bdms-sim 0.2.0__tar.gz

bdms_sim-0.2.0/.flake8

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+[flake8]
+statistics = True
+count = True
+max-line-length = 88
+extend-ignore = E203
+exclude =
+    .vscode,
+    .conda,
+    .hatch,
+    __pycache__

bdms_sim-0.2.0/.github/workflows/build-and-test.yml

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+name: build and test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build-and-test:
+    strategy:
+      matrix:
+        os: [macos-latest]
+        python-version: [3.11, 3.12]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v1
+
+      - name: Install BDMS
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+          hatch env create
+
+      - name: Lint
+        run: hatch run lint
+
+      - name: Run tests
+        run: hatch run tests
+
+      - name: Test docs build
+        run: hatch run docs

bdms_sim-0.2.0/.github/workflows/docs-build-and-deploy.yml

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+name: docs build and deploy
+
+on:
+  push:
+    branches: ["main"]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+          cache: pip
+
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v1
+
+      - name: Install BDMS
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+          hatch env create
+
+      - name: Build 🔧
+        run: |
+          hatch run docs
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

bdms_sim-0.2.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    environment: release
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip 
+        pip install hatch
+    - name: Build package
+      run: hatch build
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

bdms_sim-0.2.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/_autosummary/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# vscode
+.vscode/
+
+# hatch
+.hatch/

bdms_sim-0.2.0/CITATION.cff

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+cff-version: 1.2.0
+title: BDMS
+message: 'If you use BDMS in your work, please cite as follows.'
+type: software
+authors:
+  - given-names: William S.
+    family-names: DeWitt
+    affiliation: 'University of California, Berkeley'
+    email: wsdewitt@berkeley.edu
+    orcid: 'https://orcid.org/0000-0002-6802-9139'
+  - given-names: Michael
+    family-names: Celentano
+    affiliation: 'University of California, Berkeley'
+    email: mcelentano@berkeley.edu
+    orcid: 'https://orcid.org/0000-0001-9474-1827'
+  - given-names: Thanasi
+    family-names: Bakis
+    affiliation: 'University of California, Irvine'
+    email: abakis@uci.edu
+    orcid: 'https://orcid.org/0000-0002-5730-1483'
+  - given-names: Duncan K.
+    family-names: Ralph
+    affiliation: Fred Hutchinson Cancer Center
+    email: dralph@fredhutch.org
+    orcid: 'https://orcid.org/0000-0002-2527-8610'
+  - given-names: Sebastian
+    family-names: Prillo
+    affiliation: 'University of California, Berkeley'
+    email: sprillo@berkeley.edu
+    orcid: 'https://orcid.org/0000-0002-2427-8627'
+  - given-names: Frederick A.
+    family-names: Matsen
+    name-suffix: IV
+    affiliation: Fred Hutchinson Cancer Center
+    email: matsen@fredhutch.org
+    orcid: 'https://orcid.org/0000-0003-0607-6025'
+  - given-names: Yun S.
+    family-names: Song
+    affiliation: 'University of California, Berkeley'
+    email: yss@berkeley.edu
+    orcid: 'https://orcid.org/0000-0002-0734-9868'
+  - given-names: Volodymyr M.
+    family-names: Minin
+    affiliation: 'University of California, Irvine'
+    email: vminin@uci.edu
+    orcid: 'https://orcid.org/0000-0002-1917-9288'
+identifiers:
+  - type: doi
+    value: none
+    description: placeholder
+repository-code: 'https://github.com/WSDeWitt/BDMS'
+url: 'https://wsdewitt.github.io/BDMS'
+abstract: >-
+  BDMS is a Python package for simulating trees from
+  birth-death-mutation-sampling (BDMS) processes. It
+  is developed by collaborators at the University of
+  California, Berkeley and the University of
+  California, Irvine, and the Fred Hutchinson Cancer.
+license: MIT

bdms_sim-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 William DeWitt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bdms_sim-0.2.0/PKG-INFO

@@ -0,0 +1,27 @@
+Metadata-Version: 2.1
+Name: bdms-sim
+Version: 0.2.0
+Summary: Tree simulator for birth-death-mutation-sampling (BDMS) processes
+Project-URL: Homepage, https://github.com/WSDeWitt/BDMS
+Project-URL: Bug Tracker, https://github.com/WSDeWitt/BDMS/issues
+Project-URL: Documentation, https://wsdewitt.github.io/BDMS
+Author-email: Thanasi Bakis <abakis@uci.edu>, Michael Celentano <mcelentano@berkeley.edu>, William DeWitt <wsdewitt@gmail.com>, Frederick Matsen <ematsen@gmail.com>, Volodymyr Minin <yss@berkeley.edu>, Sebastian Prillo <sprillo@berkeley.edu>, Duncan Ralph <dkralph@gmail.com>, Yoonseo Song <ysong07@cs.washington.edu>, Yun Song <yss@berkeley.edu>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Requires-Dist: ete3
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pyqt5
+Requires-Dist: scipy
+Description-Content-Type: text/markdown
+
+[![build and test](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml)
+[![docs build and deploy](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml)
+
+# BDMS
+Tree simulator for birth-death-mutation-sampling (BDMS) processes
+
+Documentation: https://wsdewitt.github.io/BDMS

