tree-annotated-plot 0.3.0__tar.gz → 0.4.0__tar.gz

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/CHANGELOG.md

@@ -7,6 +7,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.4.0] - 2026-08-20
+
+### Added
+
+- `spacing` (default `0`): pixels of blank space between the tree panel and
+  the chart panel. `0` keeps the two butted together, as before. Distinct from
+  `shift_tree_loc`, which moves the tree within its own panel by resizing the
+  label strip. CLI form: `--spacing`.
+
+### Changed
+
+- Pin `ruff` to `>=0.16,<0.17` and state the lint rules explicitly with
+  `[tool.ruff.lint] select`. Ruff's *default* rule set widened in 0.16, which
+  turned CI red on unchanged code; the selection is now a project decision
+  rather than whatever the installed ruff defaults to. Development-only, no
+  effect on the package.
+
+### Fixed
+
+- With `connect_leader_to_label` on, strain labels were anchored exactly on the
+  tree panel's chart-facing edge, so the text ran up against the chart's frame
+  and the frame line became hard to read. The pad that the label strip already
+  reserved is now applied between the text and the chart, and the leader lines
+  stop where the text begins rather than continuing to the panel edge. The gap
+  is `max(3, strain_label_font_size * 0.2)` px, and the tree panel grows by that
+  much, so a hand-tuned `shift_tree_loc` may want the same adjustment.
+
 ## [0.3.0] - 2026-05-19
 
 ### Added

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: tree-annotated-plot
-Version: 0.3.0
+Version: 0.4.0
 Summary: Annotate the axis of an Altair / Vega-Lite plot with a phylogenetic tree.
 Project-URL: Documentation, https://jbloomlab.github.io/tree-annotated-plot/
 Project-URL: Homepage, https://github.com/jbloomlab/tree-annotated-plot
@@ -43,7 +43,7 @@ Requires-Dist: vl-convert-python>=1.9
 Provides-Extra: dev
 Requires-Dist: black>=24; extra == 'dev'
 Requires-Dist: pytest>=8; extra == 'dev'
-Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: ruff<0.17,>=0.16; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: mkdocs-click>=0.8; extra == 'docs'
 Requires-Dist: mkdocs-material>=9.5; extra == 'docs'

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "tree-annotated-plot"
-version = "0.3.0"
+version = "0.4.0"
 description = "Annotate the axis of an Altair / Vega-Lite plot with a phylogenetic tree."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -36,7 +36,7 @@ Issues = "https://github.com/jbloomlab/tree-annotated-plot/issues"
 [project.optional-dependencies]
 dev = [
     "pytest>=8",
-    "ruff>=0.6",
+    "ruff>=0.16,<0.17",
     "black>=24",
 ]
 docs = [
@@ -58,3 +58,10 @@ target-version = ["py311"]
 
 [tool.ruff]
 target-version = "py311"
+
+[tool.ruff.lint]
+# Ruff's default rule set is not stable across releases -- 0.16 broadened it,
+# which turned CI red on unchanged code. State the rules we lint against so a
+# ruff upgrade changes them only when we say so. These are ruff's pre-0.16
+# defaults, which is what this project has been checked against all along.
+select = ["E4", "E7", "E9", "F"]

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/src/tree_annotated_plot/_config.py

@@ -68,6 +68,15 @@ class PlotConfig:
         "(x-encoded).",
     ] = None
 
+    spacing: Annotated[
+        int,
+        "Pixels of blank space between the tree panel and the chart panel. "
+        "Default 0, which butts the two together. Distinct from "
+        "`shift_tree_loc`, which moves the tree within its own panel by "
+        "resizing the label strip; `spacing` sets the gap between the panels "
+        "and applies whether or not `connect_leader_to_label` is on.",
+    ] = 0
+
     tree_line_width: Annotated[
         float,
         "Stroke width (px) for the tree's branch lines. Default 2.",
@@ -155,8 +164,9 @@ class PlotConfig:
     shift_tree_loc: Annotated[
         int,
         "Pixels by which to shift the tree toward (positive) or away from "
-        "(negative) the chart. Default 0. Has no effect when "
-        "connect_leader_to_label is off.",
+        "(negative) the chart, by resizing the label strip inside the tree "
+        "panel. Default 0. Has no effect when connect_leader_to_label is off; "
+        "to set the gap between the tree and chart panels use `spacing`.",
     ] = 0
 
     color_tree_by: Annotated[

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/src/tree_annotated_plot/_plot.py

