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[ENH] Standardize configuration management for training and inference pipelines

Status: Open.

#665 In gc-os-ai/pyaptamer;

· ayushk687 opened on May 14, 2026

Unify input handling between AptaTrans and AptaNet

Status: Open.

#664 In gc-os-ai/pyaptamer;

· ayushk687 opened on May 14, 2026

[BUG] AptaTrans.__init__() raises AssertionError instead of ValueError for invalid input

Status: Open.

#658 In gc-os-ai/pyaptamer;

· onkar717 opened on May 8, 2026

[MNT] aa_props() uses 'type' as parameter name, shadowing Python builtin

Status: Open.

#656 In gc-os-ai/pyaptamer;

· onkar717 opened on May 8, 2026

[BUG] PositionalEncoding.forward() dropout check is always truthy

Status: Open.

#654 In gc-os-ai/pyaptamer;

· onkar717 opened on May 8, 2026

[BUG] AptaTransEncoderLightning crashes with NameError for invalid encoder_typ

Status: Open.

#652 In gc-os-ai/pyaptamer;

· onkar717 opened on May 8, 2026

[BUG] AptaNetClassifier/Regressor.fit() mutates global NumPy random state via np.random.seed()

Status: Open.

#650 In gc-os-ai/pyaptamer;

· onkar717 opened on May 7, 2026

[BUG] clean_protein_seq replaces invalid amino acids with Asparagine ("N") instead of removing them

Status: Open.

#648 In gc-os-ai/pyaptamer;

· onkar717 opened on May 7, 2026

[BUG] MaskedDataset masking deviates from BERT 80/10/10 masking behavior

Status: Open.

#646 In gc-os-ai/pyaptamer;

· onkar717 opened on May 7, 2026

[BUG] augment_reverse: dangling word "added." in Returns docstring

Status: Open.

#644 In gc-os-ai/pyaptamer;

· Ishiezz opened on May 6, 2026

[MNT] BaseTransform: replace ValueError with NotImplementedError for abstract methods and add missing module-level attributes

Status: Open.

#636 In gc-os-ai/pyaptamer;

· Ishiezz opened on May 3, 2026

[BUG] GreedyEncoder crashes or silently produces all-zeros output when words dict is empty

Status: Open.

#631 In gc-os-ai/pyaptamer;

· Ishiezz opened on May 2, 2026