PythiaLabelGenerator 1.1.1__tar.gz → 1.2.0__tar.gz

pythialabelgenerator-1.2.0/.gitattributes

@@ -0,0 +1 @@
+pixi.lock linguist-generated=true

pythialabelgenerator-1.2.0/.github/workflows/publish-pypi.yml

@@ -0,0 +1,63 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: pypi-${{ github.event.release.tag_name }}
+  cancel-in-progress: false
+
+jobs:
+  validate-release:
+    name: Validate release version
+    if: github.event_name == 'release' && github.event.action == 'published' && !github.event.release.draft && !github.event.release.prerelease
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out released commit
+        uses: actions/checkout@v7
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: '3.14'
+      - name: Check tag matches package version
+        env:
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+        run: |
+          python - <<'PY'
+          import os
+          import pathlib
+          import tomllib
+
+          version = tomllib.loads(pathlib.Path("pyproject.toml").read_text())["project"]["version"]
+          tag = os.environ["RELEASE_TAG"]
+          if tag != version:
+              raise SystemExit(f"Release tag {tag!r} must match package version {version!r}")
+          print(f"Validated release {version}")
+          PY
+
+  test-and-build:
+    name: Test and build release
+    needs: validate-release
+    uses: ./.github/workflows/test-label-generator.yml
+
+  publish:
+    name: Upload distributions to PyPI
+    needs: test-and-build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/PythiaLabelGenerator/
+    permissions:
+      id-token: write
+    steps:
+      - name: Download tested distributions
+        uses: actions/download-artifact@v8
+        with:
+          name: python-distributions
+          path: dist/
+      - name: Publish distributions
+        uses: pypa/gh-action-pypi-publish@v1.14.2

pythialabelgenerator-1.2.0/.github/workflows/test-label-generator.yml

@@ -0,0 +1,89 @@
+name: Build and test LabelGenerator
+run-name: Build and test the LabelGenerator Python library
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+  workflow_call:
+
+permissions:
+  contents: read
+
+jobs:
+  pixi-tests:
+    name: Pixi tests (${{ matrix.os }}, ${{ matrix.environment }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        environment: [py311, py314, legacy-raxml]
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v7
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.10.2
+        with:
+          pixi-version: v0.77.0
+          environments: ${{ matrix.environment }}
+          frozen: true
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+      - name: Check the lock file
+        run: pixi lock --check
+      - name: Check RAxML-NG and IQ-TREE
+        run: pixi run --frozen --environment ${{ matrix.environment }} binary-smoke
+      - name: Run the test suite
+        run: pixi run --frozen --environment ${{ matrix.environment }} test
+      - name: Check the CLI
+        run: pixi run --frozen --environment ${{ matrix.environment }} cli-smoke
+
+  package-smoke:
+    name: Python package smoke test (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v7
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.10.2
+        with:
+          pixi-version: v0.77.0
+          environments: build
+          frozen: true
+          cache: true
+      - name: Check the lock file
+        run: pixi lock --check
+      - name: Build and verify distributions
+        run: pixi run --frozen package-smoke
+      - name: Check distribution filenames
+        run: |
+          pixi run --frozen --environment build python - <<'PY'
+          import pathlib
+          import tomllib
+
+          version = tomllib.loads(pathlib.Path("pyproject.toml").read_text())["project"]["version"]
+          expected = {
+              f"pythialabelgenerator-{version}-py3-none-any.whl",
+              f"pythialabelgenerator-{version}.tar.gz",
+          }
+          actual = {path.name for path in pathlib.Path("dist").iterdir()}
+          if actual != expected:
+              raise SystemExit(f"Expected distributions {sorted(expected)}, found {sorted(actual)}")
+          PY
+      - name: Upload tested distributions
+        if: matrix.os == 'ubuntu-latest'
+        uses: actions/upload-artifact@v7
+        with:
+          name: python-distributions
+          path: |
+            dist/*.whl
+            dist/*.tar.gz
+          if-no-files-found: error
+          overwrite: true

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/.gitignore

@@ -2,6 +2,9 @@
 **/*.log
 **/*.csv
 
+# Pixi environments
+.pixi/
+
 *.raxml.*
 !tests/**/*.raxml.*
 

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v6.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
     -   id: detect-private-key
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.7
+    rev: v0.16.6
     hooks:
     # Run the linter.
     -   id: ruff

pythialabelgenerator-1.1.1/README.md → pythialabelgenerator-1.2.0/PKG-INFO

@@ -1,3 +1,23 @@
+Metadata-Version: 2.5
+Name: PythiaLabelGenerator
+Version: 1.2.0
+Summary: Command line tool to generate the ground-truth phylogenetic difficulty of MSAs
+Project-URL: Homepage, https://github.com/tschuelia/PythiaLabelGenerator
+Author-email: Julia Haag <info@juliaschmid.com>
+License-Expression: GPL-3.0-or-later
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.11
+Requires-Dist: loguru
+Requires-Dist: pythiaphylopredictor>=2.1.0
+Requires-Dist: regex
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
 # Pythia Difficulty Label Generator (PyDLG)
 
 ![Label Generator GH actions CI](https://github.com/tschuelia/PythiaLabelGenerator/actions/workflows/test-label-generator.yml/badge.svg)
@@ -39,6 +59,18 @@ Per default, the difficulty is based on $`N_{\text{all}}=100`$ ML trees.
 Note that this number can be adjusted by the user, however, the difficulty will only be an approximation if the number
 of trees is changed.
 
