Fix ID processing (int->str) - #12
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🟢 Approval recommended
No unresolved blocking issues were identified.
Review effort: Lite
Findings: None
What changed in this PR
This PR preserves ChEBI IDs as strings during parsing, corrects split-based filtering, and raises the minimum Python version to 3.11.
Changes:
- Parse split IDs as strings.
- Filter samples using split IDs.
- Require Python 3.11+.
| File | Description |
|---|---|
pyproject.toml |
Raises the minimum Python version. |
chebILP/molecule_processing/data_preparation.py |
Preserves split IDs as strings. |
chebILP/ilp_problem_builder.py |
Corrects split-based sample filtering. |
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IDs are handled as strings in chebILP. However, pandas handles them as numbers by default unless we tell pandas not to.
This issue was also addressed in 1ba9d51, but only for the ILPProblemBuilder, not generally (which did not matter so far since it is the only place using the splits). This PR implements the cleaner solution and addresses the problem right at the parsing stage.
Also, we now require python >=3.11 since networkx does not work with 3.10.