Clip painted regions to chromosome outlines

[wyim-pgl]

python -m jcvi.graphics.chromosome features.bed idmap --size=sizes paints each BED feature as a full-width Rectangle, so a feature at a chromosome end sticks out past the rounded cap.

This change keeps painted regions inside the outline:

• Chromosome, HorizontalChromosome and ChromosomeWithCentromere keep their outline (self.outline, or a compound path of both arms for the centromere glyph) and gain a clip(artist) helper.
• draw_chromosomes clips every painted rectangle to the glyph that contains it. Features that extend beyond the chromosome length are clipped at the cap; features entirely beyond it become invisible instead of floating past the end.
• The glyphs' own patch= rectangles are clipped the same way. Clipping happens after add_patches() because set_clip_path() captures the outline's transform at call time, and set_transform() re-clips for callers such as karyotype that transform the glyph after construction.
• Chromosome borders and the centromere circle still draw above the painted regions. --imagemap output is unchanged.

Verified on PNG, PDF and SVG output with and without centromeres. New tests in tests/graphics/test_chromosome.py render each glyph and check pixels inside and just outside the caps; they fail on main and pass with this change.

[Adamtaranto]

Hi @wyim-pgl can you please post example before and after images showing the issue and the fix?

[wyim-pgl]

Here we go.

[Adamtaranto]

I don't see the issue with the feature sticking out past the rounded cap

[holschbachPGL]

here is some additional context

[tanghaibao]

looks good, thanks all @wyim-pgl @Adamtaranto @holschbachPGL