pycea-lineage 0.0.1__tar.gz

pycea_lineage-0.0.1/.codecov.yaml

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+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 85
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

pycea_lineage-0.0.1/.cruft.json

@@ -0,0 +1,43 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
+  "context": {
+    "cookiecutter": {
+      "project_name": "pycea",
+      "package_name": "pycea",
+      "project_description": "Scverse lineage tracing toolkit",
+      "author_full_name": "William Colgan",
+      "author_email": "wcolgan@mit.edu",
+      "github_user": "colganwi",
+      "github_repo": "pycea",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+    }
+  },
+  "directory": null
+}

pycea_lineage-0.0.1/.editorconfig

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+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

pycea_lineage-0.0.1/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

pycea_lineage-0.0.1/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

pycea_lineage-0.0.1/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for pycea
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

pycea_lineage-0.0.1/.github/workflows/build.yaml

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+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

pycea_lineage-0.0.1/.github/workflows/release.yaml

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+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pycea-lineage
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

pycea_lineage-0.0.1/.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.12"
+          - os: ubuntu-latest
+            python: "3.12"
+            pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch test --cover --python ${{ matrix.python }}
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4

pycea_lineage-0.0.1/.gitignore

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+# Temp files
+.DS_Store
+*~
+buck-out/
+.ipynb_checkpoints/
+
+# Compiled files
+.venv/
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+
+# Distribution / packaging
+/build/
+/dist/
+/*.egg-info/
+
+# Tests and coverage
+/.pytest_cache/
+/.cache/
+/data/
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# IDEs
+/.idea/
+/.vscode/
+
+# Plots
+/tests/plots/*.png
+
+# Node modules
+node_modules/
+
+# Environment
+environment.yml
+
+# Datasets
+/datasets/

pycea_lineage-0.0.1/.pre-commit-config.yaml

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+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.5.1
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.2
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

pycea_lineage-0.0.1/.readthedocs.yaml

@@ -0,0 +1,18 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
+formats:
+  - pdf

pycea_lineage-0.0.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## [Unreleased]
+
+### Added
+
+-   Basic tool, preprocessing and plotting functions

pycea_lineage-0.0.1/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, William Colgan
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pycea_lineage-0.0.1/PKG-INFO

@@ -0,0 +1,136 @@
+Metadata-Version: 2.4
+Name: pycea-lineage
+Version: 0.0.1
+Summary: Scverse lineage tracing toolkit
+Project-URL: Documentation, https://pycea.readthedocs.io/
+Project-URL: Homepage, https://github.com/YosefLab/pycea
+Project-URL: Source, https://github.com/YosefLab/pycea
+Author: William Colgan
+Maintainer-email: William Colgan <wcolgan@mit.edu>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, William Colgan
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Requires-Dist: cycler
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: requests
+Requires-Dist: scanpy>=1.10
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: session-info
+Requires-Dist: treedata>=0.2
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine>=4.0.2; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb>=1.1; extra == 'doc'
+Requires-Dist: pandas; extra == 'doc'
+Requires-Dist: setuptools; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
+Requires-Dist: sphinx-book-theme>=1; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx-tabs; extra == 'doc'
+Requires-Dist: sphinx>=4; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=1; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+[![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/YosefLab/pycea/test.yaml?branch=main
+[link-tests]: https://github.com/YosefLab/pycea/actions/workflows/test.yml
+[badge-docs]: https://img.shields.io/readthedocs/pycea
+
+<img
+  src="https://raw.githubusercontent.com/YosefLab/pycea/main/docs/_static/img/pycea_logo.svg"
+  class="dark-light" align="right" width="350" alt="image"
+/>
+
+# Pycea - lineage tracing analysis
+
+Scverse lineage tracing analysis toolkit built to work with [TreeData][treedata].
+
+To learn more about pycea, please refer to the [documentation][link-docs] or the [getting started guide][link-getting-started].
+
+## Installation
+
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+There are several alternative options to install pycea:
+
+<!--
+1) Install the latest release of `pycea` from `PyPI <https://pypi.org/project/pycea/>`_:
+
+```bash
+pip install pycea
+```
+-->
+
+1. Install the latest development version:
+
+```bash
+pip install git+https://github.com/YosefLab/pycea.git@main
+```
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+For questions and bug reports please use the [issue tracker][issue-tracker].
+
+## Citation
+
+> t.b.a
+
+[treedata]: https://treedata.readthedocs.io/
+[scverse-discourse]: https://discourse.scverse.org/
+[issue-tracker]: https://github.com/YosefLab/pycea/issues
+[changelog]: https://pycea.readthedocs.io/latest/changelog.html
+[link-docs]: https://pycea.readthedocs.io
+[link-api]: https://pycea.readthedocs.io/latest/api.html
+[link-getting-started]: https://pycea.readthedocs.io/en/latest/notebooks/getting-started.html

pycea_lineage-0.0.1/README.md

@@ -0,0 +1,58 @@
+[![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/YosefLab/pycea/test.yaml?branch=main
+[link-tests]: https://github.com/YosefLab/pycea/actions/workflows/test.yml
+[badge-docs]: https://img.shields.io/readthedocs/pycea
+
+<img
+  src="https://raw.githubusercontent.com/YosefLab/pycea/main/docs/_static/img/pycea_logo.svg"
+  class="dark-light" align="right" width="350" alt="image"
+/>
+
+# Pycea - lineage tracing analysis
+
+Scverse lineage tracing analysis toolkit built to work with [TreeData][treedata].
+
+To learn more about pycea, please refer to the [documentation][link-docs] or the [getting started guide][link-getting-started].
+
+## Installation
+
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+There are several alternative options to install pycea:
+
+<!--
+1) Install the latest release of `pycea` from `PyPI <https://pypi.org/project/pycea/>`_:
+
+```bash
+pip install pycea
+```
+-->
+
+1. Install the latest development version:
+
+```bash
+pip install git+https://github.com/YosefLab/pycea.git@main
+```
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+For questions and bug reports please use the [issue tracker][issue-tracker].
+
+## Citation
+
+> t.b.a
+
+[treedata]: https://treedata.readthedocs.io/
+[scverse-discourse]: https://discourse.scverse.org/
+[issue-tracker]: https://github.com/YosefLab/pycea/issues
+[changelog]: https://pycea.readthedocs.io/latest/changelog.html
+[link-docs]: https://pycea.readthedocs.io
+[link-api]: https://pycea.readthedocs.io/latest/api.html
+[link-getting-started]: https://pycea.readthedocs.io/en/latest/notebooks/getting-started.html

pycea_lineage-0.0.1/biome.jsonc

@@ -0,0 +1,16 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}