DEV: rebase windows-support on main (#5)

* ENH: provide piqtree_nj and nj_tree option for positive branch lengths (#165)

* ENH: parameter to restrict negative value of branch length

* TST: allow_negative correctly control the behavior of branch length in nj_tree

* ENH: add parameter allow_negative in piqtree_nj app

* MAINT: fix double return error in merge

* MAINT: ruff formatting

* TST: Use full fasta file for checking `nj_tree` negative branch lengths

* MAINT: move from `ArrayAlignment` to `Alignment` in preparation for `new_type` default

* MAINT: simplify logic for negative branch lengths

* MAINT: Sort fixtures by number of taxa

* MAINT: Remove unused test data file

---------

Co-authored-by: Robert McArthur <robert.mcarthur@anu.edu.au>

* DEV: Update minimum required `cogent3` version (support cogent3 hooks)

* TST: Remove skip for `quick_tree` `cogent3` hook as `cogent3` min version has updated

* Bump ruff from 0.11.0 to 0.11.5

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.0 to 0.11.5.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.11.0...0.11.5)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pypa/cibuildwheel from 2.23.1 to 2.23.2

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.1 to 2.23.2.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@v2.23.1...v2.23.2)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump ruff from 0.11.5 to 0.11.8

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.5 to 0.11.8.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.11.5...0.11.8)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.8
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pypa/cibuildwheel from 2.23.2 to 2.23.3

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.2 to 2.23.3.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@v2.23.2...v2.23.3)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-version: 2.23.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* MAINT: upgrade min `cogent3` and use new `Table` API

* ENH: support use of `str` for model in `build_tree` and `fit_tree`

* TST: add tests for string represnetations of models

* API: simplify expression of model in apps (match that used by `build_tree` and `fit_tree`)

* DEV: add scriv fragment

* DEV: bump version to 0.5.0

* DEV: collate scriv fragment

* DOC: fix typo in release checklist

* DEV: update trove classifiers for supported python versions

* DEV: add minimum cmake version

* Bump ruff from 0.11.8 to 0.11.9

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.8 to 0.11.9.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.11.8...0.11.9)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Yapeng Lang <u7181074@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: 3 people

.github/workflows/build_wheels.yml

@@ -61,7 +61,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v2.23.3
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh

.github/workflows/release.yml

@@ -61,7 +61,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v2.23.3
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh

build_tools/build_iqtree.sh

@@ -30,8 +30,8 @@ elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
         ..
     make -j
 else
-    echo "Building for Linux."
-    cmake -DBUILD_LIB=ON ..
+    echo "Building for linux."
+    cmake -DBUILD_LIB=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j
 fi
 

changelog.md

@@ -1,4 +1,24 @@
 
+<a id='changelog-0.5.0'></a>
+# Changes in release "0.5.0"
+
+## Contributors
+
+- @GavinHuttley added `nj_tree` as a hook for `cogent3.Alignment.quick_tree`.
+- @YapengLang handled negative branch lengths from the rapidNJ tree.
+- @rmcar17, @thomaskf general maintanence on the piqtree/IQ-TREE sides including work on windows behind the scenes.
+
+## ENH
+
+- Add support for Python 3.13, remove support for 3.10
+- IQ-TREE's rapidNJ implementation can be used as a hook for `quick_tree` on `cogent3` alignment objects. Try `Alignment.quick_tree(use_hook="piqtree")`.
+- `nj_tree` now by default does not allow negative branch lengths. Set `allow_negative=True` if this behaviour is desired.
+- Allow `str` to be used for `model` in `build_tree` and `fit_tree`. The value is automatically coerced into the `Model` class.
+
+## API
+
+- Simplify API for `piqtree_phylo` and `piqtree_fit` apps. Both now take a single parameter for the model, matching the parameter for `model` in `build_tree` and `fit_tree`.
+
 <a id='changelog-0.4.0'></a>
 # Changes in release "0.4.0"
 

docs/developers/release.md

@@ -8,7 +8,7 @@ The documentation is fetched by readthedocs from the "Build Docs" GitHub Action.
 
 - The `piqtree` version has been correctly bumped.
 - The testing, linting and type checking all pass on all supported platforms.
-- The code has been throuroughly tested (check what's been missed in the coverage report).
+- The code has been thoroughly tested (check what's been missed in the coverage report).
 - The documentation builds and appears correct.
 - The documentation has been updated on readthedocs (this must be triggered from readthedocs).
 - The "Release" GitHub Action has correctly uploaded to Test PyPI.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "piqtree"
-dependencies = ["cogent3>=2024.11.29a2", "pyyaml", "requests"]
+dependencies = ["cogent3>=2025.5.8a2", "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"}]
@@ -28,9 +28,9 @@ classifiers = [
 
