tree-annotated-plot 0.3.0__tar.gz → 0.5.0__tar.gz

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.5.0}/CHANGELOG.md

@@ -5,7 +5,69 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.5.0] - 2026-10-30
+
+### Added
+
+- `strain_label_styles` (default `None`): style a subset of the strain labels
+  rendered in the tree panel when `connect_leader_to_label` is on, e.g. to draw
+  the vaccine strains' labels in bold red. A list of rules, each naming some
+  `strains` and a `style` of Vega-Lite text properties (`fill`, `opacity`,
+  `fontWeight`, `fontStyle`). Where rules overlap, later rules win property by
+  property. An optional `when` condition applies a rule only while it holds:
+  - the name of a parameter declared in the chart, such as a checkbox;
+  - any Vega expression, e.g. `"emphasis == 'cell'"` for a radio button;
+  - in Python, an `alt.Parameter`, which is declared on the returned chart if
+    the chart doesn't already declare it.
+
+  Each styled property becomes a per-label expression on the existing label
+  layers, so no layers are added and the returned chart keeps its shape. A
+  strain that isn't a tree tip raises; strains dropped by `prune_tree_to_chart`
+  are skipped. CLI form: `--strain-label-styles` with a JSON array, where
+  `when` names a parameter saved in the chart JSON.
+  ([#12](https://github.com/jbloomlab/tree-annotated-plot/issues/12))
+
+### Fixed
+
+- A chart with selection parameters on a compound chart (layer, facet, or
+  concat) failed to render when passed to `plot()` as a JSON path, HTML path
+  or spec dict, which is every CLI use. Vega-Lite reported
+  `Duplicate signal name: "<selection>_tuple"`. This affected the flu examples'
+  CLI reproductions. The chart loader removed each selection's `views` before
+  loading, and altair then emitted empty `views`, which makes Vega-Lite define
+  the selection in every view. The loader now leaves the spec's `views` intact.
+  Live altair charts were never affected.
+- The `plot()` docstring's Returns section described the panel order wrongly
+  for a strain on `x`. The default `tree_location="bottom"` puts the chart
+  first and the tree second. The section now gives the order for each
+  `tree_location`.
+
+## [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
 

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.5.0}/CLAUDE.md

@@ -7,7 +7,9 @@
   section as you make them — new parameters, behavior changes, removed
   features, bug fixes — in [Keep a Changelog](https://keepachangelog.com/)
   format. At release time, `## [Unreleased]` is renamed to
-  `## [X.Y.Z] - YYYY-MM-DD` and a fresh `## [Unreleased]` is created.
+  `## [X.Y.Z] - YYYY-MM-DD`, with no empty `## [Unreleased]` left above it.
+  When the next change lands and there's no `## [Unreleased]` section, add
+  one at the top.
 - **Single source of truth — `pyproject.toml`**: canonical for dependencies,
   supported Python version, build config, tool settings. Don't restate any of
   these in prose; refer to `pyproject.toml`.
@@ -52,6 +54,13 @@
   on `x` or `y`, overrides its sort to match the tree's tip order, and
   hconcat's or vconcat's a tree panel on the matching side. Tree dictates
   tip ordering; plot follows.
+- **Loaded specs go to `from_dict` unmodified.** Don't strip or rewrite
+  altair's annotations when loading a dict / JSON / HTML chart. Selection
+  params' `views` in particular are valid at the top level; removing them made
+  every compound chart with a selection fail to render ("Duplicate signal
+  name"). See `_load_chart`. Likewise, declare extra params by appending to
+  the combined chart's top-level `params`, never with `add_params`, which
+  recurses into sub-charts and raises on spec-loaded ones.
 - **Two surfaces, one config**: `tree_annotated_plot.plot()` and the `tree-annotated-plot`
   CLI both accept the same parameters via `PlotConfig`. They converge on
   `_build(tree, chart, config)` so they can never disagree.
@@ -78,7 +87,10 @@
 - **Eyeball examples after any rendering change.** There are no
   image-snapshot regression tests (vl-convert/font/platform variance
   makes them flaky), so visual regressions only get caught by
-  looking. After any change to `_plot.py`, `_tree.py`, the example
+  looking. Tests may still render with `vl_convert.vegalite_to_svg`
+  to check that a spec renders at all, or to assert discrete SVG
+  attributes such as a label's `font-weight` / `fill`; those are
+  deterministic. After any change to `_plot.py`, `_tree.py`, the example
   scripts, or anything they touch: run `scripts/build_docs.sh`, open
   `site/examples.html`, and click through each example — both the
   embedded SVG and the interactive HTML link. Confirm tip-row

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: tree-annotated-plot
-Version: 0.3.0
+Version: 0.5.0
 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-0.5.0}/docs/examples.md

@@ -140,6 +140,77 @@ CLI flags: `--connect-leader-to-label --strain-label-font-size 9
 --shift-tree-loc 60`. In Python:
 `connect_leader_to_label=True, strain_label_font_size=9, shift_tree_loc=60`.
 
