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jonbrenasalimanfoo
jonbrenas
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alimanfoo
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Changed figures into optional_figures and def_figures into figures (#676)
* Changed figures into optional_figures and def_figures into figures * Used figure in optional_figure definition * ensure no duplicate window sizes --------- Co-authored-by: Alistair Miles <[email protected]>
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10 files changed

+36
-36
lines changed

10 files changed

+36
-36
lines changed

‎malariagen_data/anoph/cnv_data.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -626,7 +626,7 @@ def plot_cnv_hmm_coverage_track(
626626
show: gplt_params.show = True,
627627
x_range: Optional[gplt_params.x_range] = None,
628628
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
629-
) -> gplt_params.figure:
629+
) -> gplt_params.optional_figure:
630630
debug = self._log.debug
631631

632632
import bokeh.models as bkmod
@@ -753,7 +753,7 @@ def plot_cnv_hmm_coverage(
753753
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
754754
gene_labels: Optional[gplt_params.gene_labels] = None,
755755
gene_labelset: Optional[gplt_params.gene_labelset] = None,
756-
) -> gplt_params.figure:
756+
) -> gplt_params.optional_figure:
757757
debug = self._log.debug
758758

759759
import bokeh.layouts as bklay
@@ -821,7 +821,7 @@ def plot_cnv_hmm_heatmap_track(
821821
height: Optional[gplt_params.height] = None,
822822
show: gplt_params.show = True,
823823
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
824-
) -> gplt_params.figure:
824+
) -> gplt_params.optional_figure:
825825
debug = self._log.debug
826826

827827
import bokeh.models as bkmod
@@ -965,7 +965,7 @@ def plot_cnv_hmm_heatmap(
965965
show: gplt_params.show = True,
966966
gene_labels: Optional[gplt_params.gene_labels] = None,
967967
gene_labelset: Optional[gplt_params.gene_labelset] = None,
968-
) -> gplt_params.figure:
968+
) -> gplt_params.optional_figure:
969969
debug = self._log.debug
970970

971971
import bokeh.layouts as bklay

‎malariagen_data/anoph/fst.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -187,7 +187,7 @@ def plot_fst_gwss_track(
187187
x_range: Optional[gplt_params.x_range] = None,
188188
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
189189
clip_min: fst_params.clip_min = 0.0,
190-
) -> gplt_params.figure:
190+
) -> gplt_params.optional_figure:
191191
# compute Fst
192192
x, fst = self.fst_gwss(
193193
contig=contig,
@@ -295,7 +295,7 @@ def plot_fst_gwss(
295295
clip_min: fst_params.clip_min = 0.0,
296296
gene_labels: Optional[gplt_params.gene_labels] = None,
297297
gene_labelset: Optional[gplt_params.gene_labelset] = None,
298-
) -> gplt_params.figure:
298+
) -> gplt_params.optional_figure:
299299
# gwss track
300300
fig1 = self.plot_fst_gwss_track(
301301
contig=contig,

‎malariagen_data/anoph/g123.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -335,7 +335,7 @@ def plot_g123_gwss_track(
335335
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
336336
inline_array: base_params.inline_array = base_params.inline_array_default,
337337
chunks: base_params.chunks = base_params.native_chunks,
338-
) -> gplt_params.figure:
338+
) -> gplt_params.optional_figure:
339339
# compute G123
340340
x, g123 = self.g123_gwss(
341341
contig=contig,
@@ -440,7 +440,7 @@ def plot_g123_gwss(
440440
chunks: base_params.chunks = base_params.native_chunks,
441441
gene_labels: Optional[gplt_params.gene_labels] = None,
442442
gene_labelset: Optional[gplt_params.gene_labelset] = None,
443-
) -> gplt_params.figure:
443+
) -> gplt_params.optional_figure:
444444
# gwss track
445445
fig1 = self.plot_g123_gwss_track(
446446
contig=contig,
@@ -518,7 +518,7 @@ def plot_g123_calibration(
518518
show: gplt_params.show = True,
519519
inline_array: base_params.inline_array = base_params.inline_array_default,
520520
chunks: base_params.chunks = base_params.native_chunks,
521-
) -> gplt_params.figure:
521+
) -> gplt_params.optional_figure:
522522
# get g123 values
523523
calibration_runs = self.g123_calibration(
524524
contig=contig,

