v0.9.0

A release with a HUGE breaking change.

Until now, we have been using the word "predicate" in two contexts:

• VariantPredicate for testing if a variant meets one or more criteria (is missense, is a SNV, ...)
• genotype/phenotype predicate for assigning an individual into a genotype/phenotype category

The first context stays as is. However, from now on, we will use "classifier" and "class" for the assignment of an individual into a genotype/phenotype category.

Sadly, this results in a huge breaking change and practically all analyses will have to be updated. We outline the migration strategy below.

Migration strategy

A list of the most important updates

Item	Replacement	Comment
gpsea.analysis.predicate.genotype.VariantPredicate	gpsea.analysis.predicate.VariantPredicate	Moved with no change
gpsea.analysis.predicate.genotype.VariantPredicates	gpsea.analysis.predicate	The builtin predicates are now available in the module
gpsea.analysis.predicate.genotype.GenotypePolyPredicate	gpsea.analysis.clf.GenotypeClassifier	Moved and renamed
gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate	gpsea.analysis.clf.PhenotypeClassifier	Moved and renamed
gpsea.analysis.predicate.genotype.monoallelic_predicate	gpsea.analysis.clf.monoallelic_classifier	Moved and renamed
gpsea.analysis.predicate.genotype.biallelic_predicate	gpsea.analysis.clf.biallelic_classifier	Moved and renamed
gpsea.analysis.predicate.genotype.allele_count	gpsea.analysis.clf.allele_count	Moved and renamed
gpsea.analysis.predicate.genotype.sex_predicate	gpsea.analysis.clf.sex_classifier	Moved and renamed
gpsea.analysis.predicate.genotype.diagnosis_predicate	gpsea.analysis.clf.diagnosis_classifier	Moved and renamed
gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest	gpsea.analysis.clf.prepare_classifiers_for_terms_of_interest	Moved and renamed

Please contact ielis to help with analysis migration.

What's Changed

• Use classifiers instead of genotype/phenotype predicates. by @ielis in #381

Full Changelog: v0.8.0...v0.9.0