fix(preprocess): correct double-escaped regex in ND2 binning parser#225
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petercla0119 wants to merge 3 commits into
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fix(preprocess): correct double-escaped regex in ND2 binning parser#225petercla0119 wants to merge 3 commits into
petercla0119 wants to merge 3 commits into
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format_singlecell_anndata fails with TypeError when writing the singlecell h5ad because columns like gene_symbol_1 and gene_id_1 contain NaN (float) values mixed with strings. h5py cannot implicitly convert non-string objects to variable-length strings. Fill NaN with empty strings and cast to str for all object-typed obs columns before calling write_h5ad. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The raw-string regex in `_parse_binning_from_nd2` used `\\s` and `\\d` which in an r-string are literal backslash-s and backslash-d, never matching actual whitespace or digits. This caused binning_xy to always return None for ND2 files even when "Binning: 2x2" was present in the text_info metadata. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Docs are Markdown-only and don't use autodoc, so the package doesn't need to be installed. The full install was failing because iohub==0.3.0 doesn't exist on PyPI (only pre-releases up to 0.3.0a7). Co-Authored-By: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>
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Description
The raw-string regex in
_parse_binning_from_nd2used double-escaped sequences (\\s,\\d) which in a Pythonr"..."string are literal backslash characters, not regex metacharacters. This caused the function to never match the"Binning: 2x2"string present in ND2text_infometadata, always returningNoneforbinning_xy.Before:
r"Binning:\\s*(\\d+)x(\\d+)"— searches for literal\s*\d+x\d+After:
r"Binning:\s*(\d+)x(\d+)"— correctly matchesBinning: 2x2What is the nature of your change?
Checklist
pyproject.tomlto reflect the change as designated by semantic versioning. (N/A — this PR targets thezarr3development branch, which is already at1.5.0; no version bump needed.)ruff checkandruff format.