Drugresponseeval 1.3.0 - Bubbly Blastoise

Blastoise is a blue Pokémon whose body is mostly hidden by its tough, brown shell. The two powerful water cannons on its back can produce water blasts that can pierce steel and concrete and be used for high-speed charges and propelling itself in the air. The speed of Blastoise's charges is similar to the force of a rocket.

Added

• --custom_splitter_path to provide a Python script defining custom CV splits instead of the built-in splitting by @JudithBernett in #101
• --clean_min_responders and --clean_min_responder_frac to clean the dataset by removing responders with fewer than a certain number of responses by @JudithBernett in #101
• New models: EnsembleMF, PaccMann, SparseGO by @JudithBernett in #101

Changed

• Updated Zenodo link to latest dataset release by @JudithBernett in #101
• Simplified documentation and README by @JudithBernett in #104
• Migration to topics by @JudithBernett in #108
• Important! Template update for nf-core/tools v4.0.3 by @nf-core-bot in #97
• Important! Template update for nf-core/tools v4.1.0 by @nf-core-bot in #100
• Switch fix-linting to the hardened nf-core/actions reusable workflow by @mashehu in #102
• Move seqeralabs/action-tower-launch to @v2 (v2.4.0) by @mashehu in #103
• Update to new drevalpy version v1.6.0 by @JudithBernett in #101

Removed

• Unnecessary ext.use_gpu parameter by @JudithBernett in #101

Fixed

• The NONE.csv placeholder for PREDICT_FULL is now a real file (assets/NONE.csv), so staging no longer fails when inputs are copied instead of symlinked by @JudithBernett in #101
• Fixed a bug for training the final model on the full dataset: didn't work correctly for single drug models by @JudithBernett in #101
• Defined parameter types for boolean, integer, and float parameters because of Nextflow 26.04.0 by @JudithBernett in #101
• Merge patch into dev by @JudithBernett in #99
• Remove vulnerable PR-comment artifact pattern by @mashehu in #98

Dependencies

Dependency	Old version	New version
drevalpy	1.5.1	1.6.0
numpy	2.4.6	2.5.3
scikit-learn	1.9.0	1.9.1
scikit-posthocs	0.14.0	0.17.0
scipy	1.17.1	1.18.1
torch	2.12.0	2.14.0
pytorch-lightning	2.6.5	2.6.6
Nextflow	>= 25.10.4	>= 26.04.0

Parameters

Params	Status
--custom_splitter_path	Added
--clean_min_responders	Added
--clean_min_responder_frac	Added

Full Changelog: 1.2.2...1.3.0