bdms_sim-0.2.0/README.md

@@ -0,0 +1,7 @@
+[![build and test](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/build-and-test.yml)
+[![docs build and deploy](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml/badge.svg)](https://github.com/WSDeWitt/BDMS/actions/workflows/docs-build-and-deploy.yml)
+
+# BDMS
+Tree simulator for birth-death-mutation-sampling (BDMS) processes
+
+Documentation: https://wsdewitt.github.io/BDMS

bdms_sim-0.2.0/bdms/__init__.py

@@ -0,0 +1,9 @@
+__version__ = "0.2.0"
+
+from .tree import TreeNode as _TreeNode
+
+TreeNode = _TreeNode
+"""Alias for :py:class:`bdms.tree.TreeNode`."""
+
+Tree = _TreeNode
+"""Alias for :py:class:`bdms.tree.TreeNode`."""

bdms_sim-0.2.0/bdms/mutators.py

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+r"""Mutation effects generators.
+
+Abstract base class for defining generic mutation effect generators (i.e.
+:math:`\mathcal{p}(x\mid x')`), with arbitrary :py:class:`ete3.TreeNode` attribute
+dependence. Some concrete child classes are included.
+
+These classes are used to define mutation effects for simulations with
+:py:class:`bdms.TreeNode.evolve`.
+
+Example:
+
+    >>> import bdms
+
+    Define a discrete mutation model.
+
+    >>> mutator = bdms.mutators.DiscreteMutator(
+    ...     state_space=["a", "b", "c"],
+    ...     transition_matrix=[[0.0, 0.5, 0.5],
+    ...                        [0.5, 0.0, 0.5],
+    ...                        [0.5, 0.5, 0.0]],
+    ... )
+
+    Mutate a node.
+
+    >>> node = bdms.TreeNode(state="a")
+    >>> mutator.mutate(node, seed=0)
+    >>> node.state
+    'c'
+"""
+
+from __future__ import annotations
+from abc import ABC, abstractmethod
+from typing import Any
+from collections.abc import Sequence, Callable, Hashable
+import numpy as np
+import scipy.stats as stats
+import ete3
+
+# NOTE: sphinx is currently unable to present this in condensed form when the
+#       sphinx_autodoc_typehints extension is enabled
+# TODO: use ArrayLike in various phenotype/time methods (current float types)
+#       once it is available in a stable release
+# from numpy.typing import ArrayLike
+from numpy.typing import NDArray
+
+
+class Mutator(ABC):
+    r"""Abstract base class for mutators that mutate a specified
+    :py:class:`ete3.TreeNode` node attribute.
+
+    Args:
+        attr: Node attribute to mutate.
+    """
+
+    def __init__(self, attr: str = "state", *args: Any, **kwargs: Any) -> None:
+        self.attr = attr
+
+    @abstractmethod
+    def mutate(
+        self,
+        node: ete3.TreeNode,
+        seed: int | np.random.Generator | None = None,
+    ) -> None:
+        r"""Mutate a :py:class:`bdms.TreeNode` object in place.
+
+        Args:
+            node: A :py:class:`bdms.TreeNode` to mutate.
+            seed: A seed to initialize the random number generation. If ``None``, then
+                  fresh, unpredictable entropy will be pulled from the OS. If an
+                  ``int``, then it will be used to derive the initial state. If a
+                  :py:class:`numpy.random.Generator`, then it will be used directly.
+        """
+
+    @abstractmethod
+    def prob(self, attr1: float, attr2: float, log: bool = False) -> float:
+        r"""Probability of mutating from ``attr1`` to ``attr2``.
+
+        Args:
+            attr1: The initial attribute value.
+            attr2: The final attribute value.
+            log: If ``True``, return the log-probability.
+
+        Returns:
+            Mutation probability (or log probability).
+        """
+
+    def __repr__(self) -> str:
+        keyval_strs = (
+            f"{key}={value}"
+            for key, value in vars(self).items()
+            if not key.startswith("_")
+        )
+        return f"{self.__class__.__name__}({', '.join(keyval_strs)})"
+
+
+class GaussianMutator(Mutator):
+    r"""Gaussian mutation effects on a specified attribute.
+
+    Args:
+        shift: Mean shift wrt current attribute value.
+        scale: Standard deviation of mutation effect.
+        attr: Node attribute to mutate.
+    """
+
+    def __init__(
+        self,
+        shift: float = 0.0,
+        scale: float = 1.0,
+        attr: str = "state",
+    ):
+        super().__init__(attr=attr)
+        self.shift = shift
