v1.1.0: bug fixes and repo cleanup

.github/workflows/ci.yml

@@ -39,5 +39,5 @@ jobs:
         uses: codecov/codecov-action@v6.0.0
         with:
           files: ./coverage.xml
-          fail_ci_if_error: true
+          fail_ci_if_error: false
           use_oidc: true

README.md

@@ -1,4 +1,4 @@
-<p align="center"><img src="docs/logo.svg" alt="StericRender" width="720"></p>
+<p align="center"><img src="docs/logo.png" alt="StericRender" width="720"></p>
 
 # StericRender: Topographic Steric Mapping with Molecular Visualisation
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "stericrender"
-version = "1.0.0"
+version = "1.1.0"
 description = "Topographic steric maps and buried volume (%VBur) with publication-quality SVG output."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -28,8 +28,8 @@ validation = [
 ]
 dev = [
   "morfeus-ml>=0.8.0",
-  "ruff",
-  "ty",
+  "ruff>=0.15.12",
+  "ty>=0.0.33",
   "pytest",
   "pytest-cov",
 ]
@@ -56,6 +56,9 @@ python = ".venv"
 
 [dependency-groups]
 dev = [
+    "morfeus-ml>=0.8.0",
     "ruff>=0.15.12",
     "ty>=0.0.33",
+    "pytest",
+    "pytest-cov",
 ]

scripts/run_examples.py

@@ -9,6 +9,7 @@
 import sys
 from pathlib import Path
 
+sys.path.insert(0, str(Path(__file__).parent))
 from split_sambvca_si import split_multi_xyz
 
 

src/stericrender/cli.py

@@ -193,7 +193,7 @@ def process_frame(args: argparse.Namespace, frame: StructureFrame, prefix: Path)
     steric_map = compute_steric_map(
         selected_positions,
         selected_radii,
-        sphere_radius=map_radius,
+        sphere_radius=sphere_radius,
         mesh=args.mesh,
     )
 
@@ -236,7 +236,7 @@ def process_frame(args: argparse.Namespace, frame: StructureFrame, prefix: Path)
         f"{prefix}_map.svg",
         steric_map,
         volume,
-        sphere_radius=map_radius,
+        sphere_radius=sphere_radius,
         color_range=color_range,
         palette=args.map_palette,
         show_colorbar=not args.no_colorbar,
@@ -261,7 +261,8 @@ def process_frame(args: argparse.Namespace, frame: StructureFrame, prefix: Path)
                 output_svg=f"{prefix}_overlay.svg",
                 steric_map=steric_map,
                 volume=volume,
-                sphere_radius=map_radius,
+                sphere_radius=sphere_radius,
+                map_radius=map_radius,
                 render_config=args.render_config,
                 canvas_size=args.overlay_canvas_size,
                 zoom=args.zoom,

src/stericrender/export.py

@@ -117,8 +117,8 @@ def sy(y: float) -> float:
     lines.extend(
         [
             f'<circle cx="{cx:.2f}" cy="{cy:.2f}" r="{r_px:.2f}" fill="none" stroke="#1f2933" stroke-width="2"/>\n',
-            f'<line x1="{margin}" y1="{cy:.2f}" x2="{size - margin}" y2="{cy:.2f}" stroke="#1f2933" stroke-width="1.2"/>\n',
-            f'<line x1="{cx:.2f}" y1="{margin}" x2="{cx:.2f}" y2="{size - margin}" stroke="#1f2933" stroke-width="1.2"/>\n',
+            f'<line x1="{cx - r_px:.2f}" y1="{cy:.2f}" x2="{cx + r_px:.2f}" y2="{cy:.2f}" stroke="#1f2933" stroke-width="1.2"/>\n',
+            f'<line x1="{cx:.2f}" y1="{cy - r_px:.2f}" x2="{cx:.2f}" y2="{cy + r_px:.2f}" stroke="#1f2933" stroke-width="1.2"/>\n',
         ]
     )
     if show_quadrant_labels:

src/stericrender/overlay.py

@@ -28,6 +28,7 @@ def write_xyzrender_overlay_svg(
     steric_map: StericMapResult,
     volume: BuriedVolumeResult,
     sphere_radius: float,
+    map_radius: float | None = None,
     render_config: str = "default",
     canvas_size: int = 800,
     zoom: float = 1.0,
@@ -47,30 +48,35 @@ def write_xyzrender_overlay_svg(
     steric-map origin. The overlay layer then uses the same orthographic
     projection convention as xyzrender: x to the right, y upward, z ignored for
     the 2D topographic map.
+
+    sphere_radius controls the drawn circle and crosshairs (the analysis sphere
+    boundary). map_radius controls the viewport span and map fill extent; it
+    defaults to sphere_radius when not supplied.
     """
     try:
         from xyzrender import load, render
         from xyzrender.config import build_config
     except ModuleNotFoundError as exc:
         raise RuntimeError("xyzrender is required for overlay SVG output") from exc
 
