From 91e786754ce30ef94990eec966dc25f3a65ad448 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Fri, 20 Mar 2026 23:57:16 +0000 Subject: [PATCH 01/12] Initial move to ToyTree --- README.md | 2 - make_tree/__init__.py | 4 +- make_tree/entrypoint.py | 6 +- make_tree/make_tree.py | 389 +++++++++++++--------- pyproject.toml | 6 +- tests/test_make_tree.py | 117 +++++-- uv.lock | 715 ++++++++++++++++++++++++++++++---------- 7 files changed, 855 insertions(+), 384 deletions(-) diff --git a/README.md b/README.md index c7414f7..0f05919 100644 --- a/README.md +++ b/README.md @@ -66,8 +66,6 @@ uv run mypy make_tree tests > **Note:** tree_maker requires trees be generated from [Clustal](http://www.clustal.org/)! -> **IMPORTANT:** You will need `libgl1` to use this, `apt install libgl1` for Debian based systems. - To use Tree Maker, run the following command: ```shell diff --git a/make_tree/__init__.py b/make_tree/__init__.py index ae34d41..2fbe510 100644 --- a/make_tree/__init__.py +++ b/make_tree/__init__.py @@ -1,8 +1,8 @@ from .make_tree import ( COLOUR_LIST, + TreeParseError, export_tree, get_optimal_font_size, - get_result_dimensions, interpolate, load_tree, parse_label, @@ -12,9 +12,9 @@ __all__ = [ "COLOUR_LIST", + "TreeParseError", "export_tree", "get_optimal_font_size", - "get_result_dimensions", "interpolate", "load_tree", "parse_label", diff --git a/make_tree/entrypoint.py b/make_tree/entrypoint.py index 0fdf07b..5b14101 100644 --- a/make_tree/entrypoint.py +++ b/make_tree/entrypoint.py @@ -1,9 +1,7 @@ import argparse import sys -from ete4.parser.newick import NewickError - -from .make_tree import export_tree, load_tree +from .make_tree import TreeParseError, export_tree, load_tree def main() -> None: @@ -22,7 +20,7 @@ def main() -> None: try: t = load_tree(args.input_path) - except NewickError as e: + except TreeParseError as e: print( "Error: The tree file is not in the expected format. Please make sure it uses the standard Newick format. Details: ", e, diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index fb3493a..66d3eed 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -14,9 +14,16 @@ import os import re -from typing import Any, Dict, Optional, Tuple +from collections import defaultdict +from typing import Dict, List, Optional, Tuple -from ete4 import Tree # Tree drawing library +import toytree +import toytree.mod +import toyplot +import toyplot.reportlab +import toyplot.reportlab.pdf +import toyplot.svg +import reportlab.pdfgen.canvas as _rl_canvas COLOUR_LIST = [ "#000000", @@ -41,16 +48,28 @@ LABEL_RE = re.compile(r"(i|b)?([0-9]+)?!!(.*)") +# SVG namespace used by toyplot +_SVG_NS = "http://www.w3.org/2000/svg" + + +class TreeParseError(Exception): + """Raised when a Newick string or file cannot be parsed as a tree.""" + def parse_label(label: str) -> Tuple[Optional[str], Optional[int], str]: - """ - _summary_ + """Parse a node label encoding font style, colour index and display text. - :param label: _description_ + Labels may optionally carry a font flag (``i`` or ``b``) and a numeric + colour index from :data:`COLOUR_LIST`, separated from the actual display + text by ``!!``. Examples: ``test``, ``i!!test``, ``b2!!test``. + + :param label: Raw node name string. :type label: str - :raises ValueError: _description_ - :raises ValueError: _description_ - :return: _description_ + :raises ValueError: If the label contains ``!!`` but is not well-formed. + :raises ValueError: If the colour index is out of range. + :return: ``(font_flag, colour_index, display_text)`` where *font_flag* is + ``"i"``, ``"b"``, or ``None``; *colour_index* is an ``int`` or + ``None``. :rtype: Tuple[str | None, int | None, str] """ match = LABEL_RE.match(label) @@ -74,191 +93,249 @@ def parse_label(label: str) -> Tuple[Optional[str], Optional[int], str]: return (font, _colourindex, name) -def get_result_dimensions(result: Dict[str, Any]) -> Tuple[int, int]: - """Returns the rendered pixel width and height from an export_tree result dict.""" - w = max(m[2] for m in result["node_areas"].values()) - h = max(m[3] for m in result["node_areas"].values()) - return (w, h) +def interpolate(start: float, end: float, t: float) -> float: + """For t between 0 and 1, returns a number between start and end.""" + return (1 - t) * start + end * t -def _probe_scene_size(t: Tree, ts: Any) -> Tuple[float, float]: - """Return the (width, height) of the tree scene built in memory. +def get_optimal_font_size(t: toytree.ToyTree) -> int: + """Return an appropriate font size for the number of leaves in *t*. - Builds the full Qt scene (with all faces already applied) without writing - any file, then reads ``scene.sceneRect()``. + :param t: Tree to size labels for. + :type t: toytree.ToyTree + :return: Font size in points. + :rtype: int + """ + leaf_count = t.ntips + x = min(1, leaf_count / 120) + return round(interpolate(12, 4, x)) - The relationship between ``ts.tree_width`` and scene width is exactly linear - with a slope of 1 and a positive intercept driven by label widths and margins:: - scene_width = ts.tree_width + fixed_width +def _reverse_node(node: "toytree.Node") -> None: + """Recursively reverse the children tuple of *node* in place.""" + node._children = node._children[::-1] + for child in node._children: + _reverse_node(child) - This means the correction to ``ts.tree_width`` needed to hit a target scene - width is simply an additive delta — no ratio multiplication required, and the - result is exact regardless of label length. - """ - from ete4.treeview import drawer as _drawer - from ete4.treeview.qt_render import render as _qt_render - # render_tree also assigns _nid; mirror that here so the probe is identical - for nid, n in enumerate(t.traverse("preorder")): - n.add_prop("_nid", nid) +def reverse_tree(t: toytree.ToyTree) -> None: + """Recursively reverse the child order of every node in *t*. - scene, img = _drawer.init_scene(t, None, ts) - tree_item, n2i, n2f = _qt_render(t, img) - scene.init_values(t, img, n2i, n2f) - tree_item.setParentItem(scene.master_item) - scene.master_item.setPos(0, 0) - scene.addItem(scene.master_item) + Modifies *t* in place. The resulting tip order is the reverse of the + original parse order, preserving the historical ordering behaviour. - sr = scene.sceneRect() - return sr.width(), sr.height() + :param t: Tree to reverse. + :type t: toytree.ToyTree + """ + _reverse_node(t.treenode) + t._update() -def export_tree( - t: Tree, - output_path: str, - title: Optional[str] = None, -) -> Dict[str, Any]: - """ - Exports tree to a letter-size (8.5×11") PDF. +def process_tree_labels(t: toytree.ToyTree) -> toytree.ToyTree: + """Normalise negative branch lengths and apply REF_ROOT semantics. - The tree is scaled horizontally so that its natural aspect ratio matches - the page, preventing any distortion when Qt renders into fixed dimensions. - The ratio is probed by building the Qt scene in