11 fix rpy2 depraction of conversion rules #12
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Signed-off-by: kgoebler <[email protected]>
Signed-off-by: kgoebler <[email protected]>
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Pull Request Overview
This PR fixes rpy2 deprecation warnings by replacing the deprecated activate() conversion methods with the newer localconverter approach. The changes modernize the R interface code to use current rpy2 best practices while maintaining backward compatibility.
- Replaces deprecated
numpy2ri.activate()andpandas2ri.activate()with a local converter pattern - Adds automatic installation of the "drf" R package if not present
- Updates documentation and version number
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| causalAssembly/drf_fitting.py | Modernizes rpy2 conversion methods and adds automatic R package installation |
| VERSION | Bumps version from 1.2.0 to 1.2.1 |
| README.md | Updates citation and removes manual R package installation requirement |
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causalAssembly/drf_fitting.py
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| if not rpackages.isinstalled("drf"): | ||
| # select a mirror for R packages | ||
| utils.chooseCRANmirror(ind=1) |
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Hard-coding the CRAN mirror index to 1 is fragile and may fail if that mirror becomes unavailable. Consider using a more robust approach like utils.chooseCRANmirror(graphics=False) which automatically selects an available mirror, or handle potential failures with error handling.
| utils.chooseCRANmirror(ind=1) | |
| utils.chooseCRANmirror(graphics=False) |
| Returns: | ||
| np.ndarray: New predicted samlpe of Y. | ||
| np.ndarray: New predicted sample of Y. |
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There's a spelling error in the comment. 'samlpe' should be 'sample'. This was correctly fixed in the code.
Signed-off-by: kgoebler <[email protected]>
closes #11