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Fix xarray repr in doctests
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@tomwhite
tomwhite committed Mar 4, 2024
1 parent d32b871 commit 0764d85
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Showing 3 changed files with 29 additions and 29 deletions.
12 changes: 6 additions & 6 deletions sgkit/stats/pca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -256,16 +256,16 @@ def pca(
... .pipe(sg.pca, n_components=2, merge=False)
... )
>>> ds.compute() # doctest: +NORMALIZE_WHITESPACE
<xarray.Dataset>
<xarray.Dataset> Size: 3kB
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...
sample_pca_explained_variance (components) float32 44.24 23.49
sample_pca_explained_variance_ratio (components) float32 0.1915 0.1017
sample_pca_loading (variants, components) float32 0.639...
sample_pca_projection (samples, components) float32 1kB 0....
sample_pca_component (variants, components) float32 800B ...
sample_pca_explained_variance (components) float32 8B 44.24 23.49
sample_pca_explained_variance_ratio (components) float32 8B 0.1915 0.1017
sample_pca_loading (variants, components) float32 800B ...
>>> # Visualize first two PCs
>>> ax = (
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8 changes: 4 additions & 4 deletions sgkit/stats/regenie.py
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Original file line number Diff line number Diff line change
Expand Up @@ -859,14 +859,14 @@ def regenie(
>>> ds["sample_trait"] = (("samples", "traits"), rs.normal(size=(n_sample, n_trait)))
>>> res = regenie(ds, dosage="call_dosage", covariates="sample_covariate", traits="sample_trait", merge=False)
>>> res.compute() # doctest: +NORMALIZE_WHITESPACE
<xarray.Dataset>
<xarray.Dataset> Size: 26kB
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
regenie_loco_prediction (contigs, samples, outcomes) float64 0.4886 ... ...
regenie_base_prediction (blocks, alphas, samples, outcomes) float64 20kB ...
regenie_meta_prediction (samples, outcomes) float64 2kB -0.4588 ... 0.3734
regenie_loco_prediction (contigs, samples, outcomes) float64 4kB 0.4886 ...
References
----------
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38 changes: 19 additions & 19 deletions sgkit/window.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,23 +70,23 @@ def window_by_variant(
>>> # Contiguous windows, each with the same number of variants (3)
>>> # except for the last window of each contig
>>> sg.window_by_variant(ds, size=3, merge=False)
<xarray.Dataset>
<xarray.Dataset> Size: 96B
Dimensions: (windows: 4)
Dimensions without coordinates: windows
Data variables:
window_contig (windows) int64 0 0 1 1
window_start (windows) int64 0 3 5 8
window_stop (windows) int64 3 5 8 10
window_contig (windows) int64 32B 0 0 1 1
window_start (windows) int64 32B 0 3 5 8
window_stop (windows) int64 32B 3 5 8 10
>>> # Overlapping windows
>>> sg.window_by_variant(ds, size=3, step=2, merge=False)
<xarray.Dataset>
<xarray.Dataset> Size: 144B
Dimensions: (windows: 6)
Dimensions without coordinates: windows
Data variables:
window_contig (windows) int64 0 0 0 1 1 1
window_start (windows) int64 0 2 4 5 7 9
window_stop (windows) int64 3 5 5 8 10 10
window_contig (windows) int64 48B 0 0 0 1 1 1
window_start (windows) int64 48B 0 2 4 5 7 9
window_stop (windows) int64 48B 3 5 5 8 10 10
"""
step = step or size
return _window_per_contig(ds, variant_contig, merge, _get_windows, size, step)
Expand Down Expand Up @@ -170,13 +170,13 @@ def window_by_position(
>>> # and using offset to start windows at 1
>>> ds_w1 = sg.window_by_position(ds, size=10, offset=1, merge=False)
>>> ds_w1
<xarray.Dataset>
<xarray.Dataset> Size: 192B
Dimensions: (windows: 8)
Dimensions without coordinates: windows
Data variables:
window_contig (windows) int64 0 0 1 1 1 1 1 1
window_start (windows) int64 0 4 5 6 6 8 9 9
window_stop (windows) int64 4 5 6 6 8 9 9 10
window_contig (windows) int64 64B 0 0 1 1 1 1 1 1
window_start (windows) int64 64B 0 4 5 6 6 8 9 9
window_stop (windows) int64 64B 4 5 6 6 8 9 9 10
>>> [ds.variant_position.values[i:j] for i, j in zip(ds_w1.window_start.values, ds_w1.window_stop.values) if i != j] # doctest: +NORMALIZE_WHITESPACE
[array([1, 4, 6, 8]),
array([12]),
Expand All @@ -189,13 +189,13 @@ def window_by_position(
>>> # each 10 base pairs in size. Also known as "locus windows".
>>> ds_w2 = sg.window_by_position(ds, size=10, offset=-5, window_start_position="variant_position", merge=False)
>>> ds_w2
<xarray.Dataset>
<xarray.Dataset> Size: 240B
Dimensions: (windows: 10)
Dimensions without coordinates: windows
Data variables:
window_contig (windows) int64 0 0 0 0 0 1 1 1 1 1
window_start (windows) int64 0 0 0 1 3 5 6 6 8 9
window_stop (windows) int64 2 4 4 5 5 6 8 8 9 10
window_contig (windows) int64 80B 0 0 0 0 0 1 1 1 1 1
window_start (windows) int64 80B 0 0 0 1 3 5 6 6 8 9
window_stop (windows) int64 80B 2 4 4 5 5 6 8 8 9 10
>>> [ds.variant_position.values[i:j] for i, j in zip(ds_w2.window_start.values, ds_w2.window_stop.values)] # doctest: +NORMALIZE_WHITESPACE
[array([1, 4]),
array([1, 4, 6, 8]),
Expand Down Expand Up @@ -382,12 +382,12 @@ def window_by_genome(
>>> import sgkit as sg
>>> ds = sg.simulate_genotype_call_dataset(n_variant=10, n_sample=2, n_contig=2)
>>> sg.window_by_genome(ds, merge=False)
<xarray.Dataset>
<xarray.Dataset> Size: 16B
Dimensions: (windows: 1)
Dimensions without coordinates: windows
Data variables:
window_start (windows) int64 0
window_stop (windows) int64 10
window_start (windows) int64 8B 0
window_stop (windows) int64 8B 10
"""
new_ds = create_dataset(
{
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