+        self.scale = scale
+        self._distribution = stats.norm(loc=self.shift, scale=self.scale)
+
+    def mutate(
+        self,
+        node: ete3.TreeNode,
+        seed: int | np.random.Generator | None = None,
+    ) -> None:
+        current_state = getattr(node, self.attr)
+        Δ = self._distribution.rvs(random_state=seed)
+        setattr(node, self.attr, current_state + Δ)
+
+    def prob(self, attr1: float, attr2: float, log: bool = False) -> float:
+        Δ = np.asarray(attr2) - np.asarray(attr1)
+        if log:
+            return self._distribution.logpdf(Δ)  # type:ignore
+        return self._distribution.pdf(Δ)  # type:ignore
+
+
+class KdeMutator(Mutator):
+    r"""Gaussian kernel density estimator (KDE) for mutation effect on a specified
+    attribute.
+
+    Args:
+        data: Data to fit the KDE to.
+        attr: Node attribute to mutate.
+        bw_method: KDE bandwidth (see :py:class:`scipy.stats.gaussian_kde`).
+        weights: Weights of data points (see :py:class:`scipy.stats.gaussian_kde`).
+    """
+
+    def __init__(
+        self,
+        data: NDArray[np.float64],
+        attr: str = "state",
+        bw_method: str | float | Callable[..., float] | None = None,
+        weights: NDArray[np.float64] | None = None,
+    ):
+        super().__init__(attr=attr)
+        self._distribution = stats.gaussian_kde(data, bw_method, weights)
+
+    def mutate(
+        self,
+        node: ete3.TreeNode,
+        seed: int | np.random.Generator | None = None,
+    ) -> None:
+        current_state = getattr(node, self.attr)
+        Δ = self._distribution.resample(size=1, seed=seed)[0, 0]
+        setattr(node, self.attr, current_state + Δ)
+
+    def prob(self, attr1: float, attr2: float, log: bool = False) -> float:
+        Δ = np.asarray(attr2) - np.asarray(attr1)
+        if log:
+            return self._distribution.logpdf(Δ)
+        return self._distribution.pdf(Δ)
+
+
+class DiscreteMutator(Mutator):
+    r"""Mutations on a discrete space with a stochastic matrix.
+
+    Args:
+        state_space: hashable state values.
+        transition_matrix: Right-stochastic matrix, where column and row orders match
+                           the order of `state_space`.
+        attr: Node attribute to mutate.
+    """
+
+    def __init__(
+        self,
+        state_space: Sequence[Hashable],
+        transition_matrix: NDArray[np.float64],
+        attr: str = "state",
+    ):
+        transition_matrix = np.asarray(transition_matrix, dtype=float)
+        if not (
+            transition_matrix.ndim == 2
+            and transition_matrix.shape[0]
+            == transition_matrix.shape[1]
+            == len(state_space)
+        ):
+            raise ValueError(
+                f"Transition matrix shape {transition_matrix.shape} "
+                f"does not match state space size {state_space}"
+            )
+        if (
+            np.any(transition_matrix < 0)
+            or np.any(transition_matrix > 1)
+            or not np.allclose(transition_matrix.sum(axis=1), 1)
+        ):
+            raise ValueError(
+                f"Transition matrix {transition_matrix} is not a valid stochastic"
+                " matrix."
+            )
+
+        super().__init__(attr=attr)
+
+        self.state_space: dict[Any, int] = {
+            state: index for index, state in enumerate(state_space)
+        }
+        """Mapping from state values to their indices in the transition matrix."""
+        self.transition_matrix = transition_matrix
+
+    def mutate(
+        self,
+        node: ete3.TreeNode,
+        seed: int | np.random.Generator | None = None,
+    ) -> None:
+        rng = np.random.default_rng(seed)
+        transition_probs = self.transition_matrix[
+            self.state_space[getattr(node, self.attr)], :
+        ]
+        new_value = rng.choice(list(self.state_space.keys()), p=transition_probs)
+        setattr(node, self.attr, new_value)
+
+    def prob(self, attr1: float, attr2: float, log: bool = False) -> float:
+        result = self.transition_matrix[
+            self.state_space[attr1], self.state_space[attr2]
+        ]
+        if log:
+            result = np.log(result)
+        return result