v1.1.0: bug fixes and repo cleanup#4
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Bug fixes: - Fix crosshair lines in standalone map SVG extending beyond the circle boundary into the %VBur label area (export.py now uses cx±r_px / cy±r_px, matching the overlay convention) - Fix sphere_radius/map_radius conflation in CLI pipeline: compute_steric_map, write_map_svg, and write_xyzrender_overlay_svg now each receive the correct parameter independently - Fix CSD radii fallback returning default*1.17 instead of default, making unknown-element behaviour inconsistent across radius sets Quality / hygiene: - Fix ruff format violation in tests/test_multi_xyz.py (was blocking CI) - Fix colorbar unit label (A) -> (Å) in visual.py - Fix fragile local import in scripts/run_examples.py via sys.path.insert - Replace logo SVG (SVG wrapper around a 5.9 MB embedded PNG) with the extracted PNG directly; update README reference - Consolidate duplicate dev dependency groups in pyproject.toml - Remove scripts/validate_references.py (superseded by test_validation.py and test_sambvca_examples.py) - Remove test_readme_steric_map_example_has_no_quadrant_labels which read committed assets rather than testing live code paths; covered by test_map_svg_quadrant_labels_are_opt_in using tmp_path
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JamesOBrien2
marked this pull request as ready for review
June 25, 2026 12:00
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Several bugs found during a post-release review, fixed alongside general repo tidying.
The crosshair lines in standalone map SVGs were drawn using the full SVG canvas extent rather than the circle boundary, causing them to overshoot into the %VBur label area. The
--map-radiusand--sphere-radiusparameters were being conflated in the CLI pipeline,compute_steric_mapand the map SVG writer were receiving the display radius instead of the analysis radius, so the two flags were not truly independent. The CSD radii fallback for unknown elements was returningdefault × 1.17rather thandefault, making the behaviour inconsistent with the Bondi sets. The colorbar unit label read(A)rather than(Å).On the repo side, the logo was an SVG file wrapping a 5.9 MB embedded PNG with no vector content, replaced here with the PNG directly. A developer script for validation was removed as it duplicated what the test suite already covers. Dependency group definitions in
pyproject.tomlwere consolidated. A test that read committed gallery assets rather than exercising live code was replaced by the equivalenttmp_path-based test that already existed.