memory (no file I/O) and - reading ``scene.sceneRect()`` before the single final render. + Steps performed (in order): - :param t: Tree to render. - :type t: Tree - :param output_path: Destination file path (PDF recommended). - :type output_path: str - :param title: Optional title drawn at the top of the page. - :type title: str | None - :return: ete4 image-map dict with ``node_areas``, ``nodes``, and ``faces``. - :rtype: Dict[str, Any] + 1. For any node with a negative ``dist``, shift ``abs(dist)`` onto each + sibling edge and zero the negative edge. + 2. If any node name contains ``REF_ROOT`` or ``REF_ROOT_HIDE``, reroot + the tree on that node. + 3. If any node name contains ``REF_ROOT_HIDE``, drop that tip from the + tree and clean up any resulting unary nodes. + + Because rerooting and tip-removal return new :class:`toytree.ToyTree` + objects, always use the *returned* tree rather than the argument. + + :param t: Tree to preprocess. + :type t: toytree.ToyTree + :return: Preprocessed tree (may be a new object if rerooted/pruned). + :rtype: toytree.ToyTree """ - from ete4.treeview import TextFace, TreeStyle - from ete4.treeview import drawer as _drawer - - # PyQt6 requires this on headless servers. - # More info: https://github.com/NVlabs/instant-ngp/discussions/300#discussioncomment-4814215 - os.environ["QT_QPA_PLATFORM"] = "offscreen" - - ts = TreeStyle() - ts.show_leaf_name = False - ts.margin_left = 15 - ts.margin_right = 15 - ts.branch_vertical_margin = -2 # only affects trees with many leaves - ts.min_leaf_separation = 0 - - if title: - ts.title.add_face(TextFace(title, fsize=12, bold=True), column=0) - - # Apply visual styles once, before probing — the probe must see the same - # faces that the final render will use so the ratio measurement is accurate. - _apply_node_styles(t) - - # Probe the natural scene dimensions in memory (no file write). - # When both w and h are fixed, ete4 uses IgnoreAspectRatio, which distorts - # the tree if its intrinsic ratio differs from the target page ratio. - # Since scene_width = ts.tree_width + fixed_width (slope == 1, exactly), - # the required correction is a plain additive delta — no ratio multiply needed. - PAGE_W, PAGE_H = 8.5, 11.0 - scene_w, scene_h = _probe_scene_size(t, ts) - target_scene_w = scene_h * PAGE_W / PAGE_H - ts.tree_width += target_scene_w - scene_w - - return _drawer.render_tree( - t, output_path, w=PAGE_W, h=PAGE_H, units="in", tree_style=ts - ) + # Fix negative branch lengths + for node in t.traverse(): + if node.dist is not None and node.dist < 0: + d = abs(node.dist) + for sibling in node.up.children: + sibling._dist = (sibling.dist or 0) + d + node._dist = 0.0 + t._update() + # Reroot on the first node whose name contains REF_ROOT or REF_ROOT_HIDE + for node in t.traverse(): + if node.name and ( + "REF_ROOT" in node.name or "REF_ROOT_HIDE" in node.name + ): + t = t.root(node.name) + break -def reverse_tree(node: Tree) -> None: - node.children = node.children[::-1] - for child in node.children: - reverse_tree(child) + # Drop the REF_ROOT_HIDE tip and clean up any resulting unary nodes + for node in t.traverse(): + if node.name and "REF_ROOT_HIDE" in node.name and node.is_leaf(): + t = toytree.mod.drop_tips(t, node.name) + t = toytree.mod.remove_unary_nodes(t) + break + return t -def interpolate(start: float, end: float, t: float) -> float: - """For t between 0 and 1, returns a number between start and end.""" - return (1 - t) * start + end * t +def _collect_node_styles(t: toytree.ToyTree) -> List[Dict]: + """Return a list of style dicts for every node in idx order. -def get_optimal_font_size(t: Tree) -> int: + Each dict has keys: ``text`` (display string), ``color`` (hex), + ``bold`` (bool), ``italic`` (bool). """ - Performs a calculation for the best font size with respect to the number of - leaves in the tree + result = [] + for node in t[:]: # idx-ordered slice + if node.name: + font, ci, text = parse_label(node.name) + else: + font, ci, text = None, None, "" + result.append( + { + "text": text, + "color": COLOUR_LIST[ci or 0], + "bold": font == "b", + "italic": font == "i", + } + ) + return result - :param t: ... - :type t: Tree - :return: ... - :rtype: int - """ - leaf_count = sum(1 for _ in t.leaves()) - x = min(1, leaf_count / 120) - return round(interpolate(12, 4, x)) +def _apply_italic_to_svg(svg_elem, italic_texts: set) -> None: + """Inject ``font-style:italic`` into matching ```` SVG elements. -def process_tree_labels(t: Tree) -> None: - # Some edge lengths can be negative. - # For those cases we follow instructions from http://www.icp.ucl.ac.be/~opperd/private/neighbor.html - for node in t.traverse(): - if node.dist is not None and node.dist < 0: - d = abs(node.dist) - for c in node.up.children: - c.dist = (c.dist or 0) + d - node.dist = 0 + toyplot's style validator rejects ``font-style``, so italic must be + applied via direct XML manipulation after the element tree is built. + The reportlab renderer honours ``font-style:italic`` in element ``style`` + attributes, producing correctly italicised PDF output. + """ + for text_elem in svg_elem.iter(f"{{{_SVG_NS}}}text"): + if text_elem.text in italic_texts: + existing = text_elem.get("style", "") + if existing: + text_elem.set("style", existing + ";font-style:italic") + else: + text_elem.set("style", "font-style:italic") - # Sometimes the tree root can be moved to a chosen node. - # It is signified by the label "REF_ROOT" or "REF_ROOT_HIDE". - for node in t.traverse(): - if node.name and ("REF_ROOT" in node.name or "REF_ROOT_HIDE" in node.name): - t.set_outgroup(node) - # Node with label "REF_ROOT_HIDE" must not be visible on the resulting picture. - # We simply remove it from the tree. It is not expected to be the actual tree root. - for node in t.traverse(): - if node.name and "REF_ROOT_HIDE" in node.name and node.up: - node.up.children.remove(node) +def export_tree( + t: toytree.ToyTree, + output_path: str, + title: Optional[str] = None, +) -> None: + """Export *t* to a letter-size (8.5 x 11 in) PDF. + Renders a rectangular phylogram with per-node label colours and + bold/italic styling derived from the :func:`parse_label` encoding. + All named nodes — tips and internal — receive labels. -def _apply_node_styles(t: Tree) -> None: - """Apply visual styles (TextFace, NodeStyle) to all nodes. Requires PyQt6.""" - from ete4.treeview import NodeStyle, TextFace + PDF output uses toyplot and reportlab; no Qt or PyQt dependency is + required. SVG output is also supported when *output_path* ends with + ``.svg``. + + :param t: Preprocessed tree to render. + :type t: toytree.ToyTree + :param output_path: Destination file path (PDF or SVG). + :type output_path: str + :param title: Optional title drawn above the tree. + :type title: str | None + :return: None + """ + # Letter size: 8.5 x 11 inches expressed as points (1 pt = 1/72 in) + PAGE_W, PAGE_H = 612.0, 792.0 fsize = get_optimal_font_size(t) - for node in t.traverse(): - (font, colourindex, name) = ( - parse_label(node.name) if node.name else (None, None, "") + node_styles = _collect_node_styles(t) + nnodes = t.nnodes + + # Group nodes by (bold, italic, color) — one add_node_labels() per group + groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict( + list + ) + for idx, info in enumerate(node_styles): + if info["text"]: + key = (info["bold"], info["italic"], info["color"]) + groups[key].append((idx, info["text"])) + + italic_texts: set = set() + + # Draw the tree onto a letter-sized canvas + canvas, axes, mark = t.draw( + layout="r", + width=PAGE_W, + height=PAGE_H, + node_sizes=0, + node_mask=True, + tip_labels=False, + label=title or "", + ) + + # Add per-node labels, one call per unique (bold, italic, color) group + for (bold, italic, color), node_list in groups.items(): + labels: List[str] = [""] * nnodes + mask: List[bool] = [False] * nnodes # False = hidden by default + for idx, text in node_list: + labels[idx] = text + mask[idx] = True # True = show + if italic: + italic_texts.add(text) + + style = {"font-weight": "bold"} if bold else None + t.annotate.add_node_labels( + axes, + labels, + mask=mask, + color=color, + font_size=fsize, + style=style, ) - colour = COLOUR_LIST[colourindex or 0] - bold = font == "b" - fstyle = "italic" if font == "i" else "normal" - face = TextFace(name, fgcolor=colour, bold=bold, fstyle=fstyle, fsize=fsize) - nstyle = NodeStyle() - nstyle["size"] = 0 - nstyle["hz_line_width"] = 1 - nstyle["vt_line_width"] = 1 + is_pdf = output_path.lower().endswith(".pdf") - node.set_style(nstyle) - node.add_face(face, column=0) + # Obtain the SVG element for post-processing (italic) and/or PDF render + svg_elem = toyplot.svg.render(canvas) + if italic_texts: + _apply_italic_to_svg(svg_elem, italic_texts) + if is_pdf: + surface = _rl_canvas.Canvas(output_path, pagesize=(PAGE_W, PAGE_H)) + surface.translate(0, PAGE_H) + surface.scale(1, -1) + toyplot.reportlab.render(svg_elem, surface) + surface.showPage() + surface.save() + else: + # SVG and other formats: serialize the (possibly italic-patched) tree + import xml.etree.ElementTree as ET + + ET.register_namespace("", _SVG_NS) + ET.register_namespace("xlink", "http://www.w3.org/1999/xlink") + ET.register_namespace("toyplot", "http://www.sandia.gov/toyplot") + ET.ElementTree(svg_elem).write( + output_path, xml_declaration=True, encoding="utf-8" + ) -def load_tree(input_path: str) -> Tree: - """ - Load a tree into a Tree object. - :param input_path: Can be either a file path or a newick string. - For example `(A,B,C);` +def load_tree(input_path: str) -> toytree.ToyTree: + """Load a tree from a file path or a raw Newick string. + + After parsing, the tree is preprocessed by :func:`reverse_tree` and + :func:`process_tree_labels`. + + :param input_path: Either a path to a Newick file or a Newick string + such as ``"(A,B,C);"`` :type input_path: str - :return: ... - :rtype: Tree + :raises TreeParseError: If the input cannot be parsed as a valid tree. + :return: Loaded and preprocessed tree. + :rtype: toytree.ToyTree """ - if os.path.isfile(input_path): - with open(input_path) as f: - t = Tree(f) - else: - t = Tree(input_path) + try: + t = toytree.tree(input_path) + except Exception as exc: + raise TreeParseError( + f"Could not parse tree from {input_path!r}: {exc}" + ) from exc + reverse_tree(t) - process_tree_labels(t) + t = process_tree_labels(t) return t diff --git a/pyproject.toml b/pyproject.toml index 3e9703e..455be8e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ description = 'Simple script for drawing phylogenetic trees' readme = "README.md" requires-python = ">=3.9" license = "GPL-3.0" -keywords = ["ete4", "tree maker", "pdf"] +keywords = ["toytree", "tree maker", "pdf"] authors = [ { name = "Vitaliy Mysak", email = "vmysak@bccfe.ca" }, ] @@ -25,8 +25,8 @@ classifiers = [ "Programming Language :: Python :: Implementation :: PyPy", ] dependencies = [ - "ete4", - "PyQt6; sys_platform != 'win32'", + "toytree>=3.0.11", + "toyplot", ] dynamic = ["version"] diff --git a/tests/test_make_tree.py b/tests/test_make_tree.py index 840d764..fe6f196 100644 --- a/tests/test_make_tree.py +++ b/tests/test_make_tree.py @@ -3,9 +3,10 @@ from typing import Optional, Tuple import pytest -from ete4 import Tree +import toytree from make_tree.make_tree import ( + TreeParseError, export_tree, get_optimal_font_size, interpolate, @@ -37,22 +38,20 @@ def test_parse_label_errors(input: str) -> None: @pytest.mark.parametrize( - "tree_input, expected_output", + "tree_input, original_tips, expected_reversed", [ - (None, None), - ("(A);", "(A);"), - ("(A,B,C);", "(C,B,A);"), - ("(A,B,(C,D,(E,F)));", "(((F,E),D,C),B,A);"), + ("(A,B,C);", ["A", "B", "C"], ["C", "B", "A"]), + ("(A,B,(C,D,(E,F)));", ["A", "B", "C", "D", "E", "F"], ["F", "E", "D", "C", "B", "A"]), ], - ids=["Empty Tree", "One Node", "Three Node", "Six Node"], + ids=["Three Node", "Six Node"], ) def test_reverse_tree( - tree_input: Optional[str], expected_output: Optional[str] + tree_input: str, original_tips: list, expected_reversed: list ) -> None: - t = Tree(tree_input) if tree_input is not None else Tree() + t = toytree.tree(tree_input) + assert list(t.get_tip_labels()) == original_tips reverse_tree(t) - expected = Tree(expected_output) if expected_output is not None else Tree() - assert str(t) == str(expected) + assert list(t.get_tip_labels()) == expected_reversed @pytest.mark.parametrize( @@ -64,45 +63,78 @@ def test_interpolate(a: float, b: float, c: float, exp_output: float) -> None: def test_get_optimal_font_size_small_tree() -> None: - t = Tree("(A,B,C);") + t = toytree.tree("(A,B,C);") assert get_optimal_font_size(t) > 8 def test_get_optimal_font_size_big_tree() -> None: - t = Tree("(" + "A,B,C" * 100 + ");") + tips = ",".join(f"T{i}" for i in range(200)) + t = toytree.tree(f"({tips});") assert get_optimal_font_size(t) < 8 def test_process_tree_labels_idempotent() -> None: - t = Tree("(A,B,(C,D),E);") - process_tree_labels(t) - s1 = str(t) - process_tree_labels(t) - s2 = str(t) - assert s1 == s2 + t = toytree.tree("(A,B,(C,D),E);") + tips_before = list(t.get_tip_labels()) + t = process_tree_labels(t) + tips_after = list(t.get_tip_labels()) + # A tree without REF_ROOT should have the same tip set + assert set(tips_before) == set(tips_after) @pytest.mark.parametrize( - "tree_str", ["(A,B,(C,REF_ROOT),E);", "(A,B,(C,REF_ROOT_HIDE),E);"] + "tree_str, ref_root_name", + [ + ("(A,B,(C,REF_ROOT),E);", "REF_ROOT"), + ("(A,B,(C,REF_ROOT_HIDE),E);", "REF_ROOT_HIDE"), + ], ) -def test_process_tree_labels_reroots(tree_str: str) -> None: - t = Tree(tree_str) - s1 = str(t) - process_tree_labels(t) - s2 = str(t) - assert s1 != s2 +def test_process_tree_labels_reroots(tree_str: str, ref_root_name: str) -> None: + t = toytree.tree(tree_str) + original_tips = set(t.get_tip_labels()) + t2 = process_tree_labels(t) + # Tree should now be rooted differently + root_children_names = {n.name for n in t2.treenode.children} + assert ref_root_name in root_children_names or ref_root_name not in t2.get_tip_labels(), ( + f"{ref_root_name} should be near the root or already removed" + ) + + +def test_process_tree_labels_hides_ref_root_hide() -> None: + t = toytree.tree("(A,B,(C,REF_ROOT_HIDE),E);") + t2 = process_tree_labels(t) + assert "REF_ROOT_HIDE" not in t2.get_tip_labels() + + +def test_export_pdf(tmp_path: Path) -> None: + t = toytree.tree("(A,B,(C,D),E);") + output_path = str(tmp_path / "output.pdf") + result = export_tree(t, output_path, "my title") + assert result is None + assert os.path.exists(output_path) + assert os.path.getsize(output_path) > 0 -def test_export(tmp_path: Path) -> None: - t = Tree("(A,B,(C,D),E);") - output_path = os.path.join(tmp_path, "output.pdf") - result = export_tree(t, output_path, "my title") - assert isinstance(result, dict) +def test_export_svg(tmp_path: Path) -> None: + t = toytree.tree("(A,B,C);") + output_path = str(tmp_path / "output.svg") + result = export_tree(t, output_path) + assert result is None + assert os.path.exists(output_path) + content = open(output_path).read() + assert " None: + t = toytree.tree("(b2!!BoldRed,i!!ItalicBlack,plain);") + output_path = str(tmp_path / "styled.pdf") + export_tree(t, output_path, "Styled Tree") assert os.path.exists(output_path) + assert os.path.getsize(output_path) > 0 @pytest.mark.parametrize( - "input", + "newick", [ "(A,B,(C,D),E);", "(A);", @@ -110,9 +142,22 @@ def test_export(tmp_path: Path) -> None: "(A,B,(C,D,(E,F)));", ], ) -def test_load_tree(input: str) -> None: - t1 = Tree(input) +def test_load_tree_reverses_tips(newick: str) -> None: + original = toytree.tree(newick) + original_tips = list(original.get_tip_labels()) + + loaded = load_tree(newick) + loaded_tips = list(loaded.get_tip_labels()) + + # load_tree reverses the tree, so tip order should be reversed + assert loaded_tips == original_tips[::-1] + + +def test_load_tree_bad_newick_raises() -> None: + with pytest.raises(TreeParseError): + load_tree("not_a_newick_string!!!") - t2 = load_tree(input) - assert [str(line) for line in t1][::-1] == [str(line) for line in t2] +def test_load_tree_missing_file_raises() -> None: + with pytest.raises(TreeParseError): + load_tree("/nonexistent/path/to/tree.nwk") diff --git a/uv.lock b/uv.lock index a1b1875..8aa45ab3 100644 --- a/uv.lock +++ b/uv.lock @@ -2,86 +2,27 @@ version = 1 revision = 3 requires-python = ">=3.9" resolution-markers = [ - 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02/12] Fix CI errors --- make_tree/make_tree.py | 26 ++++++++++---------------- tests/test_make_tree.py | 26 ++++++++++++++------------ 2 files changed, 24 insertions(+), 28 deletions(-) diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index 66d3eed..b9d2fe6 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -12,18 +12,18 @@ Basically it's (i)talic/(b)old flag first, then colour index, then the actual label. """ -import os import re +import xml.etree.ElementTree as ET from collections import defaultdict -from typing import Dict, List, Optional, Tuple +from typing import Any, Dict, List, Optional, Set, Tuple -import toytree -import toytree.mod +import reportlab.pdfgen.canvas as _rl_canvas import toyplot import toyplot.reportlab import toyplot.reportlab.pdf import toyplot.svg -import reportlab.pdfgen.canvas as _rl_canvas +import toytree +import toytree.mod COLOUR_LIST = [ "#000000", @@ -162,9 +162,7 @@ def process_tree_labels(t: toytree.ToyTree) -> toytree.ToyTree: # Reroot on the first node whose name contains REF_ROOT or REF_ROOT_HIDE for node in t.traverse(): - if node.name and ( - "REF_ROOT" in node.name or "REF_ROOT_HIDE" in node.name - ): + if node.name and ("REF_ROOT" in node.name or "REF_ROOT_HIDE" in node.name): t = t.root(node.name) break @@ -178,7 +176,7 @@ def process_tree_labels(t: toytree.ToyTree) -> toytree.ToyTree: return t -def _collect_node_styles(t: toytree.ToyTree) -> List[Dict]: +def _collect_node_styles(t: toytree.ToyTree) -> List[Dict[str, Any]]: """Return a list of style dicts for every node in idx order. Each dict has keys: ``text`` (display string), ``color`` (hex), @@ -201,7 +199,7 @@ def _collect_node_styles(t: toytree.ToyTree) -> List[Dict]: return result -def _apply_italic_to_svg(svg_elem, italic_texts: set) -> None: +def _apply_italic_to_svg(svg_elem: ET.Element, italic_texts: Set[str]) -> None: """Inject ``font-style:italic`` into matching ```` SVG elements. toyplot's style validator rejects ``font-style``, so italic must be @@ -249,15 +247,13 @@ def export_tree( nnodes = t.nnodes # Group nodes by (bold, italic, color) — one add_node_labels() per group - groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict( - list - ) + groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict(list) for idx, info in enumerate(node_styles): if info["text"]: key = (info["bold"], info["italic"], info["color"]) groups[key].append((idx, info["text"])) - italic_texts: set = set() + italic_texts: Set[str] = set() # Draw the tree onto a letter-sized canvas canvas, axes, mark = t.draw( @@ -306,8 +302,6 @@ def export_tree( surface.save() else: # SVG and other formats: serialize the (possibly italic-patched) tree - import xml.etree.ElementTree as ET - ET.register_namespace("", _SVG_NS) ET.register_namespace("xlink", "http://www.w3.org/1999/xlink") ET.register_namespace("toyplot", "http://www.sandia.gov/toyplot") diff --git a/tests/test_make_tree.py b/tests/test_make_tree.py index fe6f196..38b275d 100644 --- a/tests/test_make_tree.py +++ b/tests/test_make_tree.py @@ -1,6 +1,6 @@ import os from pathlib import Path -from typing import Optional, Tuple +from typing import List, Optional, Tuple import pytest import toytree @@ -41,12 +41,16 @@ def test_parse_label_errors(input: str) -> None: "tree_input, original_tips, expected_reversed", [ ("(A,B,C);", ["A", "B", "C"], ["C", "B", "A"]), - ("(A,B,(C,D,(E,F)));", ["A", "B", "C", "D", "E", "F"], ["F", "E", "D", "C", "B", "A"]), + ( + "(A,B,(C,D,(E,F)));", + ["A", "B", "C", "D", "E", "F"], + ["F", "E", "D", "C", "B", "A"], + ), ], ids=["Three Node", "Six Node"], ) def test_reverse_tree( - tree_input: str, original_tips: list, expected_reversed: list + tree_input: str, original_tips: List[str], expected_reversed: List[str] ) -> None: t = toytree.tree(tree_input) assert list(t.get_tip_labels()) == original_tips @@ -91,13 +95,12 @@ def test_process_tree_labels_idempotent() -> None: ) def test_process_tree_labels_reroots(tree_str: str, ref_root_name: str) -> None: t = toytree.tree(tree_str) - original_tips = set(t.get_tip_labels()) t2 = process_tree_labels(t) # Tree should now be rooted differently root_children_names = {n.name for n in t2.treenode.children} - assert ref_root_name in root_children_names or ref_root_name not in t2.get_tip_labels(), ( - f"{ref_root_name} should