DEV: update cogent3

.github/workflows/ci.yml

@@ -42,7 +42,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
-        python-version: ["3.11", "3.12", "3.13"] 
+        python-version: ["3.11", "3.12", "3.13.5"] 
     steps:
       - uses: actions/checkout@v4
         with:
@@ -96,7 +96,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.13"]
+        python-version: ["3.13.5"]
         os: [ubuntu-latest]
 
     steps:
@@ -121,7 +121,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.13"]
+        python-version: ["3.13.5"]
         os: [ubuntu-latest]
 
     steps:

noxfile.py

@@ -3,9 +3,10 @@
 import nox
 
 _py_versions = range(11, 14)
+_python_sessions = [f"3.{v}" + (".5" if v == 13 else "") for v in _py_versions]
 
 
-@nox.session(python=[f"3.{v}" for v in _py_versions])
+@nox.session(python=_python_sessions)
 def test(session):
     posargs = list(session.posargs)
     env = os.environ.copy()
@@ -15,7 +16,7 @@ def test(session):
     session.run("pytest", *posargs, env=env)
 
 
-@nox.session(python=[f"3.{v}" for v in _py_versions])
+@nox.session(python=_python_sessions)
 def type_check(session):
     posargs = list(session.posargs)
     env = os.environ.copy()
@@ -25,7 +26,7 @@ def type_check(session):
     session.run("mypy", "src", "tests", *posargs, env=env)
 
 
-@nox.session(python=[f"3.{v}" for v in _py_versions])
+@nox.session(python=_python_sessions)
 def ruff(session):
     posargs = list(session.posargs)
     env = os.environ.copy()

pyproject.toml

@@ -4,15 +4,15 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "piqtree"
-dependencies = ["cogent3>=2025.5.8a2", "pyyaml", "requests"]
+dependencies = ["cogent3>=2025.5.8a7", "pyyaml", "requests"]
 requires-python = ">=3.11, <3.14"
 
 authors = [
     { name = "Gavin Huttley" },
     { name = "Robert McArthur" },
     { name = "Bui Quang Minh " },
     { name = "Richard Morris" },
-    { name = "Thomas Wong" },
+    { name = "Thomas Wong" }
 ]
 description = "Python bindings for IQTree"
 readme = "README.md"
@@ -38,7 +38,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 
-    "Typing :: Typed",
+    "Typing :: Typed"
 ]
 
 [project.urls]
@@ -54,7 +54,7 @@ dev = [
     "scriv",
     "piqtree[test]",
     "piqtree[lint]",
-    "piqtree[typing]",
+    "piqtree[typing]"
 ]
 test = ["pytest", "pytest-cov", "nox"]
 lint = ["ruff==0.11.13"]
@@ -71,7 +71,7 @@ doc = [
     "cogent3[extra]",
     "diverse-seq",
     "jupyter",
-    "ipywidgets",
+    "ipywidgets"
 ]
 
 [project.entry-points."cogent3.app"]
@@ -116,7 +116,7 @@ exclude = [
     "dist",
     "node_modules",
     "site-packages",
-    "venv",
+    "venv"
 ]
 
 # Same as Black.
@@ -141,33 +141,33 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
 [tool.ruff.lint.per-file-ignores]
 "tests/**/*.py" = [
-    "S101",   # asserts allowed in tests...
+    "S101", # asserts allowed in tests...
     "INP001", # __init__.py files are not required...
-    "N802",   # allow non snake_case function names for fixtures
-    "N803",   # allow use of fixture constants
+    "N802", # allow non snake_case function names for fixtures
+    "N803", # allow use of fixture constants
     "SLF001", # private member access is useful for testing
     "FBT001", # allow bool pos args for parameterisation
-    "D",      # don't require docstrings
+    "D" # don't require docstrings
 ]
 "docs/**/*.py" = ["B018", "E402", "ERA001", "INP001"]
 "noxfile.py" = [
-    "S101",   # asserts allowed in tests...
+    "S101", # asserts allowed in tests...
     "INP001", # __init__.py files are not required...
     "ANN",
     "N802",
     "N803",
-    "D",
+    "D"
 ]
 "src/piqtree/_app/__init__.py" = [
-    "N801", # apps follow function naming convention
+    "N801" # apps follow function naming convention
 ]
 "src/piqtree/__init__.py" = [
-    "E402",   # handle DLLs before imports
+    "E402", # handle DLLs before imports
     "PTH118", # os operations for DLL path
-    "PTH120", # os operations for DLL path
+    "PTH120" # os operations for DLL path
 ]
 "src/piqtree/model/_substitution_model.py" = [
-    "N815", # use IQ-TREE naming scheme
+    "N815" # use IQ-TREE naming scheme
 ]
 
 [tool.ruff.format]
@@ -205,7 +205,7 @@ categories = [
     "BUG",
     "DOC",
     "Deprecations",
-    "Discontinued",
+    "Discontinued"
 ]
 output_file = "changelog.md"
 version = "literal: src/piqtree/__init__.py: __version__"

tests/conftest.py

@@ -1,7 +1,8 @@
 import pathlib
 
 import pytest
-from cogent3 import Alignment, load_aligned_seqs
+from cogent3 import load_aligned_seqs
+from cogent3.core.alignment import Alignment
 
 
 @pytest.fixture(scope="session")

tests/test_iqtree/test_build_tree.py

@@ -1,7 +1,8 @@
 import re
 
 import pytest
-from cogent3 import Alignment, make_tree
+from cogent3 import make_tree
+from cogent3.core.alignment import Alignment
 
 import piqtree
 from piqtree.exceptions import IqTreeError

tests/test_iqtree/test_distance.py

@@ -1,4 +1,4 @@
-from cogent3 import Alignment
+from cogent3.core.alignment import Alignment
 
 from piqtree import jc_distances
 

tests/test_iqtree/test_fit_tree.py

@@ -1,6 +1,7 @@
 import pytest
-from cogent3 import Alignment, get_app, make_tree
+from cogent3 import get_app, make_tree
 from cogent3.app.result import model_result
+from cogent3.core.alignment import Alignment
 from cogent3.core.tree import PhyloNode
 
 import piqtree

tests/test_iqtree/test_model_finder.py

@@ -1,7 +1,7 @@
 import multiprocessing
 
 import pytest
-from cogent3 import Alignment
+from cogent3.core.alignment import Alignment
 
 from piqtree.iqtree import ModelFinderResult, ModelResultValue, model_finder
 

tests/test_iqtree/test_nj_tree.py

@@ -2,7 +2,8 @@
 
 import numpy as np
 import pytest
-from cogent3 import Alignment, make_tree
+from cogent3 import make_tree
+from cogent3.core.alignment import Alignment
 
 from piqtree import jc_distances, nj_tree