+## RAxML-NG 2 Compatibility
+
+When using RAxML-NG 2, PyDLG automatically passes the following flags to preserve the label-generation procedure
+used in our publications:
+
+- `--adaptive off` disables adaptive search and its early-stopping rule. This ensures that tree searches are not
+  cut short based on estimated difficulty and that label computation follows our published difficulty definition.
+- `--extra brlen-start-fixed` restores the initial branch-length behavior of RAxML-NG 1.2, so labels are computed
+  using the same initialization as in our publications.
+
+These flags are applied automatically; no additional `label` arguments are required.
+
 ## Prediction of Phylogenetic Difficulty
 
 As stated above, computing the ground-truth difficulty for an MSA is very time-consuming and requires a lot of
@@ -62,7 +94,7 @@ biological morphological data, Pythia should work just fine 😉
 To use PyDLG, you need to install
 
 - RAxML-NG: See [the RAxML-NG GitHub repository](https://github.com/amkozlov/raxml-ng) for installation instructions.
-  Please make sure that you install a RAxML-NG version < 2.
+  PyDLG supports both RAxML-NG 1.x and 2.x.
 - IQ-TREE: See [the IQ-TREE website](http://www.iqtree.org) for installation instructions. Please install IQ-TREE
   version 2 or higher.
 
@@ -82,6 +114,38 @@ You can install the package using pip:
 pip install pythialabelgenerator
 ```
 
+This installs the Python package but not RAxML-NG or IQ-TREE. Install both programs separately as described in
+[Requirements](#requirements).
+
+#### Develop using Pixi
+
+Pixi is the supported way to create a development environment containing the Python package and both phylogenetic
+binaries:
+
+```bash
+git clone https://github.com/tschuelia/PythiaLabelGenerator.git
+cd PythiaLabelGenerator
+pixi install --frozen
+pixi run binary-smoke
+pixi run cli-smoke
+pixi run test
+```
+
+Unlike released-package installations, these project-local Pixi environments install the tested binaries from
+Bioconda. The default environment contains RAxML-NG 2.0.2 and IQ-TREE 2.4.0, while `legacy-raxml` contains RAxML-NG
+1.2.2. PyPythia 2.1.0 or newer is installed from conda-forge.
+
+The default environment uses Python 3.14 and RAxML-NG 2.0.2. Use `pixi run --environment py311 ...` or
+`pixi run --environment py314 ...` to reproduce the minimum and maximum Python versions tested in CI, or
+`pixi run --environment legacy-raxml ...` to test with RAxML-NG 1.2.2. PyDLG supports Python 3.11 through Python 3.14.
+
+Install the pre-commit hooks once and run all checks on demand using the dedicated environment:
+
+```bash
+pixi run --environment pre-commit pre-commit-install
+pixi run --environment pre-commit pre-commit-run
+```
+
 ## Usage
 
 PyDLG is primarily a command line tool. You can call it using the `label` command, for instance, to
@@ -96,9 +160,9 @@ to the console.
 The output will look something like this:
 
 ```text
-PyDLG version 1.0.1 released by The Exelixis Lab
+PyDLG version 1.2.0 released by The Exelixis Lab
 Developed by: Julia Haag
-Latest version: https://github.com/tschuelia/LabelGenerator
+Latest version: https://github.com/tschuelia/PythiaLabelGenerator
 Questions/problems/suggestions? Please open an issue on GitHub.
 
 LabelGenerator was called at 06-Mar-2025 15:15:03 as follows:
@@ -126,14 +190,14 @@ Depending on your system setup, you might need to pass a RAxML-NG and IQ-TREE bi
 You can do this using the `-r` and `-i` options, respectively. This is required in case `raxml-ng` and/or `iqtree2` are
 not in your `$PATH`.
 