‎malariagen_data/anoph/genome_features.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -193,7 +193,7 @@ def plot_transcript(
193193
gplt_params.toolbar_location
194194
] = gplt_params.toolbar_location_default,
195195
title: gplt_params.title = True,
196-
) -> gplt_params.figure:
196+
) -> gplt_params.optional_figure:
197197
debug = self._log.debug
198198

199199
debug("Find the transcript annotation.")
@@ -335,7 +335,7 @@ def plot_genes(
335335
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
336336
gene_labels: Optional[gplt_params.gene_labels] = None,
337337
gene_labelset: Optional[gplt_params.gene_labelset] = None,
338-
) -> gplt_params.figure:
338+
) -> gplt_params.optional_figure:
339339
debug = self._log.debug
340340

341341
debug("handle region parameter - this determines the genome region to plot")

‎malariagen_data/anoph/gplt_params.py‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -79,16 +79,16 @@
7979
# Use quite a broad type here to accommodate both single-panel figures
8080
# created via bokeh.plotting and multi-panel figures created via
8181
# bokeh.layouts.
82-
Optional[bokeh.model.Model],
83-
"A bokeh figure (only returned if show=False).",
82+
bokeh.model.Model,
83+
"A bokeh figure.",
8484
]
8585

86-
def_figure: TypeAlias = Annotated[
86+
optional_figure: TypeAlias = Annotated[
8787
# Use quite a broad type here to accommodate both single-panel figures
8888
# created via bokeh.plotting and multi-panel figures created via
8989
# bokeh.layouts.
90-
bokeh.model.Model,
91-
"A bokeh figure.",
90+
Optional[figure],
91+
"A bokeh figure (only returned if show=False).",
9292
]
9393

9494
output_backend: TypeAlias = Annotated[

‎malariagen_data/anoph/h12.py‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -149,7 +149,7 @@ def plot_h12_calibration(
149149
show: bool = True,
150150
chunks: base_params.chunks = base_params.native_chunks,
151151
inline_array: base_params.inline_array = base_params.inline_array_default,
152-
) -> gplt_params.figure:
152+
) -> gplt_params.optional_figure:
153153
# Get H12 values.
154154
calibration_runs = self.h12_calibration(
155155
contig=contig,
@@ -369,7 +369,7 @@ def plot_h12_gwss_track(
369369
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
370370
chunks: base_params.chunks = base_params.native_chunks,
371371
inline_array: base_params.inline_array = base_params.inline_array_default,
372-
) -> gplt_params.figure:
372+
) -> gplt_params.optional_figure:
373373
# Compute H12.
374374
x, h12, contigs = self.h12_gwss(
375375
contig=contig,
@@ -474,7 +474,7 @@ def plot_h12_gwss(
474474
inline_array: base_params.inline_array = base_params.inline_array_default,
475475
gene_labels: Optional[gplt_params.gene_labels] = None,
476476
gene_labelset: Optional[gplt_params.gene_labelset] = None,
477-
) -> gplt_params.figure:
477+
) -> gplt_params.optional_figure:
478478
# Plot GWSS track.
479479
fig1 = self.plot_h12_gwss_track(
480480
contig=contig,
@@ -558,7 +558,7 @@ def plot_h12_gwss_multi_overlay_track(
558558
show: gplt_params.show = True,
559559
x_range: Optional[gplt_params.x_range] = None,
560560
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
561-
) -> gplt_params.figure:
561+
) -> gplt_params.optional_figure:
562562
cohort_queries = self._setup_cohort_queries(
563563
cohorts=cohorts,
564564
sample_sets=sample_sets,
@@ -679,7 +679,7 @@ def plot_h12_gwss_multi_overlay(
679679
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
680680
gene_labels: Optional[gplt_params.gene_labels] = None,
681681
gene_labelset: Optional[gplt_params.gene_labelset] = None,
682-
) -> gplt_params.figure:
682+
) -> gplt_params.optional_figure:
683683
# Plot GWSS track.
684684
fig1 = self.plot_h12_gwss_multi_overlay_track(
685685
contig=contig,
@@ -764,7 +764,7 @@ def plot_h12_gwss_multi_panel(
764764
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
765765
gene_labels: Optional[gplt_params.gene_labels] = None,
766766
gene_labelset: Optional[gplt_params.gene_labelset] = None,
767-
) -> gplt_params.figure:
767+
) -> gplt_params.optional_figure:
768768
cohort_queries = self._setup_cohort_queries(
769769
cohorts=cohorts,
770770
sample_sets=sample_sets,
@@ -781,7 +781,7 @@ def plot_h12_gwss_multi_panel(
781781
raise ValueError("Cohorts and window_sizes should have the same keys.")
782782

