diff --git a/setup.cfg b/setup.cfg index 096628c01..586fe9eae 100644 --- a/setup.cfg +++ b/setup.cfg @@ -73,8 +73,7 @@ bgen = fail_under = 100 [tool:pytest] -# TODO: remove ignored doctests below once Xarray>0.18.2 is released (with https://github.com/pydata/xarray/pull/4753) -addopts = --doctest-modules --ignore=validation --cov-fail-under=100 --ignore=sgkit/stats/regenie.py --ignore=sgkit/stats/pca.py +addopts = --doctest-modules --ignore=validation --cov-fail-under=100 norecursedirs = .eggs build docs filterwarnings = error diff --git a/sgkit/stats/pca.py b/sgkit/stats/pca.py index eff18ecfb..91fe0aadb 100644 --- a/sgkit/stats/pca.py +++ b/sgkit/stats/pca.py @@ -257,8 +257,9 @@ def pca( ... ) >>> ds.compute() # doctest: +NORMALIZE_WHITESPACE - Dimensions: (components: 2, samples: 150, variants: 100) - Dimensions without coordinates: components, samples, variants + Dimensions: (samples: 150, components: 2, + variants: 100) + Dimensions without coordinates: samples, components, variants Data variables: sample_pca_projection (samples, components) float32 0.0103... sample_pca_component (variants, components) float32 0.096... @@ -273,7 +274,7 @@ def pca( ... .plot.scatter(x=("sample_pca_projection", 0), y=("sample_pca_projection", 1)) ... ) >>> ax - + References ---------- diff --git a/sgkit/stats/regenie.py b/sgkit/stats/regenie.py index b76fd6672..ddab2a7ee 100644 --- a/sgkit/stats/regenie.py +++ b/sgkit/stats/regenie.py @@ -860,8 +860,9 @@ def regenie( >>> res = regenie(ds, dosage="call_dosage", covariates="sample_covariate", traits="sample_trait", merge=False) >>> res.compute() # doctest: +NORMALIZE_WHITESPACE - Dimensions: (alphas: 5, blocks: 2, contigs: 2, outcomes: 5, samples: 50) - Dimensions without coordinates: alphas, blocks, contigs, outcomes, samples + Dimensions: (blocks: 2, alphas: 5, samples: 50, outcomes: 5, + contigs: 2) + Dimensions without coordinates: blocks, alphas, samples, outcomes, contigs Data variables: regenie_base_prediction (blocks, alphas, samples, outcomes) float64 0.33... regenie_meta_prediction (samples, outcomes) float64 -0.4588 0.78 ... 0.3734