+### Optional: emphasize some strains' labels
+
+With label connection on, you can also style a subset of the labels, for
+example so the vaccine strains are easy to pick out. Pass
+`strain_label_styles`, a list of rules. Each rule names some `strains`
+(tree tip identifiers, i.e. `tree_strain_field` values) and a `style` built
+from Vega-Lite text properties: `fill`, `opacity`, `fontWeight` and
+`fontStyle`. A rule can also take a `when` condition, usually the name of a
+checkbox parameter, so the style applies only while the box is ticked.
+Where rules overlap, later rules win.
+
+The example below draws the labels of the H3N2 recent vaccine strains in
+bold red, with a checkbox that turns the emphasis off and on:
+
+![H3N2 with vaccine-strain labels in bold red](images/h3n2_combined_label_styles.svg)
+
+[Open the interactive chart in a new tab →](charts/h3n2_combined_label_styles.html){target="_blank"}
+
+From the CLI, a `when` parameter has to be declared in the saved chart, so
+add it before saving:
+
+```python
+chart = chart.add_params(
+    alt.param(
+        name="vaccine_strains",
+        value=True,
+        bind=alt.binding_checkbox(name="highlight vaccine strains "),
+    )
+)
+chart.save("titers.json")
+```
+
+then pass the rules as a JSON array, alongside the label-connection flags
+above:
+
+```bash
+--connect-leader-to-label --strain-label-styles \
+    '[{"strains": ["J.2.4", "J.2:S145N"],
+       "style": {"fill": "#d62728", "fontWeight": "bold"},
+       "when": "vaccine_strains"}]'
+```
+
+In Python, pass the parameter object itself. If your chart doesn't already
+declare it, it is declared on the returned chart for you:
+
+```python
+vaccine_strains = alt.param(
+    name="vaccine_strains",
+    value=True,
+    bind=alt.binding_checkbox(name="highlight vaccine strains "),
+)
+tree_annotated_plot.plot(
+    ...,
+    connect_leader_to_label=True,
+    strain_label_styles=[
+        {
+            "strains": ["J.2.4", "J.2:S145N"],
+            "style": {"fill": "#d62728", "fontWeight": "bold"},
+            "when": vaccine_strains,
+        }
+    ],
+)
+```
+
+Leave out `when` for a style that is always on. `when` can be any Vega
+expression, so other inputs work too. For example, with a radio button
+`alt.param(name="emphasis", value="cell", bind=alt.binding_radio(options=["cell", "egg"]))`
+declared on the chart, one rule with `"when": "emphasis == 'cell'"` and
+another with `"when": "emphasis == 'egg'"` switch the emphasis between two
+groups of strains.
+
 ### Color the tree
 
 Pass `color_tree_by` to color the tree's branches and tip circles by

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.5.0}/examples/flu-seqneut-2025to2026_titer_charts.py

@@ -131,6 +131,17 @@ def strain_plot_order(viruses_subset: pd.DataFrame) -> list[str]:
     return sorted_df["virus"].tolist()
 
 
+def vaccine_axis_labels(viruses: pd.DataFrame, subtype: str) -> list[str]:
+    """Axis labels of the `RECENT_VACCINE_STRAINS` in `subtype`, in table order.
+
+    These are the strain-axis values the chart (and so the tree's tips) use for
+    the vaccine strains, e.g. for `strain_label_styles`."""
+    is_vaccine = (viruses["subtype"] == subtype) & viruses["virus"].isin(
+        RECENT_VACCINE_STRAINS
+    )
+    return viruses.loc[is_vaccine, "axis_label"].tolist()
+
+
 def make_chart(
     subtype: str,
     chart_type: str,

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.5.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "tree-annotated-plot"
-version = "0.3.0"
+version = "0.5.0"
 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-0.5.0}/scripts/generate_docs_assets.py

@@ -25,6 +25,8 @@ import sys
 from pathlib import Path
 from types import ModuleType
 
+import altair as alt
+
 import tree_annotated_plot
 
 REPO = Path(__file__).resolve().parent.parent
@@ -163,6 +165,47 @@ def _render_kikawa() -> None:
     )
     _save_pair(out, "h3n2_combined_label_connect")
 