783783
# Plot GWSS track.
784-
figs: list[gplt_params.def_figure] = []
784+
figs: list[gplt_params.figure] = []
785785
for i, (cohort_label, cohort_query) in enumerate(cohort_queries.items()):
786786
params = dict(
787787
contig=contig,

‎malariagen_data/anoph/h1x.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -196,7 +196,7 @@ def plot_h1x_gwss_track(
196196
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
197197
chunks: base_params.chunks = base_params.native_chunks,
198198
inline_array: base_params.inline_array = base_params.inline_array_default,
199-
) -> gplt_params.figure:
199+
) -> gplt_params.optional_figure:
200200
# Compute H1X.
201201
x, h1x, contigs = self.h1x_gwss(
202202
contig=contig,
@@ -306,7 +306,7 @@ def plot_h1x_gwss(
306306
inline_array: base_params.inline_array = base_params.inline_array_default,
307307
gene_labels: Optional[gplt_params.gene_labels] = None,
308308
gene_labelset: Optional[gplt_params.gene_labelset] = None,
309-
) -> gplt_params.figure:
309+
) -> gplt_params.optional_figure:
310310
# Plot GWSS track.
311311
fig1 = self.plot_h1x_gwss_track(
312312
contig=contig,

‎malariagen_data/anoph/snp_data.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1307,7 +1307,7 @@ def plot_snps(
13071307
show: gplt_params.show = True,
13081308
gene_labels: Optional[gplt_params.gene_labels] = None,
13091309
gene_labelset: Optional[gplt_params.gene_labelset] = None,
1310-
) -> gplt_params.figure:
1310+
) -> gplt_params.optional_figure:
13111311
# Plot SNPs track.
13121312
fig1 = self.plot_snps_track(
13131313
region=region,
@@ -1379,7 +1379,7 @@ def plot_snps_track(
13791379
x_range: Optional[gplt_params.x_range] = None,
13801380
show: gplt_params.show = True,
13811381
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
1382-
) -> gplt_params.figure:
1382+
) -> gplt_params.optional_figure:
13831383
# Normalise params.
13841384
site_mask_prepped = self._prep_site_mask_param(site_mask=site_mask)
13851385
del site_mask

‎malariagen_data/anopheles.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -359,7 +359,7 @@ def plot_heterozygosity_track(
359359
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
360360
chunks: base_params.chunks = base_params.native_chunks,
361361
inline_array: base_params.inline_array = base_params.inline_array_default,
362-
) -> gplt_params.figure:
362+
) -> gplt_params.optional_figure:
363363
debug = self._log.debug
364364