@@ -49,6 +49,7 @@ def plot(
     branch_length: Literal["div", "num_date"],
     tree_size: int = 100,
     tree_location: TreeLocation | None = None,
+    spacing: int = 0,
     tree_line_width: float = 2.0,
     tree_node_size: float = 45,
     leader_line_width: float = 1.0,
@@ -77,6 +78,7 @@ def plot(
             branch_length=branch_length,
             tree_size=tree_size,
             tree_location=tree_location,
+            spacing=spacing,
             tree_line_width=tree_line_width,
             tree_node_size=tree_node_size,
             leader_line_width=leader_line_width,
@@ -281,7 +283,10 @@ def _build(
     hoisted_config, hoisted_other = _pop_toplevel_only_attrs(new_chart)
 
     combined = _concat_for_location(
-        tree_chart=tree_chart, user_chart=new_chart, location=location
+        tree_chart=tree_chart,
+        user_chart=new_chart,
+        location=location,
+        spacing=config.spacing,
     )
     _apply_combined_config(combined, hoisted_config)
     for k, v in hoisted_other.items():
@@ -320,6 +325,7 @@ def _concat_for_location(
     tree_chart: alt.TopLevelMixin,
     user_chart: alt.TopLevelMixin,
     location: TreeLocation,
+    spacing: int,
 ) -> alt.HConcatChart | alt.VConcatChart:
     """Concat tree and chart in the order implied by the tree's location.
 
@@ -333,19 +339,19 @@ def _concat_for_location(
     user-chart marks whose color values aren't in the tree's domain.
     """
     if location == "left":
-        return alt.hconcat(tree_chart, user_chart, spacing=0).resolve_scale(
+        return alt.hconcat(tree_chart, user_chart, spacing=spacing).resolve_scale(
             y="independent", color="independent"
         )
     if location == "right":
-        return alt.hconcat(user_chart, tree_chart, spacing=0).resolve_scale(
+        return alt.hconcat(user_chart, tree_chart, spacing=spacing).resolve_scale(
             y="independent", color="independent"
         )
     if location == "top":
-        return alt.vconcat(tree_chart, user_chart, spacing=0).resolve_scale(
+        return alt.vconcat(tree_chart, user_chart, spacing=spacing).resolve_scale(
             x="independent", color="independent"
         )
     if location == "bottom":
-        return alt.vconcat(user_chart, tree_chart, spacing=0).resolve_scale(
+        return alt.vconcat(user_chart, tree_chart, spacing=spacing).resolve_scale(
             x="independent", color="independent"
         )
     raise ValueError(f"unreachable: tree_location={location!r}")
@@ -1475,6 +1481,11 @@ def _build_scale_bar_layer(
 
 _LABEL_PAD_PX_MIN = 4
 _LABEL_PAD_RATIO = 0.4  # `LABEL_PAD_PX = max(MIN, font_size * RATIO)`
+# Gap between the labels and the chart, kept separate from the tree-facing pad
+# above because it clears the chart's frame rather than the deepest tip, and so
+# wants a small fixed clearance rather than the pad's larger, faster-growing one.
+_LABEL_CHART_GAP_PX_MIN = 3
+_LABEL_CHART_GAP_RATIO = 0.2  # `LABEL_CHART_GAP_PX = max(MIN, font_size * RATIO)`
 _LABEL_CHAR_PX_RATIO = 0.6  # rough proportional sans-serif glyph-width estimate
 _LABEL_HALO_RATIO = 0.6  # white-halo strokeWidth as a fraction of font_size
 
