Update Keras to Keras3 #12
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dan-knight
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dan-knight
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Looks good to me! Makes sense to update to the new keras package. Just update the version and date in DESCRIPTION and document this change in NEWS.
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Pull request overview
This pull request migrates the iSubGen package from using the legacy keras package to the modern keras3 package. The update affects dependencies, imports, API calls, file formats, and documentation across the codebase.
Changes:
- Updated package dependencies and imports from
kerastokeras3in DESCRIPTION, NAMESPACE, and metadata.yaml - Modified code to use keras3 API: changed
load_model_hdf5()toload_model(), updatedmodel$inputtomodel$inputs, and changed file extension from.hdf5to.keras - Updated documentation and examples in README, vignette, and help files to reference keras3 package
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| DESCRIPTION | Updated Imports to replace keras with keras3 |
| NAMESPACE | Updated import statement from keras to keras3 |
| metadata.yaml | Updated Dependencies list to replace keras with keras3 |
| R/create.autoencoder.R | Changed output file extension from .hdf5 to .keras |
| R/create.autoencoder.irf.matrix.R | Updated to use load_model() instead of load_model_hdf5(), changed file extension check from hdf5 to keras, and updated model property from model$input to model$inputs |
| man/create.autoencoder.Rd | Updated documentation to reference keras file format and removed trailing whitespace |
| README.md | Updated package references to keras3, added explicit library loading for tensorflow/keras3/reticulate |
| vignettes/iSubGenGuide.Rnw | Updated package references and URLs to point to keras3 |
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Pull request overview
Copilot reviewed 10 out of 11 changed files in this pull request and generated 2 comments.
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tnyamaguchi
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tnyamaguchi
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@maotian06 The last two comments from copilot make sense. Do you want to accept the suggestions or any reason you want to skip them? Otherwise, looks good to me.
Co-authored-by: Copilot <[email protected]>
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Pull request overview
Copilot reviewed 10 out of 11 changed files in this pull request and generated no new comments.
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Description
Closes #...
Analysis Results
Checklist
This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
Disclosing PHI is a major problem1 - Even a small leak can be costly2.
This PR does NOT contain germline genetic data3, RNA-Seq, DNA methylation, microbiome or other molecular data4.
.png, .jpeg),.pdf,.RData,.xlsx,.doc,.ppt, or other output files.To automatically exclude such files using a .gitignore file, see here for example.
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have set up or verified the
mainbranch protection rule following the github standards before opening this pull request.The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have added the major changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.Footnotes
UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩
The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩
Genetic information is considered PHI.
Forensic assays can identify patients with as few as 21 SNPs ↩
RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