be near the root or already removed" - ) + assert ( + ref_root_name in root_children_names or ref_root_name not in t2.get_tip_labels() + ), f"{ref_root_name} should be near the root or already removed" def test_process_tree_labels_hides_ref_root_hide() -> None: @@ -109,8 +112,7 @@ def test_process_tree_labels_hides_ref_root_hide() -> None: def test_export_pdf(tmp_path: Path) -> None: t = toytree.tree("(A,B,(C,D),E);") output_path = str(tmp_path / "output.pdf") - result = export_tree(t, output_path, "my title") - assert result is None + export_tree(t, output_path, "my title") assert os.path.exists(output_path) assert os.path.getsize(output_path) > 0 @@ -118,10 +120,10 @@ def test_export_pdf(tmp_path: Path) -> None: def test_export_svg(tmp_path: Path) -> None: t = toytree.tree("(A,B,C);") output_path = str(tmp_path / "output.svg") - result = export_tree(t, output_path) - assert result is None + export_tree(t, output_path) assert os.path.exists(output_path) - content = open(output_path).read() + with open(output_path) as fh: + content = fh.read() assert " Date: Sat, 21 Mar 2026 00:02:50 +0000 Subject: [PATCH 03/12] Do not support python 3.9 --- .github/workflows/main.yml | 2 +- pyproject.toml | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c4b80a9..a255e4e 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -14,7 +14,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-latest] - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 diff --git a/pyproject.toml b/pyproject.toml index 455be8e..be4112b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "hatchling.build" name = "make_tree" description = 'Simple script for drawing phylogenetic trees' readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.10" license = "GPL-3.0" keywords = ["toytree", "tree maker", "pdf"] authors = [ @@ -17,7 +17,6 @@ classifiers = [ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: OS Independent", "Programming Language :: Python", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", From 12825c49362c1cebce3f25616c1632e7de5b97e0 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Sat, 21 Mar 2026 00:03:50 +0000 Subject: [PATCH 04/12] Support newer versions of python --- .github/workflows/main.yml | 2 +- pyproject.toml | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a255e4e..a1edc29 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -14,7 +14,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-latest] - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] steps: - uses: actions/checkout@v3 diff --git a/pyproject.toml b/pyproject.toml index be4112b..5224efa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 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b/make_tree/make_tree.py index b9d2fe6..9062ebe 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -199,21 +199,31 @@ def _collect_node_styles(t: toytree.ToyTree) -> List[Dict[str, Any]]: return result -def _apply_italic_to_svg(svg_elem: ET.Element, italic_texts: Set[str]) -> None: - """Inject ``font-style:italic`` into matching ```` SVG elements. +def _apply_text_styles_to_svg( + svg_elem: ET.Element, + italic_texts: Set[str], + bold_texts: Set[str], +) -> None: + """Inject ``font-style`` / ``font-weight`` overrides into SVG ```` elements. toyplot's style validator rejects ``font-style``, so italic must be applied via direct XML manipulation after the element tree is built. - The reportlab renderer honours ``font-style:italic`` in element ``style`` - attributes, producing correctly italicised PDF output. + Bold is handled the same way for tip labels (which have no per-label + bold API), and harmlessly reinforces bold already set on internal labels. + The reportlab renderer honours both properties in element ``style`` + attributes. """ for text_elem in svg_elem.iter(f"{{{_SVG_NS}}}text"): - if text_elem.text in italic_texts: - existing = text_elem.get("style", "") - if existing: - text_elem.set("style", existing + ";font-style:italic") - else: - text_elem.set("style", "font-style:italic") + text = text_elem.text + if text not in italic_texts and text not in bold_texts: + continue + extra: List[str] = [] + if text in italic_texts: + extra.append("font-style:italic") + if text in bold_texts: + extra.append("font-weight:bold") + existing = text_elem.get("style", "") + text_elem.set("style", existing + ";" + ";".join(extra) if existing else ";".join(extra)) def export_tree( @@ -244,54 +254,75 @@ def export_tree( fsize = get_optimal_font_size(t) node_styles = _collect_node_styles(t) + ntips = t.ntips nnodes = t.nnodes - # Group nodes by (bold, italic, color) — one add_node_labels() per group - groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict(list) - for idx, info in enumerate(node_styles): + # --- Tip labels: handed to draw() for native right-aligned positioning --- + tip_texts: List[str] = [node_styles[i]["text"] for i in range(ntips)] + tip_colors: List[str] = [node_styles[i]["color"] for i in range(ntips)] + + # --- Internal node labels: grouped by (bold, italic, color) --- + int_groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict( + list + ) + for idx in range(ntips, nnodes): + info = node_styles[idx] if info["text"]: key = (info["bold"], info["italic"], info["color"]) - groups[key].append((idx, info["text"])) + int_groups[key].append((idx, info["text"])) + # Collect texts that need SVG font-style / font-weight injection italic_texts: Set[str] = set() + bold_texts: Set[str] = set() + for _idx, info in enumerate(node_styles): + if info["text"]: + if info["italic"]: + italic_texts.add(info["text"]) + if info["bold"]: + bold_texts.add(info["text"]) - # Draw the tree onto a letter-sized canvas + # Draw the base tree canvas, axes, mark = t.draw( layout="r", width=PAGE_W, height=PAGE_H, + padding=50, node_sizes=0, node_mask=True, - tip_labels=False, + # Tip labels: built-in positioning with a right-side padding gap + tip_labels=tip_texts, + tip_labels_colors=tip_colors, + tip_labels_style={ + "-toyplot-anchor-shift": "10px", + "font-size": f"{fsize}px", + }, + # Slightly thicker, softer edges + edge_widths=1.5, + edge_style={"stroke": "#2c3e50", "stroke-linecap": "round"}, label=title or "", ) - # Add per-node labels, one call per unique (bold, italic, color) group - for (bold, italic, color), node_list in groups.items(): + # Add internal-node labels, one call per unique (bold, italic, color) group + for (_bold, _italic, color), node_list in int_groups.items(): labels: List[str] = [""] * nnodes - mask: List[bool] = [False] * nnodes # False = hidden by default + mask: List[bool] = [False] * nnodes for idx, text in node_list: labels[idx] = text - mask[idx] = True # True = show - if italic: - italic_texts.add(text) - - style = {"font-weight": "bold"} if bold else None + mask[idx] = True t.annotate.add_node_labels( axes, labels, mask=mask, color=color, font_size=fsize, - style=style, ) is_pdf = output_path.lower().endswith(".pdf") - # Obtain the SVG element for post-processing (italic) and/or PDF render + # SVG post-processing: inject italic / bold into matching text elements svg_elem = toyplot.svg.render(canvas) - if italic_texts: - _apply_italic_to_svg(svg_elem, italic_texts) + if italic_texts or bold_texts: + _apply_text_styles_to_svg(svg_elem, italic_texts, bold_texts) if is_pdf: surface = _rl_canvas.Canvas(output_path, pagesize=(PAGE_W, PAGE_H)) From 089879fd28bf76b0bd9a27b96e9d6f39c825dc36 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Sat, 21 Mar 2026 00:13:41 +0000 Subject: [PATCH 07/12] Reduce the shift --- make_tree/make_tree.