365365
# Normalise parameters.
@@ -424,7 +424,7 @@ def plot_heterozygosity(
424424
inline_array: base_params.inline_array = base_params.inline_array_default,
425425
gene_labels: Optional[gplt_params.gene_labels] = None,
426426
gene_labelset: Optional[gplt_params.gene_labelset] = None,
427-
) -> gplt_params.figure:
427+
) -> gplt_params.optional_figure:
428428
debug = self._log.debug
429429

430430
# normalise to support multiple samples
@@ -619,7 +619,7 @@ def plot_roh_track(
619619
x_range: Optional[gplt_params.x_range] = None,
620620
title: Optional[gplt_params.title] = None,
621621
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
622-
) -> gplt_params.figure:
622+
) -> gplt_params.optional_figure:
623623
debug = self._log.debug
624624

625625
debug("handle region parameter - this determines the genome region to plot")
@@ -723,7 +723,7 @@ def plot_roh(
723723
inline_array: base_params.inline_array = base_params.inline_array_default,
724724
gene_labels: Optional[gplt_params.gene_labels] = None,
725725
gene_labelset: Optional[gplt_params.gene_labelset] = None,
726-
) -> gplt_params.figure:
726+
) -> gplt_params.optional_figure:
727727
debug = self._log.debug
728728

729729
resolved_region: Region = parse_single_region(self, region)
@@ -1476,7 +1476,7 @@ def plot_ihs_gwss_track(
14761476
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
14771477
chunks: base_params.chunks = base_params.native_chunks,
14781478
inline_array: base_params.inline_array = base_params.inline_array_default,
1479-
) -> gplt_params.figure:
1479+
) -> gplt_params.optional_figure:
14801480
# compute ihs
14811481
x, ihs = self.ihs_gwss(
14821482
contig=contig,
@@ -1621,7 +1621,7 @@ def plot_xpehh_gwss(
16211621
inline_array: base_params.inline_array = base_params.inline_array_default,
16221622
gene_labels: Optional[gplt_params.gene_labels] = None,
16231623
gene_labelset: Optional[gplt_params.gene_labelset] = None,
1624-
) -> gplt_params.figure:
1624+
) -> gplt_params.optional_figure:
16251625
# gwss track
16261626
fig1 = self.plot_xpehh_gwss_track(
16271627
contig=contig,
@@ -1726,7 +1726,7 @@ def plot_ihs_gwss(
17261726
inline_array: base_params.inline_array = base_params.inline_array_default,
17271727
gene_labels: Optional[gplt_params.gene_labels] = None,
17281728
gene_labelset: Optional[gplt_params.gene_labelset] = None,
1729-
) -> gplt_params.figure:
1729+
) -> gplt_params.optional_figure:
17301730
# gwss track
17311731
fig1 = self.plot_ihs_gwss_track(
17321732
contig=contig,
@@ -2009,7 +2009,7 @@ def plot_xpehh_gwss_track(
20092009
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
20102010
chunks: base_params.chunks = base_params.native_chunks,
20112011
inline_array: base_params.inline_array = base_params.inline_array_default,
2012-
) -> gplt_params.figure:
2012+
) -> gplt_params.optional_figure:
20132013
# compute xpehh
20142014
x, xpehh = self.xpehh_gwss(
20152015
contig=contig,

‎tests/anoph/test_h12.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -103,7 +103,7 @@ def test_h12_calibration(fixture, api: AnophelesH12Analysis):
103103
# Set up test parameters.
104104
all_sample_sets = api.sample_sets()["sample_set"].to_list()
105105
window_sizes = np.random.randint(100, 500, size=random.randint(2, 5)).tolist()
106-
window_sizes = sorted([int(x) for x in window_sizes])
106+
window_sizes = sorted(set([int(x) for x in window_sizes]))
107107
h12_params = dict(
108108
contig=random.choice(api.contigs),
109109
sample_sets=[random.choice(all_sample_sets)],

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