-Note that this `examply.phy` MSA is not the same exemplary MSA as we provide in the PyPythia repository, so please don't compare this ground-truth lable to the exemplary prediction in PyPythia 😉
+Note that this `example.phy` MSA is not the same exemplary MSA as we provide in the PyPythia repository, so please don't compare this ground-truth label to the exemplary prediction in PyPythia 😉
 
 For a full list of command line options, run `label -h`:
 
 ```text
-PyDLG version 1.0.1 released by The Exelixis Lab
+PyDLG version 1.2.0 released by The Exelixis Lab
 Developed by: Julia Haag
-Latest version: https://github.com/tschuelia/LabelGenerator
+Latest version: https://github.com/tschuelia/PythiaLabelGenerator
 Questions/problems/suggestions? Please open an issue on GitHub.
 
 usage: label [-h] -m MSA -r RAXMLNG -i IQTREE [-t THREADS] [-s SEED] [-p PREFIX] [--model MODEL] [--ntrees NTREES] [--redo] [-V]

pythialabelgenerator-1.1.1/PKG-INFO → pythialabelgenerator-1.2.0/README.md

@@ -1,23 +1,3 @@
-Metadata-Version: 2.4
-Name: PythiaLabelGenerator
-Version: 1.1.1
-Summary: Command line tool to generate the ground-truth phylogenetic difficulty of MSAs
-Project-URL: Homepage, https://github.com/tschuelia/PythiaLabelGenerator
-Author-email: Julia Haag <info@juliaschmid.com>
-License-Expression: GPL-3.0-or-later
-License-File: LICENSE
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Python: <3.13,>=3.9
-Requires-Dist: loguru
-Requires-Dist: pythiaphylopredictor>=2.0.0
-Requires-Dist: regex
-Provides-Extra: test
-Requires-Dist: pytest; extra == 'test'
-Description-Content-Type: text/markdown
-
 # Pythia Difficulty Label Generator (PyDLG)
 
 ![Label Generator GH actions CI](https://github.com/tschuelia/PythiaLabelGenerator/actions/workflows/test-label-generator.yml/badge.svg)
@@ -59,6 +39,18 @@ Per default, the difficulty is based on $`N_{\text{all}}=100`$ ML trees.
 Note that this number can be adjusted by the user, however, the difficulty will only be an approximation if the number
 of trees is changed.
 
+## RAxML-NG 2 Compatibility
+
+When using RAxML-NG 2, PyDLG automatically passes the following flags to preserve the label-generation procedure
+used in our publications:
+
+- `--adaptive off` disables adaptive search and its early-stopping rule. This ensures that tree searches are not
+  cut short based on estimated difficulty and that label computation follows our published difficulty definition.
+- `--extra brlen-start-fixed` restores the initial branch-length behavior of RAxML-NG 1.2, so labels are computed
+  using the same initialization as in our publications.
+
+These flags are applied automatically; no additional `label` arguments are required.
+
 ## Prediction of Phylogenetic Difficulty
 
 As stated above, computing the ground-truth difficulty for an MSA is very time-consuming and requires a lot of
@@ -82,7 +74,7 @@ biological morphological data, Pythia should work just fine 😉
 To use PyDLG, you need to install
 
 - RAxML-NG: See [the RAxML-NG GitHub repository](https://github.com/amkozlov/raxml-ng) for installation instructions.
-  Please make sure that you install a RAxML-NG version < 2.
+  PyDLG supports both RAxML-NG 1.x and 2.x.
 - IQ-TREE: See [the IQ-TREE website](http://www.iqtree.org) for installation instructions. Please install IQ-TREE
   version 2 or higher.
 
@@ -102,6 +94,38 @@ You can install the package using pip:
 pip install pythialabelgenerator
 ```
 
+This installs the Python package but not RAxML-NG or IQ-TREE. Install both programs separately as described in
+[Requirements](#requirements).
+
+#### Develop using Pixi
+
+Pixi is the supported way to create a development environment containing the Python package and both phylogenetic
+binaries:
+
+```bash
+git clone https://github.com/tschuelia/PythiaLabelGenerator.git
+cd PythiaLabelGenerator
+pixi install --frozen
+pixi run binary-smoke
+pixi run cli-smoke
+pixi run test
+```
+
+Unlike released-package installations, these project-local Pixi environments install the tested binaries from
+Bioconda. The default environment contains RAxML-NG 2.0.2 and IQ-TREE 2.4.0, while `legacy-raxml` contains RAxML-NG
+1.2.2. PyPythia 2.1.0 or newer is installed from conda-forge.
+
+The default environment uses Python 3.14 and RAxML-NG 2.0.2. Use `pixi run --environment py311 ...` or
+`pixi run --environment py314 ...` to reproduce the minimum and maximum Python versions tested in CI, or
+`pixi run --environment legacy-raxml ...` to test with RAxML-NG 1.2.2. PyDLG supports Python 3.11 through Python 3.14.
+
+Install the pre-commit hooks once and run all checks on demand using the dedicated environment:
+
+```bash
+pixi run --environment pre-commit pre-commit-install
+pixi run --environment pre-commit pre-commit-run
+```
+
 ## Usage
 