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index 9062ebe..d171d2b 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -223,7 +223,9 @@ def _apply_text_styles_to_svg( if text in bold_texts: extra.append("font-weight:bold") existing = text_elem.get("style", "") - text_elem.set("style", existing + ";" + ";".join(extra) if existing else ";".join(extra)) + text_elem.set( + "style", existing + ";" + ";".join(extra) if existing else ";".join(extra) + ) def export_tree( @@ -262,9 +264,7 @@ def export_tree( tip_colors: List[str] = [node_styles[i]["color"] for i in range(ntips)] # --- Internal node labels: grouped by (bold, italic, color) --- - int_groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict( - list - ) + int_groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict(list) for idx in range(ntips, nnodes): info = node_styles[idx] if info["text"]: @@ -293,7 +293,7 @@ def export_tree( tip_labels=tip_texts, tip_labels_colors=tip_colors, tip_labels_style={ - "-toyplot-anchor-shift": "10px", + "-toyplot-anchor-shift": "1px", "font-size": f"{fsize}px", }, # Slightly thicker, softer edges From a99d1cc0145cd03eb96ddf09dcd3ab461bf2e85c Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Sat, 21 Mar 2026 00:17:33 +0000 Subject: [PATCH 08/12] Add scale bar --- make_tree/make_tree.py | 1 + 1 file changed, 1 insertion(+) diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index d171d2b..d30edfc 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -283,6 +283,7 @@ def export_tree( # Draw the base tree canvas, axes, mark = t.draw( + scale_bar=True, layout="r", width=PAGE_W, height=PAGE_H, From 5a248c696f7aa0c117803236e1a94090211fcb0f Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Sat, 21 Mar 2026 00:22:07 +0000 Subject: [PATCH 09/12] Simplify infrastructure --- .github/workflows/lint.yml | 2 +- .github/workflows/main.yml | 13 +++---------- .github/workflows/typecheck.yml | 2 +- Dockerfile | 24 ------------------------ README.md | 2 +- make_tree/make_tree.py | 30 +++++++++++++++--------------- pyproject.toml | 2 +- tests/test_make_tree.py | 5 ++--- 8 files changed, 24 insertions(+), 56 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 7dd2afb..41529d3 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v5 diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a1edc29..5df14c9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -14,20 +14,16 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-latest] - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.10", "3.11", "3.12", "3.13"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v5 with: python-version: ${{ matrix.python-version }} - - name: Install system dependencies - if: runner.os == 'Linux' - run: sudo apt-get install -y libegl1 libzstd1 - - name: Install dependencies run: uv sync --extra test @@ -41,16 +37,13 @@ jobs: name: Test and report on ubuntu-latest runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v5 with: python-version: "3.11" - - name: Install system dependencies - run: sudo apt-get install -y libegl1 libzstd1 - - name: Install dependencies run: uv sync --extra test diff --git a/.github/workflows/typecheck.yml b/.github/workflows/typecheck.yml index 157d1df..c704ab9 100644 --- a/.github/workflows/typecheck.yml +++ b/.github/workflows/typecheck.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v5 diff --git a/Dockerfile b/Dockerfile index ed9eebe..f6e5a28 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,29 +1,5 @@ FROM python:3.11-slim -# Install system dependencies: -# build-essential – gcc + libc6-dev (stdlib.h) needed to compile ete4's Cython extensions -# libegl1 – PyQt6 offscreen rendering backend -# libzstd1 – runtime dependency of the PyQt6 wheel -# libglib2.0-0 – GLib/Qt integration -# libgl1 – OpenGL (Qt fallback) -# libdbus-1-3 – D-Bus (Qt platform plugin) -# libxcb1 – X11 client library (loaded even in offscreen mode) -# libfontconfig1 – font handling for Qt -# libxkbcommon0 – keyboard input handling for Qt -# libx11-6 – X11 base library -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential \ - libegl1 \ - libzstd1 \ - libglib2.0-0 \ - libgl1 \ - libdbus-1-3 \ - libxcb1 \ - libfontconfig1 \ - libxkbcommon0 \ - libx11-6 \ - && rm -rf /var/lib/apt/lists/* - # Install uv from its official image COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv diff --git a/README.md b/README.md index 0f05919..8ffeeaa 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ Tree Maker is a Python script that allows you to create and visualize phylogenet - Produces phylogenetic trees in PDF format. - Customizable label colors and styles. -- Supports Python 3.8 and higher. +- Supports Python 3.10 and higher. ## Installation diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index d30edfc..3461a59 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -15,7 +15,7 @@ import re import xml.etree.ElementTree as ET from collections import defaultdict -from typing import Any, Dict, List, Optional, Set, Tuple +from typing import Any import reportlab.pdfgen.canvas as _rl_canvas import toyplot @@ -56,7 +56,7 @@ class TreeParseError(Exception): """Raised when a Newick string or file cannot be parsed as a tree.""" -def parse_label(label: str) -> Tuple[Optional[str], Optional[int], str]: +def parse_label(label: str) -> tuple[str | None, int | None, str]: """Parse a node label encoding font style, colour index and display text. Labels may optionally carry a font flag (``i`` or ``b``) and a numeric @@ -73,7 +73,7 @@ def parse_label(label: str) -> Tuple[Optional[str], Optional[int], str]: :rtype: Tuple[str | None, int | None, str] """ match = LABEL_RE.match(label) - _colourindex: Optional[int] = None + _colourindex: int | None = None font, colourindex, name = (None, None, label) if match: @@ -176,7 +176,7 @@ def process_tree_labels(t: toytree.ToyTree) -> toytree.ToyTree: return t -def _collect_node_styles(t: toytree.ToyTree) -> List[Dict[str, Any]]: +def _collect_node_styles(t: toytree.ToyTree) -> list[dict[str, Any]]: """Return a list of style dicts for every node in idx order. Each dict has keys: ``text`` (display string), ``color`` (hex), @@ -201,8 +201,8 @@ def _collect_node_styles(t: toytree.ToyTree) -> List[Dict[str, Any]]: def _apply_text_styles_to_svg( svg_elem: ET.Element, - italic_texts: Set[str], - bold_texts: Set[str], + italic_texts: set[str], + bold_texts: set[str], ) -> None: """Inject ``font-style`` / ``font-weight`` overrides into SVG ```` elements. @@ -217,7 +217,7 @@ def _apply_text_styles_to_svg( text = text_elem.text if text not in italic_texts and text not in bold_texts: continue - extra: List[str] = [] + extra: list[str] = [] if text in italic_texts: extra.append("font-style:italic") if text in bold_texts: @@ -231,7 +231,7 @@ def _apply_text_styles_to_svg( def export_tree( t: toytree.ToyTree, output_path: str, - title: Optional[str] = None, + title: str | None = None, ) -> None: """Export *t* to a letter-size (8.5 x 11 in) PDF. @@ -260,11 +260,11 @@ def export_tree( nnodes = t.nnodes # --- Tip labels: handed to draw() for native right-aligned positioning --- - tip_texts: List[str] = [node_styles[i]["text"] for i in range(ntips)] - tip_colors: List[str] = [node_styles[i]["color"] for i in range(ntips)] + tip_texts: list[str] = [node_styles[i]["text"] for i in range(ntips)] + tip_colors: list[str] = [node_styles[i]["color"] for i in range(ntips)] # --- Internal node labels: grouped by (bold, italic, color) --- - int_groups: Dict[Tuple[bool, bool, str], List[Tuple[int, str]]] = defaultdict(list) + int_groups: dict[tuple[bool, bool, str], list[tuple[int, str]]] = defaultdict(list) for idx in range(ntips, nnodes): info = node_styles[idx] if info["text"]: @@ -272,8 +272,8 @@ def export_tree( int_groups[key].append((idx, info["text"])) # Collect texts that need SVG font-style / font-weight injection - italic_texts: Set[str] = set() - bold_texts: Set[str] = set() + italic_texts: set[str] = set() + bold_texts: set[str] = set() for _idx, info in enumerate(node_styles): if info["text"]: if info["italic"]: @@ -305,8 +305,8 @@ def export_tree( # Add internal-node labels, one call per unique (bold, italic, color) group for (_bold, _italic, color), node_list in int_groups.items(): - labels: List[str] = [""] * nnodes - mask: List[bool] = [False] * nnodes + labels: list[str] = [""] * nnodes + mask: list[bool] = [False] * nnodes for idx, text in node_list: labels[idx] = text mask[idx] = True diff --git a/pyproject.toml b/pyproject.toml index 5224efa..2366540 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -112,7 +112,7 @@ disallow_untyped_decorators = false [tool.ruff] line-length = 88 -target-version = "py38" +target-version = "py310" [tool.ruff.lint] select = [ diff --git a/tests/test_make_tree.py b/tests/test_make_tree.py index 38b275d..bfa23d0 100644 --- a/tests/test_make_tree.py +++ b/tests/test_make_tree.py @@ -1,6 +1,5 @@ import os from pathlib import Path -from typing import List, Optional, Tuple import pytest import toytree @@ -26,7 +25,7 @@ ], ) def test_parse_label_basic( - input: str, exp_output: Tuple[Optional[str], Optional[int], str] + input: str, exp_output: tuple[str | None, int | None, str] ) -> None: assert parse_label(input) == exp_output @@ -50,7 +49,7 @@ def test_parse_label_errors(input: str) -> None: ids=["Three Node", "Six Node"], ) def test_reverse_tree( - tree_input: str, original_tips: List[str], expected_reversed: List[str] + tree_input: str, original_tips: list[str], expected_reversed: list[str] ) -> None: t = toytree.tree(tree_input) assert list(t.get_tip_labels()) == original_tips From 9ad19f6b78c72167393c5bb094a9bcbc3513c777 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Mon, 23 Mar 2026 17:22:10 +0000 Subject: [PATCH 10/12] Improve bolding --- make_tree/make_tree.py | 97 ++++++++---------------------------------- 1 file changed, 17 insertions(+), 80 deletions(-) diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index 3461a59..58c5794 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -13,7 +13,6 @@ """ import re -import xml.etree.ElementTree as ET from collections import defaultdict from typing import Any @@ -48,9 +47,6 @@ LABEL_RE = re.compile(r"(i|b)?([0-9]+)?!!(.*)") -# SVG namespace used by toyplot -_SVG_NS = "http://www.w3.org/2000/svg" - class TreeParseError(Exception): """Raised when a Newick string or file cannot be parsed as a tree.""" @@ -180,7 +176,7 @@ def _collect_node_styles(t: toytree.ToyTree) -> list[dict[str, Any]]: """Return a list of style dicts for every node in idx order. Each dict has keys: ``text`` (display string), ``color`` (hex), - ``bold`` (bool), ``italic`` (bool). + ``bold`` (bool). """ result = [] for node in t[:]: # idx-ordered slice @@ -193,41 +189,11 @@ def _collect_node_styles(t: toytree.ToyTree) -> list[dict[str, Any]]: "text": text, "color": COLOUR_LIST[ci or 0], "bold": font == "b", - "italic": font == "i", } ) return result -def _apply_text_styles_to_svg( - svg_elem: ET.Element, - italic_texts: set[str], - bold_texts: set[str], -) -> None: - """Inject ``font-style`` / ``font-weight`` overrides into SVG ```` elements. - - toyplot's style validator rejects ``font-style``, so italic must be - applied via direct XML manipulation after the element tree is built. - Bold is handled the same way for tip labels (which have no per-label - bold API), and harmlessly reinforces bold already set on internal labels. - The reportlab renderer honours both properties in element ``style`` - attributes. - """ - for text_elem in svg_elem.iter(f"{{{_SVG_NS}}}text"): - text = text_elem.text - if text not in italic_texts and text not in bold_texts: - continue - extra: list[str] = [] - if text in italic_texts: - extra.append("font-style:italic") - if text in bold_texts: - extra.append("font-weight:bold") - existing = text_elem.get("style", "") - text_elem.set( - "style", existing + ";" + ";".join(extra) if existing else ";".join(extra) - ) - - def export_tree( t: toytree.ToyTree, output_path: str, @@ -236,7 +202,7 @@ def export_tree( """Export *t* to a letter-size (8.5 x 11 in) PDF. Renders a rectangular phylogram with per-node label colours and - bold/italic styling derived from the :func:`parse_label` encoding. + bold styling derived from the :func:`parse_label` encoding. All named nodes — tips and internal — receive labels. PDF output uses toyplot and reportlab; no Qt or PyQt dependency is @@ -259,73 +225,50 @@ def export_tree( ntips = t.ntips nnodes = t.nnodes - # --- Tip labels: handed to draw() for native right-aligned positioning --- - tip_texts: list[str] = [node_styles[i]["text"] for i in range(ntips)] - tip_colors: list[str] = [node_styles[i]["color"] for i in range(ntips)] - - # --- Internal node labels: grouped by (bold, italic, color) --- - int_groups: dict[tuple[bool, bool, str], list[tuple[int, str]]] = defaultdict(list) - for idx in range(ntips, nnodes): - info = node_styles[idx] - if info["text"]: - key = (info["bold"], info["italic"], info["color"]) - int_groups[key].append((idx, info["text"])) - - # Collect texts that need SVG font-style / font-weight injection - italic_texts: set[str] = set() - bold_texts: set[str] = set() - for _idx, info in enumerate(node_styles): + # Group