HDF5 attribute writing by sanitizing attribute values before calling setncattr, addressing failures when attributes contain unsupported (e.g., object) dtypes.
Changes:
- Added helpers to detect HDF5-compatible NumPy dtypes and to coerce unsupported attribute values to HDF5-storable types.
- Updated global attribute writing to route all attributes (including history) through the sanitizer.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+166
to
+168
| # Everything else: encode to string bytes | ||
| str_value = value if isinstance(value, str) else str(value) | ||
| return np.bytes_(str_value.encode("ascii")) |
There was a problem hiding this comment.
str_value.encode("ascii") will raise UnicodeEncodeError for any non-ASCII attribute (e.g., filenames, user-supplied metadata). Consider adding an error strategy (e.g., errors="backslashreplace"/"replace") or falling back to UTF-8 encoding so NetCDF writing can’t crash on valid Unicode metadata.
LDeakin
marked this pull request as ready for review
April 23, 2026 23:35
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Addresses
TypeError: Object dtype dtype('O') has no native HDF5 equivalentonsetncattr, which I was hitting running the cylinder unwrapping CLI.