 PyDLG is primarily a command line tool. You can call it using the `label` command, for instance, to
@@ -116,9 +140,9 @@ to the console.
 The output will look something like this:
 
 ```text
-PyDLG version 1.0.1 released by The Exelixis Lab
+PyDLG version 1.2.0 released by The Exelixis Lab
 Developed by: Julia Haag
-Latest version: https://github.com/tschuelia/LabelGenerator
+Latest version: https://github.com/tschuelia/PythiaLabelGenerator
 Questions/problems/suggestions? Please open an issue on GitHub.
 
 LabelGenerator was called at 06-Mar-2025 15:15:03 as follows:
@@ -146,14 +170,14 @@ Depending on your system setup, you might need to pass a RAxML-NG and IQ-TREE bi
 You can do this using the `-r` and `-i` options, respectively. This is required in case `raxml-ng` and/or `iqtree2` are
 not in your `$PATH`.
 
-Note that this `examply.phy` MSA is not the same exemplary MSA as we provide in the PyPythia repository, so please don't compare this ground-truth lable to the exemplary prediction in PyPythia 😉
+Note that this `example.phy` MSA is not the same exemplary MSA as we provide in the PyPythia repository, so please don't compare this ground-truth label to the exemplary prediction in PyPythia 😉
 
 For a full list of command line options, run `label -h`:
 
 ```text
-PyDLG version 1.0.1 released by The Exelixis Lab
+PyDLG version 1.2.0 released by The Exelixis Lab
 Developed by: Julia Haag
-Latest version: https://github.com/tschuelia/LabelGenerator
+Latest version: https://github.com/tschuelia/PythiaLabelGenerator
 Questions/problems/suggestions? Please open an issue on GitHub.
 
 usage: label [-h] -m MSA -r RAXMLNG -i IQTREE [-t THREADS] [-s SEED] [-p PREFIX] [--model MODEL] [--ntrees NTREES] [--redo] [-V]

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/labelgenerator/iqtree.py

@@ -1,6 +1,5 @@
 import pathlib
 import subprocess
-from typing import Optional
 
 from pypythia.custom_types import DataType
 
@@ -49,7 +48,7 @@ def run_statstests(
     model: str,
     prefix: pathlib.Path,
     seed: int = 0,
-    threads: Optional[int] = None,
+    threads: int | None = None,
     is_morph: bool = False,
     redo: bool = False,
 ) -> None:

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/labelgenerator/label.py

@@ -1,7 +1,6 @@
 import pathlib
-from typing import Optional
 
-from pypythia.msa import DataType, MSA
+from pypythia.msa import MSA, DataType
 
 from labelgenerator.iqtree import (
     filter_plausible_trees,
@@ -92,9 +91,9 @@ def get_label(
     label = total / 5
 
     eps = 1e-9
-    assert (
-        -eps <= label <= 1 + eps
-    ), f"Label {label} is not between 0 and 1. Check the input values."
+    assert -eps <= label <= 1 + eps, (
+        f"Label {label} is not between 0 and 1. Check the input values."
+    )
 
     return label
 
@@ -105,10 +104,10 @@ def compute_label(
     raxmlng: pathlib.Path,
     iqtree: pathlib.Path,
     prefix: pathlib.Path,
-    model: Optional[str] = None,
+    model: str | None = None,
     n_trees: int = 100,
     seed: int = 0,
-    threads: Optional[int] = None,
+    threads: int | None = None,
     redo: bool = False,
     log_info: bool = True,
 ) -> float:

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/labelgenerator/logger.py

@@ -3,6 +3,7 @@ import textwrap
 import time
 
 import loguru
+
 from labelgenerator import __version__
 
 SCRIPT_START = time.perf_counter()
@@ -17,7 +18,7 @@ def get_header():
     return textwrap.dedent(
         f"PyDLG version {__version__} released by The Exelixis Lab\n"
         f"Developed by: Julia Haag\n"
-        f"Latest version: https://github.com/tschuelia/LabelGenerator\n"
+        f"Latest version: https://github.com/tschuelia/PythiaLabelGenerator\n"
         f"Questions/problems/suggestions? Please open an issue on GitHub.\n",
     )
 

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/labelgenerator/main.py

@@ -3,7 +3,10 @@ import pathlib
 import shutil
 import sys
 import time
-from typing import Optional
+
+from pypythia.msa import parse_msa
+from pypythia.prediction import collect_features
+from pypythia.raxmlng import RAxMLNG
 
 from labelgenerator import __version__
 from labelgenerator.label import compute_label
@@ -14,9 +17,6 @@ from labelgenerator.logger import (
     log_runtime_information,
     logger,
 )
-from pypythia.msa import parse_msa
-from pypythia.prediction import collect_features
-from pypythia.raxmlng import RAxMLNG
 
 DEFAULT_RAXMLNG_EXE = (
     pathlib.Path(shutil.which("raxml-ng")) if shutil.which("raxml-ng") else None
@@ -27,7 +27,7 @@ DEFAULT_IQTREE_EXE = (
 )
 
 
-def _parse_cli(arg_list: Optional[list[str]] = None):
+def _parse_cli(arg_list: list[str] | None = None):
     parser = argparse.ArgumentParser(
         description="Generate the ground truth difficulty for the given MSA."
     )
@@ -118,7 +118,7 @@ def _parse_cli(arg_list: Optional[list[str]] = None):
     return parser.parse_args(arg_list)
 