@@ -1614,9 +1625,15 @@ def _build_tree_chart(
         max_name_len = max((len(n) for n in names), default=0)
         char_px = strain_label_font_size * _LABEL_CHAR_PX_RATIO
         label_pad_px = max(_LABEL_PAD_PX_MIN, strain_label_font_size * _LABEL_PAD_RATIO)
+        chart_gap_px = max(
+            _LABEL_CHART_GAP_PX_MIN, strain_label_font_size * _LABEL_CHART_GAP_RATIO
+        )
         # Strip needs to fit the longest label plus `halo_px / 2` of halo
-        # extension on the leader-facing side, plus a small fixed pad.
-        label_pixel_width = label_pad_px + max_name_len * char_px + halo_px / 2
+        # extension on the leader-facing side, a pad between the tree and the
+        # text, and a smaller gap between the text and the chart.
+        label_pixel_width = (
+            label_pad_px + chart_gap_px + max_name_len * char_px + halo_px / 2
+        )
         strip_pixel_width = label_pixel_width - shift_tree_loc
         if strip_pixel_width <= 0:
             raise ValueError(
@@ -1629,9 +1646,13 @@ def _build_tree_chart(
         per_pixel = branch_span / tree_size if tree_size else 0.0
         extra_branch_units = strip_pixel_width * per_pixel
         chart_edge_branch = branch_max + extra_branch_units
-        tips_df = tips_df.assign(x_label=chart_edge_branch)
-        leader_df = tips_df[tips_df["x"] < chart_edge_branch].assign(
-            x2=chart_edge_branch
+        # Anchor the labels `chart_gap_px` *inside* the chart-facing edge rather
+        # than on it, so the text does not run up against the chart's frame. The
+        # leaders stop at the same place, where the text begins.
+        label_anchor_branch = chart_edge_branch - chart_gap_px * per_pixel
+        tips_df = tips_df.assign(x_label=label_anchor_branch)
+        leader_df = tips_df[tips_df["x"] < label_anchor_branch].assign(
+            x2=label_anchor_branch
         )
         extended_tree_size = tree_size + strip_pixel_width
     else:
@@ -1680,9 +1701,9 @@ def _build_tree_chart(
         # When connect_leader_to_label is on, the branch domain is extended
         # past `branch_max` to `chart_edge_branch` so the label strip has
         # data-units to occupy; tips at `branch_max` still sit at pixel
-        # `tree_size` on the panel. Each label's chart-facing edge is
-        # anchored at `chart_edge_branch` and aligned outward (right for
-        # tree on the left, left for tree on the right).
+        # `tree_size` on the panel. Each label's chart-facing edge sits
+        # `chart_gap_px` inside `chart_edge_branch`, aligned outward (right
+        # for tree on the left, left for tree on the right).
         if tree_location == "left":
             branch_domain = [branch_min, chart_edge_branch]
             text_align = "right"
@@ -1783,7 +1804,8 @@ def _build_tree_chart(
         # strip at bottom, opposite the chart above).
         # tree_location="bottom" → root at bottom → branch_max at top (label
         # strip at top, opposite the chart below).
-        # Each label's chart-facing edge is anchored at `chart_edge_branch`.
+        # Each label's chart-facing edge sits `chart_gap_px` inside
+        # `chart_edge_branch`.
         # The text mark is rotated 270° (reads bottom-to-top), which maps
         # pre-rotation `align="right"` to a top anchor (text extends down)
         # and `align="left"` to a bottom anchor (text extends up). For tree

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/tests/test_appearance_tuning.py

@@ -795,3 +795,30 @@ def test_cli_scale_bar_font_size(tmp_path):
     collect_text_marks(tree_panel, text_marks)
     sizes = [m.get("fontSize") for m in text_marks if "fontSize" in m]
     assert 16.0 in sizes or 16 in sizes
+
+
+def test_cli_spacing(tmp_path):
+    """`--spacing` reaches the saved spec's top-level concat gap."""
+    tree_path, chart_path, out_path = _cli_setup(
+        tmp_path, _attr_auspice(), _vertical_chart(["A", "B", "C", "D"])
+    )
+    _run_cli(
+        [
+            "--tree",
+            str(tree_path),
+            "--chart",
+            str(chart_path),
+            "--output",
+            str(out_path),
+            "--chart-strain-field",
+            "strain",
+            "--tree-strain-field",
+            "name",
+            "--branch-length",
+            "div",
+            "--spacing",
+            "9",
+        ]
+    )
+    spec = json.loads(out_path.read_text())
+    assert spec["spacing"] == 9

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/tests/test_cli.py

@@ -45,6 +45,7 @@ def test_help_lists_auto_generated_options() -> None:
         "--branch-length",
         "--tree-size",
         "--tree-location",
+        "--spacing",
         "--tree-line-width",
         "--scale-bar / --no-scale-bar",
         "--strict-version / --no-strict-version",

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/tests/test_label_connection.py

@@ -285,9 +285,9 @@ def test_default_leader_endpoint_stops_at_branch_max() -> None:
 
