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Fixes
- Fix
devicekwarg colliding with the default in neural net constructors - Fix
qsar()/pcm()crashing on insufficient training data for non-year splits - Fix missing
source_pathinfrom_dataframetest calls - Cast
Yearto int32 when converting bioactivity data to Parquet - Raise a clear
ImportErrorinstead ofNameErrorwhen torch/skorch are missing - Coerce
Yearcolumn to numeric before temporal split comparison
Additions
- Add
download_if_missingoption toPapyrusDataset.from_dataframe
Docs
- Document Windows CUDA wheel install for the
dnnextra
Notebook examples overhaul
- New
protein_descriptors.ipynb: fetching ProDEC amino-acid-scale descriptors, the fixed-lengthAVG/ACC/PDT/FFTtransforms, aligning short sequences with pyFAMSA for comparable raw descriptors, andpcm()modelling with both gradient boosting and the DNN classes (single-task, multi-task classifier) advanced_querying.ipynb: fixed the mold2 sentinel-NaN (~1e38) values not being unmasked before scaling, fixed DNN checkpoint paths colliding acrossMultiTaskNNRegressorruns, and added new sections covering therandom/cluster/custom-cluster/customsplit strategies and how to pullX_train/y_train/X_valid/y_validarrays directlymatchRCSB.ipynb: fixed the Colab setup cell's%%capturemagic being placed after another comment line, which silently broke output suppressionsimple_examples.ipynb: added printed result counts to the similarity/substructure search examples and cleaned up stale imports/descriptor references