nodes by (is_tip, bold, color) — one add_node_labels() per group. + # Tip labels receive an xshift so they don't overlap branch lines. + groups: dict[tuple[bool, bool, str], list[tuple[int, str]]] = defaultdict(list) + for idx, info in enumerate(node_styles): if info["text"]: - if info["italic"]: - italic_texts.add(info["text"]) - if info["bold"]: - bold_texts.add(info["text"]) + key = (idx < ntips, info["bold"], info["color"]) + groups[key].append((idx, info["text"])) - # Draw the base tree + # Draw the base tree (tip labels off — handled uniformly by add_node_labels) canvas, axes, mark = t.draw( - scale_bar=True, layout="r", width=PAGE_W, height=PAGE_H, padding=50, node_sizes=0, node_mask=True, - # Tip labels: built-in positioning with a right-side padding gap - tip_labels=tip_texts, - tip_labels_colors=tip_colors, - tip_labels_style={ - "-toyplot-anchor-shift": "1px", - "font-size": f"{fsize}px", - }, - # Slightly thicker, softer edges + tip_labels=False, edge_widths=1.5, edge_style={"stroke": "#2c3e50", "stroke-linecap": "round"}, label=title or "", ) - # Add internal-node labels, one call per unique (bold, italic, color) group - for (_bold, _italic, color), node_list in int_groups.items(): + # Add labels for each (is_tip, bold, color) group + for (is_tip, bold, color), node_list in groups.items(): labels: list[str] = [""] * nnodes mask: list[bool] = [False] * nnodes for idx, text in node_list: labels[idx] = text mask[idx] = True + style: dict[str, str] = {"font-weight": "bold"} if bold else {} t.annotate.add_node_labels( axes, labels, mask=mask, color=color, font_size=fsize, + xshift=10 if is_tip else 0, + style=style or None, ) is_pdf = output_path.lower().endswith(".pdf") - # SVG post-processing: inject italic / bold into matching text elements - svg_elem = toyplot.svg.render(canvas) - if italic_texts or bold_texts: - _apply_text_styles_to_svg(svg_elem, italic_texts, bold_texts) - if is_pdf: + svg_elem = toyplot.svg.render(canvas) surface = _rl_canvas.Canvas(output_path, pagesize=(PAGE_W, PAGE_H)) surface.translate(0, PAGE_H) surface.scale(1, -1) @@ -333,13 +276,7 @@ def export_tree( surface.showPage() surface.save() else: - # SVG and other formats: serialize the (possibly italic-patched) tree - ET.register_namespace("", _SVG_NS) - ET.register_namespace("xlink", "http://www.w3.org/1999/xlink") - ET.register_namespace("toyplot", "http://www.sandia.gov/toyplot") - ET.ElementTree(svg_elem).write( - output_path, xml_declaration=True, encoding="utf-8" - ) + toyplot.svg.render(canvas, output_path) def load_tree(input_path: str) -> toytree.ToyTree: From 09b954a3ecf22a95072870f2783463443608cca4 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Mon, 23 Mar 2026 17:44:51 +0000 Subject: [PATCH 11/12] Improve italization --- make_tree/make_tree.py | 21 +++++++++++++-------- tests/test_make_tree.py | 10 ++++++++++ 2 files changed, 23 insertions(+), 8 deletions(-) diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index 58c5794..0b79567 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -176,7 +176,7 @@ def _collect_node_styles(t: toytree.ToyTree) -> list[dict[str, Any]]: """Return a list of style dicts for every node in idx order. Each dict has keys: ``text`` (display string), ``color`` (hex), - ``bold`` (bool). + ``bold`` (bool), ``italic`` (bool). """ result = [] for node in t[:]: # idx-ordered slice @@ -189,6 +189,7 @@ def _collect_node_styles(t: toytree.ToyTree) -> list[dict[str, Any]]: "text": text, "color": COLOUR_LIST[ci or 0], "bold": font == "b", + "italic": font == "i", } ) return result @@ -202,7 +203,7 @@ def export_tree( """Export *t* to a letter-size (8.5 x 11 in) PDF. Renders a rectangular phylogram with per-node label colours and - bold styling derived from the :func:`parse_label` encoding. + bold/italic styling derived from the :func:`parse_label` encoding. All named nodes — tips and internal — receive labels. PDF output uses toyplot and reportlab; no Qt or PyQt dependency is @@ -225,12 +226,14 @@ def export_tree( ntips = t.ntips nnodes = t.nnodes - # Group nodes by (is_tip, bold, color) — one add_node_labels() per group. + # Group nodes by (is_tip, bold, italic, color) — one add_node_labels() per group. # Tip labels receive an xshift so they don't overlap branch lines. - groups: dict[tuple[bool, bool, str], list[tuple[int, str]]] = defaultdict(list) + groups: dict[tuple[bool, bool, bool, str], list[tuple[int, str]]] = defaultdict( + list + ) for idx, info in enumerate(node_styles): if info["text"]: - key = (idx < ntips, info["bold"], info["color"]) + key = (idx < ntips, info["bold"], info["italic"], info["color"]) groups[key].append((idx, info["text"])) # Draw the base tree (tip labels off — handled uniformly by add_node_labels) @@ -247,12 +250,14 @@ def export_tree( label=title or "", ) - # Add labels for each (is_tip, bold, color) group - for (is_tip, bold, color), node_list in groups.items(): + # Add labels for each (is_tip, bold, italic, color) group. + # Italic is expressed via toyplot rich-text … markup in the label + # text itself, because toyplot's CSS validator does not allow font-style. + for (is_tip, bold, italic, color), node_list in groups.items(): labels: list[str] = [""] * nnodes mask: list[bool] = [False] * nnodes for idx, text in node_list: - labels[idx] = text + labels[idx] = f"{text}" if italic else text mask[idx] = True style: dict[str, str] = {"font-weight": "bold"} if bold else {} t.annotate.add_node_labels( diff --git a/tests/test_make_tree.py b/tests/test_make_tree.py index bfa23d0..fcd7728 100644 --- a/tests/test_make_tree.py +++ b/tests/test_make_tree.py @@ -6,6 +6,7 @@ from make_tree.make_tree import ( TreeParseError, + _collect_node_styles, export_tree, get_optimal_font_size, interpolate, @@ -126,6 +127,15 @@ def test_export_svg(tmp_path: Path) -> None: assert " None: + t = toytree.tree("(i!!A,b2!!B,C);") + styles = _collect_node_styles(t) + texts = [s for s in styles if s["text"]] + assert any(s["text"] == "A" and s["italic"] for s in texts) + assert any(s["text"] == "B" and s["bold"] for s in texts) + assert any(s["text"] == "C" and not s["italic"] and not s["bold"] for s in texts) + + def test_export_with_styled_labels(tmp_path: Path) -> None: t = toytree.tree("(b2!!BoldRed,i!!ItalicBlack,plain);") output_path = str(tmp_path / "styled.pdf") From efe8477892426106b487a7c64bda6cf683cbb057 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Mon, 23 Mar 2026 17:45:47 +0000 Subject: [PATCH 12/12] Bring back the scale bar --- make_tree/make_tree.py | 1 + 1 file changed, 1 insertion(+) diff --git a/make_tree/make_tree.py b/make_tree/make_tree.py index 0b79567..a2eaeb9 100644 --- a/make_tree/make_tree.py +++ b/make_tree/make_tree.py @@ -238,6 +238,7 @@ def export_tree( # Draw the base tree (tip labels off — handled uniformly by add_node_labels) canvas, axes, mark = t.draw( + scale_bar=True, layout="r", width=PAGE_W, height=PAGE_H,