 def test_vertical_left_renders_text_with_right_align() -> None:
     """Vertical layout with `connect_leader_to_label=True` and default
-    `tree_location="left"`: tree on left, chart on right; labels flush
-    against the chart on the panel's right (chart-facing) edge. Text
-    mark uses `align="right"` and `x_label > branch_max`."""
+    `tree_location="left"`: tree on left, chart on right; labels sit just
+    inside the panel's right (chart-facing) edge. Text mark uses
+    `align="right"` and `x_label > branch_max`."""
     out = tree_annotated_plot.plot(_auspice(), _vertical_chart(), **_on_kw())
     text = _text_layer(out)
     assert text is not None
@@ -557,3 +557,48 @@ def test_default_off_keeps_user_axis_labels_intact() -> None:
     assert axis.get("labelFontWeight") == "bold"
     assert axis.get("labels") is not False
     assert axis.get("ticks") is not False
+
+
+# ---------- label inset from the chart-facing edge ----------
+
+
+def test_labels_sit_inside_the_chart_facing_edge() -> None:
+    """Labels are anchored one pad *inside* `chart_edge_branch` rather than on
+    it, so the glyphs do not run up against the chart panel's frame. The panel
+    itself still extends to `chart_edge_branch`, which is the chart-facing end
+    of the branch scale's domain."""
+    out = tree_annotated_plot.plot(_auspice(), _vertical_chart(), **_on_kw())
+    text = _text_layer(out)
+    assert text is not None
+    # tree on the left → branch domain is [branch_min, chart_edge_branch]
+    chart_edge_branch = text["encoding"]["x"]["scale"]["domain"][1]
+    rows = _resolve_dataset(out.to_dict(), text)
+    assert rows
+    for row in rows:
+        assert row["x_label"] < chart_edge_branch
+
+
+def test_labels_sit_inside_the_chart_facing_edge_horizontal() -> None:
+    """Same inset in horizontal layout, where the default tree_location is
+    "bottom" and the branch domain runs [branch_min, chart_edge_branch] on y."""
+    out = tree_annotated_plot.plot(_auspice(), _horizontal_chart(), **_on_kw())
+    text = _text_layer(out)
+    assert text is not None
+    chart_edge_branch = text["encoding"]["y"]["scale"]["domain"][1]
+    rows = _resolve_dataset(out.to_dict(), text)
+    assert rows
+    for row in rows:
+        assert row["x_label"] < chart_edge_branch
+
+
+def test_leaders_stop_where_the_labels_begin() -> None:
+    """The leaders run to the label anchor rather than on to the panel edge, so
+    the dashed line meets the text instead of passing under it to the frame."""
+    out = tree_annotated_plot.plot(_auspice(), _vertical_chart(), **_on_kw())
+    text = _text_layer(out)
+    assert text is not None
+    anchors = {row["x_label"] for row in _resolve_dataset(out.to_dict(), text)}
+    assert len(anchors) == 1, f"expected one shared label anchor, got {anchors}"
+    (anchor,) = anchors
+    for row in _resolve_dataset(out.to_dict(), _leader_layer(out)):
+        assert row["x2"] == pytest.approx(anchor)

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.4.0}/tests/test_tree_location.py

@@ -181,3 +181,55 @@ def test_right_with_x_encoded_strain_raises() -> None:
         tree_annotated_plot.plot(
             _auspice_4_tip(), _horizontal_chart(), tree_location="right", **_kw()
         )
+
+
+# ---------- spacing between the tree and chart panels ----------
+
+
+@pytest.mark.parametrize(
+    ("chart_fn", "location"),
+    [
+        (_vertical_chart, "left"),
+        (_vertical_chart, "right"),
+        (_horizontal_chart, "top"),
+        (_horizontal_chart, "bottom"),
+    ],
+)
+def test_spacing_defaults_to_zero(chart_fn, location) -> None:
+    """The default butts the two panels together, as before `spacing` existed."""
+    out = tree_annotated_plot.plot(
+        _auspice_4_tip(), chart_fn(), tree_location=location, **_kw()
+    )
+    assert out.to_dict()["spacing"] == 0
+
+
+@pytest.mark.parametrize(
+    ("chart_fn", "location"),
+    [
+        (_vertical_chart, "left"),
+        (_vertical_chart, "right"),
+        (_horizontal_chart, "top"),
+        (_horizontal_chart, "bottom"),
+    ],
+)
+def test_spacing_propagates_to_the_concat(chart_fn, location) -> None:
+    """An explicit `spacing` reaches the top-level concat spec, for every
+    `tree_location` — the gap is between the two panels, so it applies
+    uniformly to the hconcat and vconcat forms alike."""
+    out = tree_annotated_plot.plot(
+        _auspice_4_tip(), chart_fn(), tree_location=location, spacing=7, **_kw()
+    )
+    assert out.to_dict()["spacing"] == 7
+
+
+def test_spacing_does_not_disturb_panel_sizes() -> None:
+    """Spacing is applied along the branch axis, between panels, so neither
+    panel's own dimensions change and strain-row alignment is untouched."""
+    out_zero = tree_annotated_plot.plot(_auspice_4_tip(), _vertical_chart(), **_kw())
+    out_gap = tree_annotated_plot.plot(
+        _auspice_4_tip(), _vertical_chart(), spacing=12, **_kw()
+    )
+    d_zero, d_gap = out_zero.to_dict(), out_gap.to_dict()
+    for i in (0, 1):
+        assert d_zero["hconcat"][i]["width"] == d_gap["hconcat"][i]["width"]
+        assert d_zero["hconcat"][i].get("height") == d_gap["hconcat"][i].get("height")