 
-def main(arg_list: Optional[list[str]] = None):
+def main(arg_list: list[str] | None = None):
     logger.info(get_header())
     args = _parse_cli(arg_list)
 

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/labelgenerator/raxmlng.py

@@ -1,6 +1,5 @@
 import math
 import pathlib
-from typing import Optional
 
 from pypythia.raxmlng import RAxMLNG, get_raxmlng_rfdist_results, run_raxmlng_command
 
@@ -38,7 +37,7 @@ def infer_ml_trees(
     prefix: pathlib.Path,
     n_trees: int = 100,
     seed: int = 0,
-    threads: Optional[int] = None,
+    threads: int | None = None,
     redo: bool = False,
 ) -> None:
     """
@@ -74,6 +73,8 @@ def infer_ml_trees(
     if not redo and _inference_results_exist_and_correct(prefix, n_trees):
         return
 
+    raxmlng_major_version = RAxMLNG(raxmlng)._major_version
+
     n_pars_trees = math.ceil(n_trees / 2)
     n_rand_trees = n_trees - n_pars_trees
     rand_string = f",rand{{{n_rand_trees}}}" if n_rand_trees > 0 else ""
@@ -95,6 +96,11 @@ def infer_ml_trees(
     if threads is not None:
         cmd.extend(["--threads", threads])
 
+    if raxmlng_major_version >= 2:
+        # Preserve the v1.2 search and fixed parsimony starting branch lengths.
+        # Disabling adaptive search alone leaves v2's new initialization enabled.
+        cmd.extend(["--adaptive", "off", "--extra", "brlen-start-fixed"])
+
     if redo:
         cmd.append("--redo")
 
@@ -130,7 +136,7 @@ def rf_distance(
     ml_trees: pathlib.Path,
     prefix: pathlib.Path,
     raxmlng: pathlib.Path,
-    n_trees: Optional[int] = None,
+    n_trees: int | None = None,
     redo: bool = False,
 ) -> tuple[int, float]:
     """

pythialabelgenerator-1.2.0/pixi.toml

@@ -0,0 +1,55 @@
+[workspace]
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64", "osx-64", "osx-arm64"]
+requires-pixi = ">=0.76.1"
+
+[dependencies]
+pythiaphylopredictor = ">=2.1.0"
+regex = "*"
+loguru = "*"
+iqtree = "==2.4.0"
+
+[pypi-dependencies]
+PythiaLabelGenerator = { path = ".", editable = true }
+
+[feature.py311.dependencies]
+python = "3.11.*"
+
+[feature.py314.dependencies]
+python = "3.14.*"
+
+[feature.test.dependencies]
+pytest = "*"
+
+[feature.raxml1.dependencies]
+raxml-ng = "==1.2.2"
+
+[feature.raxml2.dependencies]
+raxml-ng = "==2.0.2"
+
+[feature.pre-commit.dependencies]
+pre-commit = "*"
+
+[feature.pre-commit.tasks]
+pre-commit-install = "pre-commit install"
+pre-commit-run = "pre-commit run --all-files"
+
+[feature.build.dependencies]
+hatchling = "*"
+pip = "*"
+python-build = "*"
+
+[environments]
+default = { features = ["py314", "raxml2", "test"] }
+py311 = { features = ["py311", "raxml2", "test"] }
+py314 = { features = ["py314", "raxml2", "test"] }
+legacy-raxml = { features = ["py311", "raxml1", "test"] }
+build = { features = ["py314", "build"] }
+pre-commit = { features = ["pre-commit"], no-default-feature = true }
+
+[tasks]
+test = "pytest -svx --color=yes"
+binary-smoke = "raxml-ng -v && iqtree2 -v"
+cli-smoke = "label --help"
+build = { cmd = "python -m build", default-environment = "build" }
+package-smoke = { cmd = "python -m pip install --force-reinstall --no-deps dist/*.whl && python -m pip check && python -c 'import labelgenerator' && label --help", depends-on = ["build"], default-environment = "build" }

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/pyproject.toml

@@ -3,18 +3,18 @@ name = "PythiaLabelGenerator"
 description = "Command line tool to generate the ground-truth phylogenetic difficulty of MSAs"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [{name = "Julia Haag", email = "info@juliaschmid.com"}]
-version = "1.1.1"
+version = "1.2.0"
 license = "GPL-3.0-or-later"
 classifiers = [
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12"
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14"
 ]
-requires-python = ">= 3.9, < 3.13"
+requires-python = ">=3.11,<3.15"
 
