Switch to ToyTree

.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

.github/workflows/main.yml

@@ -14,20 +14,16 @@ 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", "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
 

.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

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
 

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
 
@@ -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

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",

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,