+    # The same label-connect H3N2 chart, with the recent vaccine strains'
+    # labels drawn in bold red while a checkbox is ticked: `strain_label_styles`
+    # with a `when` param. The checkbox starts ticked so the static SVG shows
+    # the emphasis.
+    h3n2_chart_styles = builder.make_chart(
+        subtype="H3N2",
+        chart_type="iqr",
+        titers=titers,
+        viruses=viruses,
+        metadata=metadata,
+        all_cohorts=all_cohorts,
+    )
+    vaccine_strains = alt.param(
+        name="vaccine_strains",
+        value=True,
+        bind=alt.binding_checkbox(name="highlight vaccine strains "),
+    )
+    out = tree_annotated_plot.plot(
+        DATA_DIR / "flu-seqneut-2025to2026_H3N2.json",
+        h3n2_chart_styles,
+        chart_strain_field="axis_label",
+        tree_strain_field="derived_haplotype",
+        branch_length="div",
+        tree_size=140,
+        scale_bar=True,
+        branch_length_units="substitutions",
+        connect_leader_to_label=True,
+        strain_label_font_size=9,
+        shift_tree_loc=60,
+        color_tree_by="subclade",
+        tree_color_legend_format={"orient": "left"},
+        strain_label_styles=[
+            {
+                "strains": builder.vaccine_axis_labels(viruses, "H3N2"),
+                "style": {"fill": "#d62728", "fontWeight": "bold"},
+                "when": vaccine_strains,
+            }
+        ],
+    )
+    _save_pair(out, "h3n2_combined_label_styles")
+
     # H3N2 once more, colored by genotype at HA1 site 158: same chart and
     # default layout as `h3n2_combined`, with `color_tree_by` switched to
     # the genotype form. Site 158 has two mutations (N158K, N158D) in the

{tree_annotated_plot-0.3.0 → tree_annotated_plot-0.5.0}/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.",
@@ -152,11 +161,34 @@ class PlotConfig:
         "when `connect_leader_to_label` is on.",
     ] = "normal"
 
+    strain_label_styles: Annotated[
+        list[dict[str, Any]] | None,
+        "Style a subset of the strain labels rendered in the tree panel; "
+        "requires `connect_leader_to_label`. A list of rules, each a dict "
+        'with keys "strains" (a list of tip identifiers, i.e. '
+        '`tree_strain_field` values), "style" and, optionally, "when". '
+        '"style" holds Vega-Lite text-mark properties: "fill" (a color), '
+        '"opacity" (0 to 1), "fontWeight" ("normal", "bold", or 100-900) '
+        'and "fontStyle" ("normal" or "italic"). "when" is a Vega '
+        "expression that turns the rule on while it is truthy, usually just "
+        "the name of a parameter declared in the chart (e.g. one bound to a "
+        "checkbox), but any expression works (e.g. \"emphasis == 'cell'\" "
+        'for a radio button). Without "when" the style always applies. '
+        "Where rules overlap, later rules win property by property; "
+        "properties no rule sets keep `strain_label_font_weight` and the "
+        "default black, upright text. A strain that isn't a tree tip is an "
+        "error; strains dropped by `prune_tree_to_chart` are skipped. CLI "
+        "form: a JSON array (quote the whole argument), e.g. "
+        '\'[{"strains": ["K"], "style": {"fill": "#d62728", '
+        '"fontWeight": "bold"}, "when": "vaccine_strains"}]\'.',
+    ] = None
+
     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[
@@ -215,10 +247,25 @@ class PlotConfig:
 
 
 # Sidecar for Python-docstring-only prose, keyed by PlotConfig field name.
-# Empty by default — add an entry when a field's docstring entry needs more
-# than the CLI `--help` text covers. The extras are appended to the field's
-# description in `tree_annotated_plot.plot.__doc__`, never in CLI --help.
-PARAM_DOC_EXTRAS: dict[str, str] = {}
+# Add an entry when a field's docstring entry needs more than the CLI
+# `--help` text covers. The extras are appended to the field's description in
+# `tree_annotated_plot.plot.__doc__`, never in CLI --help.
+PARAM_DOC_EXTRAS: dict[str, str] = {
+    "strain_label_styles": (
+        'In Python, "when" may also be an `altair.Parameter`, e.g. '
+        '`alt.param(name="vaccine_strains", value=True, '
+        "bind=alt.binding_checkbox())`, which is declared on the returned "
+        "chart if your chart doesn't already declare it; or an altair "
+        'parameter expression such as `emphasis == "cell"`. Only a bare '
+        "`altair.Parameter` is declared for you: parameters that an "
+        "expression refers to must be declared on the chart, and an "
+        "expression other than a bare name isn't checked until the chart "
+        "renders. A bare name or parameter must be a variable parameter: "
+        "selection parameters are rejected, since the label data doesn't "
+        "carry the fields a selection tests. Any iterable of strings (e.g. "
+        'a pandas Series) works for "strains".'
+    ),
+}
 
 
 # Descriptions for the three data-input parameters. These can't live on