 dependencies = [
-    "pythiaphylopredictor>=2.0.0",
+    "pythiaphylopredictor>=2.1.0",
     "regex",
     "loguru"
 ]
@@ -34,34 +34,15 @@ label = "labelgenerator.main:main"
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
-[tool.black]
-exclude = '''
-/(
-    \.eggs
-  | \.git
-  | \.venv
-  | build
-  | dist
-)/
-'''
-
-[tool.isort]
-multi_line_output = 3
-include_trailing_comma = true
-ensure_newline_before_comments = true
-line_length = 88
-known_first_party = "labelgenerator"
-skip_glob = '\.eggs/*,\.git/*,\.venv/*,build/*,dist/*'
-default_section = 'THIRDPARTY'
-
-[tool.mypy]
-python_version = 3.8
-ignore_missing_imports = true
-no_implicit_optional = true
-check_untyped_defs = true
+[tool.ruff.lint]
+select = ["F", "I", "UP"]
+ignore = ["E501"]
 
 [tool.pytest.ini_options]
 addopts = "--import-mode=importlib"
 
 [tool.hatch.build.targets.wheel]
 packages = ["labelgenerator"]
+
+[tool.hatch.build.targets.sdist]
+exclude = ["/pixi.lock"]

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/tests/conftest.py

@@ -1,18 +1,29 @@
+import os
 import pathlib
+import shutil
 
 import pytest
 
-from .test_config import IQTREE_COMMAND, RAXMLNG_COMMAND
+
+def _command_path(environment_variable, executable):
+    configured_command = os.environ.get(environment_variable)
+    command = configured_command or shutil.which(executable)
+    if command is None:
+        pytest.fail(
+            f"Could not find {executable!r}. Add it to PATH or set "
+            f"{environment_variable}."
+        )
+    return pathlib.Path(command)
 
 
 @pytest.fixture
 def raxmlng_command():
-    return pathlib.Path(RAXMLNG_COMMAND)
+    return _command_path("RAXMLNG_COMMAND", "raxml-ng")
 
 
 @pytest.fixture
 def iqtree_command():
-    return pathlib.Path(IQTREE_COMMAND)
+    return _command_path("IQTREE_COMMAND", "iqtree2")
 
 
 @pytest.fixture

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/tests/test_label.py

@@ -2,12 +2,12 @@ import pathlib
 import tempfile
 
 import pytest
-
-from labelgenerator.label import get_label, compute_label
-from labelgenerator.logger import logger
 from pypythia.custom_types import DataType
 from pypythia.msa import parse_msa
 
+from labelgenerator.label import compute_label, get_label
+from labelgenerator.logger import logger
+
 
 def test_get_label_fails_for_invalid_input():
     with pytest.raises(
@@ -88,11 +88,21 @@ def test_get_label(values, expected):
 
 
 @pytest.mark.parametrize(
-    "data_type, expected_label",
-    [(DataType.DNA, 0.772), (DataType.AA, 0.04), (DataType.MORPH, 0.173)],
+    "data_type, expected_label, tolerance",
+    [
+        # Native RAxML-NG builds can select different near-optimal DNA trees.
+        (DataType.DNA, 0.772, 0.05),
+        (DataType.AA, 0.04, 0.01),
+        (DataType.MORPH, 0.173, 0.01),
+    ],
 )
 def test_compute_label(
-    raxmlng_command, iqtree_command, data_dir, data_type, expected_label
+    raxmlng_command,
+    iqtree_command,
+    data_dir,
+    data_type,
+    expected_label,
+    tolerance,
 ):
     msa_file = data_dir / f"{data_type.name}.phy"
 
@@ -109,7 +119,7 @@ def test_compute_label(
             log_info=False,
             seed=42,
         )
-        assert label == pytest.approx(expected_label, abs=0.01)
+        assert label == pytest.approx(expected_label, abs=tolerance)
 
 
 def test_compute_label_with_logging(raxmlng_command, iqtree_command, data_dir):
@@ -139,8 +149,11 @@ def test_compute_label_with_logging(raxmlng_command, iqtree_command, data_dir):
         logfile_content = logfile.read_text()
 
         assert f"Inferring {n_trees} ML trees using RAxML-NG." in logfile_content
-        assert "RF-Distance ML trees: 0.23" in logfile_content
-        assert "Unique topologies ML trees: 2" in logfile_content
-        assert "Found 10 plausible trees." in logfile_content
-        assert "RF-Distance plausible trees: 0.23" in logfile_content
-        assert "Unique topologies plausible trees: 2" in logfile_content
+        expected_lines = [
+            "RF-Distance ML trees: 0.23",
+            "Unique topologies ML trees: 2",
+            "Found 10 plausible trees.",
+            "RF-Distance plausible trees: 0.23",
+            "Unique topologies plausible trees: 2",
+        ]
+        assert all(line in logfile_content for line in expected_lines)

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/tests/test_main.py

@@ -1,21 +1,32 @@
+import pathlib
 import tempfile
-import pytest
 
 import pandas as pd
-
-from labelgenerator.main import main
-from labelgenerator import __version__
-import pathlib
-
+import pytest
 from pypythia.custom_types import DataType
 from pypythia.msa import parse_msa
 