     "Programming Language :: C++",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 
     "Typing :: Typed"
 ]
@@ -43,7 +43,7 @@ Documentation = "https://piqtree.readthedocs.io"
 [project.optional-dependencies]
 dev = ["cibuildwheel", "pybind11", "scriv", "piqtree[test]", "piqtree[lint]", "piqtree[typing]"]
 test = ["pytest", "pytest-cov", "nox"]
-lint = ["ruff==0.11.0"]
+lint = ["ruff==0.11.9"]
 typing = ["mypy==1.15.0", "piqtree[stubs]", "piqtree[test]"]
 stubs = ["types-PyYAML", "types-requests"]
 extra = ["cogent3[extra]"]

src/piqtree/__init__.py

@@ -35,7 +35,7 @@ def _add_dll_path() -> None:
     make_model,
 )
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"
 
 __all__ = [
     "Model",

src/piqtree/_app/__init__.py

@@ -23,21 +23,13 @@ class piqtree_phylo:
     @extend_docstring_from(build_tree)
     def __init__(
         self,
-        submod_type: str,
-        freq_type: str | None = None,
-        rate_model: str | None = None,
+        model: Model | str,
         *,
-        invariant_sites: bool = False,
         rand_seed: int | None = None,
         bootstrap_reps: int | None = None,
         num_threads: int | None = None,
     ) -> None:
-        self._model = Model(
-            submod_type=submod_type,
-            invariant_sites=invariant_sites,
-            rate_model=rate_model,
-            freq_type=freq_type,
-        )
+        self._model = model
         self._rand_seed = rand_seed
         self._bootstrap_reps = bootstrap_reps
         self._num_threads = num_threads
@@ -61,21 +53,13 @@ class piqtree_fit:
     def __init__(
         self,
         tree: cogent3.PhyloNode,
-        submod_type: str,
-        freq_type: str | None = None,
-        rate_model: str | None = None,
+        model: Model | str,
         *,
         rand_seed: int | None = None,
         num_threads: int | None = None,
-        invariant_sites: bool = False,
     ) -> None:
         self._tree = tree
-        self._model = Model(
-            submod_type=submod_type,
-            invariant_sites=invariant_sites,
-            rate_model=rate_model,
-            freq_type=freq_type,
-        )
+        self._model = model
         self._rand_seed = rand_seed
         self._num_threads = num_threads
 
@@ -124,8 +108,12 @@ def main(
 
 @composable.define_app
 @extend_docstring_from(nj_tree)
-def piqtree_nj(dists: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
-    tree = nj_tree(dists)
+def piqtree_nj(
+    dists: c3_types.PairwiseDistanceType,
+    *,
+    allow_negative: bool = False,
+) -> cogent3.PhyloNode:
+    tree = nj_tree(dists, allow_negative=allow_negative)
     tree.params |= {"provenance": "piqtree"}
     return tree
 

src/piqtree/iqtree/_tree.py

@@ -11,7 +11,7 @@
 
 from piqtree.exceptions import ParseIqTreeError
 from piqtree.iqtree._decorator import iqtree_func
-from piqtree.model import DnaModel, Model
+from piqtree.model import DnaModel, Model, make_model
 
 iq_build_tree = iqtree_func(iq_build_tree, hide_files=True)
 iq_fit_tree = iqtree_func(iq_fit_tree, hide_files=True)
@@ -196,7 +196,7 @@ def _process_tree_yaml(
 
 def build_tree(
     aln: c3_types.AlignedSeqsType,
-    model: Model,
+    model: Model | str,
     rand_seed: int | None = None,
     bootstrap_replicates: int | None = None,
     num_threads: int | None = None,
@@ -209,7 +209,7 @@ def build_tree(
     ----------
     aln : c3_types.AlignedSeqsType
         The sequence alignment.
-    model : Model
+    model : Model | str
         The substitution model with base frequencies and rate heterogeneity.
     rand_seed : int | None, optional
         The random seed - 0 or None means no seed, by default None.
@@ -227,6 +227,9 @@ def build_tree(
         The IQ-TREE maximum likelihood tree from the given alignment.
 
     """
+    if isinstance(model, str):
+        model = make_model(model)
+
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 
@@ -261,7 +264,7 @@ def build_tree(
 def fit_tree(
     aln: c3_types.AlignedSeqsType,
     tree: cogent3.PhyloNode,
-    model: Model,
+    model: Model | str,
     rand_seed: int | None = None,
     num_threads: int | None = None,
 ) -> cogent3.PhyloNode:
@@ -276,7 +279,7 @@ def fit_tree(
         The sequence alignment.
     tree : cogent3.PhyloNode
         The topology to fit branch lengths to.
-    model : Model
+    model : Model | str
         The substitution model with base frequencies and rate heterogeneity.
     rand_seed : int | None, optional
         The random seed - 0 or None means no seed, by default None.
@@ -290,6 +293,9 @@ def fit_tree(
         A phylogenetic tree with same given topology fitted with branch lengths.
 
     """
+    if isinstance(model, str):
+        model = make_model(model)
+
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 
@@ -312,7 +318,11 @@ def fit_tree(
     return tree
 
 
-def nj_tree(pairwise_distances: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
+def nj_tree(
+    pairwise_distances: c3_types.PairwiseDistanceType,
+    *,
+    allow_negative: bool = False,
+) -> cogent3.PhyloNode:
     """Construct a neighbour joining tree from a pairwise distance matrix.
 