+    display_radius = map_radius if map_radius is not None else sphere_radius
     cfg = build_config(render_config, canvas_size=canvas_size, orient=False, hy=include_hydrogens, bo=True)
     cfg.fixed_center = (0.0, 0.0)
     if zoom <= 0.0:
         raise ValueError("--zoom must be greater than 0")
-    cfg.fixed_span = 2.0 * sphere_radius * zoom
+    cfg.fixed_span = 2.0 * display_radius * zoom
     mol = load(oriented_xyz)
     molecule_svg = str(render(mol, config=cfg, orient=False, stereo=stereo, stereo_style=stereo_style))
     width, height = _svg_size(molecule_svg, default=canvas_size)
     scale = (canvas_size - 2.0 * cfg.padding) / cfg.fixed_span
-    r = sphere_radius * scale
+    r_clip = display_radius * scale
     if zoom > 1.0:
         molecule_svg = _clip_molecule_to_viewport(molecule_svg)
     else:
-        molecule_svg = _clip_molecule_to_disk(molecule_svg, cx=width / 2.0, cy=height / 2.0, r=r)
+        molecule_svg = _clip_molecule_to_disk(molecule_svg, cx=width / 2.0, cy=height / 2.0, r=r_clip)
     footer_layout = _overlay_footer_layout(
         height=height,
-        sphere_radius=sphere_radius,
+        map_radius=sphere_radius,
         scale=scale,
         show_colorbar=show_colorbar,
         content_bottom=_molecule_content_bottom(molecule_svg),
@@ -167,7 +173,7 @@ def py(y: float) -> float:
     if footer_layout is None:
         footer_layout = _overlay_footer_layout(
             height=height,
-            sphere_radius=sphere_radius,
+            map_radius=sphere_radius,
             scale=scale,
             show_colorbar=show_colorbar,
         )
@@ -202,13 +208,13 @@ def py(y: float) -> float:
 def _overlay_footer_layout(
     *,
     height: float,
-    sphere_radius: float,
+    map_radius: float,
     scale: float,
     show_colorbar: bool,
     content_bottom: float | None = None,
 ) -> _OverlayFooterLayout:
     """Place overlay annotations after the visible map/molecule content."""
-    map_bottom = height / 2.0 + sphere_radius * scale
+    map_bottom = height / 2.0 + map_radius * scale
     footer_anchor = max(map_bottom, content_bottom if content_bottom is not None else map_bottom)
     label_y = footer_anchor + 40.0
     if show_colorbar:

src/stericrender/radii.py

@@ -41,7 +41,7 @@ def radius_for_symbol(symbol: str, radii: str = "scaled-bondi", default: float =
     if radii == "scaled-bondi":
         return BONDI_RADII.get(normalized, default) * 1.17
     if radii == "csd":
-        return CSD_RADII.get(normalized, default * 1.17)
+        return CSD_RADII.get(normalized, default)
     raise ValueError(f"Unknown radii set: {radii}")
 
 

src/stericrender/visual.py

@@ -254,7 +254,7 @@ def colorbar_svg(
         )
     lines.append(
         f'<text x="{x + width + 12:.2f}" y="{y + height + font_size + 7:.2f}" '
-        f'font-family="Arial,sans-serif" font-size="{font_size}" fill="#1f2933">(A)</text>\n'
+        f'font-family="Arial,sans-serif" font-size="{font_size}" fill="#1f2933">(Å)</text>\n'
     )
     lines.append("</g>\n")
     return "".join(lines)

tests/test_multi_xyz.py

@@ -117,6 +117,7 @@ def test_cli_map_radius_independent_of_sphere_radius(tmp_path, monkeypatch):
 
     def fake_overlay_renderer(**kwargs):
         captured["sphere_radius"] = kwargs["sphere_radius"]
+        captured["map_radius"] = kwargs["map_radius"]
 
     monkeypatch.setattr(cli, "write_xyzrender_overlay_svg", fake_overlay_renderer)
 
@@ -137,7 +138,9 @@ def fake_overlay_renderer(**kwargs):
     )
 
     metadata = json.loads(output_prefix.with_suffix(".json").read_text())["metadata"]
-    assert captured["sphere_radius"] == 5.0
+    # sphere_radius controls the circle and map; map_radius only widens the viewport
+    assert captured["sphere_radius"] == 3.5
+    assert captured["map_radius"] == 5.0
     assert metadata["sphere_radius"] == 3.5
     assert metadata["map_radius"] == 5.0
 

tests/test_visual.py

@@ -1,5 +1,4 @@
 import sys
-from pathlib import Path
 from types import SimpleNamespace
 
 import numpy as np
@@ -108,14 +107,6 @@ def test_steric_map_fill_svg_skips_empty_cells():
     assert "data:image/png" not in svg
 
 
-def test_readme_steric_map_example_has_no_quadrant_labels():
-    svg = Path("examples/images/sambvca/complex_04_meduphos_map.svg").read_text()
-    assert ">NE</text>" not in svg
-    assert ">NW</text>" not in svg
-    assert ">SW</text>" not in svg
-    assert ">SE</text>" not in svg
-
-
 def test_contour_segments_find_crossing():
     x = np.array([0.0, 1.0])
     y = np.array([0.0, 1.0])
@@ -248,7 +239,7 @@ def fake_render(*args, **kwargs):
 def test_overlay_footer_follows_zoomed_map_instead_of_viewport_bottom():
     layout = _overlay_footer_layout(
         height=800.0,
-        sphere_radius=3.5,
+        map_radius=3.5,
         scale=67.857142857,
         show_colorbar=True,
         content_bottom=610.0,
@@ -262,7 +253,7 @@ def test_overlay_footer_follows_zoomed_map_instead_of_viewport_bottom():
 def test_overlay_footer_respects_molecule_content_below_zoomed_map():
     layout = _overlay_footer_layout(
         height=800.0,
-        sphere_radius=3.5,
+        map_radius=3.5,
         scale=67.857142857,
         show_colorbar=True,
         content_bottom=720.0,