+from labelgenerator import __version__
+from labelgenerator.main import main
+
 
 @pytest.mark.parametrize(
-    "data_type, expected_label",
-    [(DataType.DNA, 0.772), (DataType.AA, 0.04), (DataType.MORPH, 0.173)],
+    "data_type, expected_label, tolerance",
+    [
+        # Native RAxML-NG builds can select different near-optimal DNA trees.
+        (DataType.DNA, 0.772, 0.05),
+        (DataType.AA, 0.04, 0.01),
+        (DataType.MORPH, 0.173, 0.01),
+    ],
 )
-def test_main(data_type, expected_label, data_dir, raxmlng_command, iqtree_command):
+def test_main(
+    data_type,
+    expected_label,
+    tolerance,
+    data_dir,
+    raxmlng_command,
+    iqtree_command,
+):
     with tempfile.TemporaryDirectory() as tmpdir:
         # Create a temporary directory for the test
         prefix = pathlib.Path(tmpdir) / "test"
@@ -90,7 +101,7 @@ def test_main(data_type, expected_label, data_dir, raxmlng_command, iqtree_comma
 
         # Check if the label is correct
         label = features_content["difficulty"].values[0]
-        assert label == pytest.approx(expected_label, abs=0.01)
+        assert label == pytest.approx(expected_label, abs=tolerance)
 
         # Check if the log file is correct and contains the expected output
         expected_lines = [

{pythialabelgenerator-1.1.1 → pythialabelgenerator-1.2.0}/tests/test_raxmlng.py

@@ -8,6 +8,7 @@ import pytest
 from pypythia.custom_types import DataType
 from pypythia.msa import parse_msa
 
+import labelgenerator.raxmlng as raxmlng_module
 from labelgenerator.raxmlng import (
     _inference_results_exist_and_correct,
     _rfdist_results_exists_and_correct,
@@ -67,15 +68,48 @@ def test_infer_ml_trees(raxmlng_command, dna_msa, n_trees):
         expected_random = (
             f"random ({n_rand_expected}) + " if n_rand_expected > 0 else ""
         )
-        expected_parsimony = (
-            f"parsimony ({n_pars_expected})" if n_pars_expected > 0 else ""
-        )
-        expected_log = f"start tree(s): {expected_random}{expected_parsimony}"
+        expected_log = f"start tree(s): {expected_random}parsimony ({n_pars_expected})"
 
         log_file = prefix.with_suffix(".raxml.log")
         assert expected_log in log_file.read_text()
 
 
+@pytest.mark.parametrize(
+    ("major_version", "expected_adaptive_setting"),
+    [(1, None), (2, "off"), (3, "off")],
+)
+def test_infer_ml_trees_preserves_v1_search_by_raxmlng_version(
+    tmp_path, monkeypatch, major_version, expected_adaptive_setting
+):
+    class RAxMLNGStub:
+        def __init__(self, _executable):
+            self._major_version = major_version
+
+    commands = []
+    monkeypatch.setattr(raxmlng_module, "RAxMLNG", RAxMLNGStub)
+    monkeypatch.setattr(raxmlng_module, "run_raxmlng_command", commands.append)
+
+    raxmlng_module.infer_ml_trees(
+        msa=tmp_path / "msa.phy",
+        raxmlng=tmp_path / "raxml-ng",
+        model="GTR+G",
+        prefix=tmp_path / "inference",
+        n_trees=2,
+    )
+
+    command = commands[0]
+    if expected_adaptive_setting is None:
+        assert "--adaptive" not in command
+        assert "--extra" not in command
+    else:
+        adaptive_index = command.index("--adaptive")
+        assert command[adaptive_index + 1] == expected_adaptive_setting
+        assert command.count("--adaptive") == 1
+        extra_index = command.index("--extra")
+        assert command[extra_index + 1] == "brlen-start-fixed"
+        assert command.count("--extra") == 1
+
+
 @pytest.mark.parametrize("data_type", [DataType.DNA, DataType.AA, DataType.MORPH])
 def test_infer_ml_trees_for_dtypes(raxmlng_command, data_dir, data_type):
     msa = data_dir / f"{data_type.name}.phy"

pythialabelgenerator-1.1.1/.github/actions/setup-iqtree/action.yml

@@ -1,22 +0,0 @@
-name: Setup IQ-TREE
-runs:
-  using: composite
-  steps:
-    - name: Download IQ-TREE MacOS
-      if: runner.os == 'macOS'
-      run: |
-        wget https://github.com/iqtree/iqtree2/releases/download/v2.4.0/iqtree-2.4.0-macOS.zip
-        unzip iqtree-*.zip && mv iqtree-*/* .
-      shell: bash
-    - name: Download IQ-TREE Linux
-      if: runner.os == 'Linux'
-      run: |
-        wget https://github.com/iqtree/iqtree2/releases/download/v2.4.0/iqtree-2.4.0-Linux-intel.tar.gz
-        tar xvf iqtree-*.tar.gz && mv iqtree-*/* .
-      shell: bash
-    - name: Unzip IQ-TREE and set Env variable
-      run: echo iqtree2=$(pwd)/bin/iqtree2 >> $GITHUB_ENV
-      shell: bash
-    - name: Check IQ-TREE installation
-      run: $iqtree2 -v
-      shell: bash