     Parameters
@@ -334,4 +344,11 @@ def nj_tree(pairwise_distances: c3_types.PairwiseDistanceType) -> cogent3.PhyloN
         pairwise_distances.keys(),
         np.array(pairwise_distances).flatten(),
     )
-    return make_tree(newick_tree)
+
+    tree = make_tree(newick_tree)
+
+    if not allow_negative:
+        for node in tree.traverse(include_self=False):
+            node.length = max(node.length, 0)
+
+    return tree

src/piqtree/model/_options.py

@@ -3,7 +3,7 @@
 import functools
 from typing import Literal
 
-from cogent3 import _Table, make_table
+from cogent3.core.table import Table, make_table
 
 from piqtree.model._freq_type import FreqType
 from piqtree.model._rate_type import ALL_BASE_RATE_TYPES, get_description
@@ -40,7 +40,7 @@ def available_models(
     model_type: Literal["dna", "protein"] | None = None,
     *,
     show_all: bool = True,
-) -> _Table:
+) -> Table:
     """Return a table showing available substitution models.
 
     Parameters
@@ -52,7 +52,7 @@ def available_models(
 
     Returns
     -------
-    _Table
+    Table
         Table with all available models.
 
     """
@@ -78,7 +78,7 @@ def available_models(
     return table
 
 
-def available_freq_type() -> _Table:
+def available_freq_type() -> Table:
     """Return a table showing available freq type options."""
     data: dict[str, list[str]] = {"Freq Type": [], "Description": []}
 
@@ -89,7 +89,7 @@ def available_freq_type() -> _Table:
     return make_table(data=data, title="Available frequency types")
 
 
-def available_rate_type() -> _Table:
+def available_rate_type() -> Table:
     """Return a table showing available rate type options."""
     data: dict[str, list[str]] = {"Rate Type": [], "Description": []}
 

tests/conftest.py

@@ -1,7 +1,7 @@
 import pathlib
 
 import pytest
-from cogent3 import ArrayAlignment, load_aligned_seqs
+from cogent3 import Alignment, load_aligned_seqs
 
 
 @pytest.fixture(scope="session")
@@ -10,21 +10,27 @@ def DATA_DIR() -> pathlib.Path:
 
 
 @pytest.fixture
-def three_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+def three_otu(DATA_DIR: pathlib.Path) -> Alignment:
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
 
 
 @pytest.fixture
-def four_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+def four_otu(DATA_DIR: pathlib.Path) -> Alignment:
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
 
 
 @pytest.fixture
-def five_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+def five_otu(DATA_DIR: pathlib.Path) -> Alignment:
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Manatee", "Dugong"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
+
+
+@pytest.fixture
+def all_otu(DATA_DIR: pathlib.Path) -> Alignment:
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
+    return aln.omit_gap_pos(allowed_gap_frac=0)

tests/test_app/test_app.py

@@ -1,21 +1,20 @@
 import pytest
-from cogent3 import __version__ as cogent3_vers
 from cogent3 import get_app, make_tree
 from cogent3.core.new_alignment import Alignment
 
 import piqtree
-from piqtree import jc_distances
+from piqtree import jc_distances, make_model
 
 
 def test_piqtree_phylo(four_otu: Alignment) -> None:
     expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
-    app = get_app("piqtree_phylo", submod_type="JC")
+    app = get_app("piqtree_phylo", model="JC")
     got = app(four_otu)
     assert expected.same_topology(got)
 
 
 def test_piqtree_phylo_support(four_otu: Alignment) -> None:
-    app = get_app("piqtree_phylo", submod_type="JC", bootstrap_reps=1000)
+    app = get_app("piqtree_phylo", model=make_model("JC"), bootstrap_reps=1000)
     got = app(four_otu)
     supports = [
         node.params.get("support", None)
@@ -29,7 +28,7 @@ def test_piqtree_fit(three_otu: Alignment) -> None:
     tree = make_tree(tip_names=three_otu.names)
     app = get_app("model", "JC69", tree=tree)
     expected = app(three_otu)
-    piphylo = get_app("piqtree_fit", tree=tree, submod_type="JC")
+    piphylo = get_app("piqtree_fit", tree=tree, model="JC")
     got = piphylo(three_otu)
     assert got.params["lnL"] == pytest.approx(expected.lnL)
 
@@ -112,7 +111,6 @@ def test_mfinder_result_roundtrip(five_otu: Alignment) -> None:
     assert str(got.best_aicc) == str(inflated.best_aicc)
 
 
-@pytest.mark.skipif(cogent3_vers < "2025.3.1", reason="requires cogent3 >= 2025.3.1")
 @pytest.mark.parametrize("use_hook", [None, "piqtree"])
 def test_quick_tree_hook(four_otu: Alignment, use_hook: str | None) -> None:
     tree = four_otu.quick_tree(use_hook=use_hook)