pythialabelgenerator-1.1.1/.github/actions/setup-raxmlng/action.yml

@@ -1,20 +0,0 @@
-name: Setup RAxML-NG
-runs:
-  using: composite
-  steps:
-    - name: Download RAxML-NG MacOS
-      if: runner.os == 'macOS'
-      run: wget https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_macos.zip
-      shell: bash
-    - name: Download RAxML-NG Linux
-      if: runner.os == 'Linux'
-      run: wget https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_linux_x86_64.zip
-      shell: bash
-    - name: Unzip RAxML-NG and set Env variable
-      run: |
-        unzip raxml-ng_*.zip
-        echo raxmlng=$(pwd)/raxml-ng >> $GITHUB_ENV
-      shell: bash
-    - name: Check RAxML-NG installation
-      run: $raxmlng -v
-      shell: bash

pythialabelgenerator-1.1.1/.github/actions/test-label-cli/action.yml

@@ -1,12 +0,0 @@
-name: Test Label CLI
-inputs:
-  msa-file:
-    description: MSA file to test Label CLI with
-    default: examples/example.phy
-runs:
-  using: composite
-  steps:
-    - name: Run Label CLI with an exemplary MSA to make sure everything is working
-      run: |
-        label -m ${{ inputs.msa-file }} -r ${{ env.raxmlng }} -i ${{ env.iqtree2 }} --ntrees 4
-      shell: bash -el {0}

pythialabelgenerator-1.1.1/.github/workflows/test-label-generator.yml

@@ -1,72 +0,0 @@
-name: Build and test LabelGenerator
-run-name: Build and run the tests of the LabelGenerator python library.
-on:
-  push:
-    paths-ignore:
-      - 'docs/**'
-jobs:
-  Run-Label-Generator-Tests:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.12"]
-    steps:
-      - name: Check out repository code
-        uses: actions/checkout@v3
-      - name: Setup Conda
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: etc/environment.yml
-          cache-environment: true
-          create-args:
-            python=${{ matrix.python-version }}
-          generate-run-shell: false
-          post-cleanup: none
-      - name: Setup RAxML-NG and RAxML-NG env variable
-        uses: ./.github/actions/setup-raxmlng
-      - name: Setup IQ-TREE and IQ-TREE env variable
-        uses: ./.github/actions/setup-iqtree
-      - name: Install LabelGenerator and setup requirements
-        run: |
-          pip install -e . --no-deps
-          rm tests/test_config.py
-          echo "RAXMLNG_COMMAND = '${{ env.raxmlng }}'" >> tests/test_config.py
-          echo "IQTREE_COMMAND = '${{ env.iqtree2 }}'" >> tests/test_config.py
-          cat tests/test_config.py
-        shell: bash -el {0}
-#      - name: Setup tmate session
-#        uses: mxschmitt/action-tmate@v3
-      - name: Run LabelGenerator tests
-        run: |
-          PYTHONPATH=. pytest -svx --color=yes
-        shell: bash -el {0}
-
-  Install-using-conda:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.12"]
-    steps:
-      - name: Check out repository code
-        uses: actions/checkout@v3
-      - name: Setup Conda
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: etc/environment.yml
-          cache-environment: true
-          create-args:
-            python=${{ matrix.python-version }}
-          generate-run-shell: false
-          post-cleanup: none
-      - name: Install LabelGenerator  # Install LabelGenerator manually to get the correct branch
-        run: |
-          pip install -e . --no-deps
-        shell: bash -el {0}
-      - name: Setup RAxML-NG and RAxML-NG env variable
-        uses: ./.github/actions/setup-raxmlng
-      - name: Setup IQ-TREE and IQ-TREE env variable
-        uses: ./.github/actions/setup-iqtree
-      - name: Test installation by running the CLI
-        uses: ./.github/actions/test-label-cli

pythialabelgenerator-1.1.1/etc/environment.yml

@@ -1,9 +0,0 @@
-name: labelGenerator
-channels:
-  - conda-forge
-  - nodefaults
-dependencies:
-  - regex
-  - loguru
-  - pytest
-  - pythiaphylopredictor >=2.0.0

pythialabelgenerator-1.1.1/tests/test_config.py

@@ -1,2 +0,0 @@
-RAXMLNG_COMMAND = "/Users/julia/Software/raxml-ng_v1.2.0/raxml-ng"
-IQTREE_COMMAND = "/Users/julia/Software/iqtree-2.1.3-MacOSX/bin/iqtree2"