cellflow-tools 0.0.2__tar.gz

cellflow_tools-0.0.2/.codecov.yaml

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+codecov:
+  require_ci_to_pass: true
+  strict_yaml_branch: main
+
+coverage:
+  range: "80...100"
+  status:
+    project:
+      default:
+        target: 75%
+        threshold: 1%
+    patch: off
+
+comment:
+  layout: "reach, diff, files"
+  behavior: default
+  require_changes: true
+  branches: [main]

cellflow_tools-0.0.2/.cruft.json

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+{
+	"template": "https://github.com/scverse/cookiecutter-scverse",
+	"commit": "aa877587e59c855e2464d09ed7678af00999191a",
+	"checkout": null,
+	"context": {
+		"cookiecutter": {
+			"project_name": "cell_flow_perturbation",
+			"package_name": "cellflow",
+			"project_description": "Modeling complex perturbations with flow matching and optimal transport",
+			"author_full_name": "Dominik Klein",
+			"author_email": "dominik.klein@helmholtz-munich.de",
+			"github_user": "MUCDK",
+			"project_repo": "https://github.com/theislab/cell_flow_perturbation",
+			"license": "BSD 3-Clause License",
+			"_copy_without_render": [
+				".github/workflows/build.yaml",
+				".github/workflows/test.yaml",
+				"docs/_templates/autosummary/**.rst"
+			],
+			"_render_devdocs": false,
+			"_jinja2_env_vars": {
+				"lstrip_blocks": true,
+				"trim_blocks": true
+			},
+			"_template": "https://github.com/scverse/cookiecutter-scverse"
+		}
+	},
+	"directory": null
+}

cellflow_tools-0.0.2/.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}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

cellflow_tools-0.0.2/.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: Version information
+      description: |
+        Please paste below the output of
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```
+      placeholder: |
+        -----
+        anndata             0.8.0rc2.dev27+ge524389
+        session_info        1.0.0
+        -----
+        asttokens           NA
+        awkward             1.8.0
+        backcall            0.2.0
+        cython_runtime      NA
+        dateutil            2.8.2
+        debugpy             1.6.0
+        decorator           5.1.1
+        entrypoints         0.4
+        executing           0.8.3
+        h5py                3.7.0
+        ipykernel           6.15.0
+        jedi                0.18.1
+        mpl_toolkits        NA
+        natsort             8.1.0
+        numpy               1.22.4
+        packaging           21.3
+        pandas              1.4.2
+        parso               0.8.3
+        pexpect             4.8.0
+        pickleshare         0.7.5
+        pkg_resources       NA
+        prompt_toolkit      3.0.29
+        psutil              5.9.1
+        ptyprocess          0.7.0
+        pure_eval           0.2.2
+        pydev_ipython       NA
+        pydevconsole        NA
+        pydevd              2.8.0
+        pydevd_file_utils   NA
+        pydevd_plugins      NA
+        pydevd_tracing      NA
+        pygments            2.12.0
+        pytz                2022.1
+        scipy               1.8.1
+        setuptools          62.5.0
+        setuptools_scm      NA
+        six                 1.16.0
+        stack_data          0.3.0
+        tornado             6.1
+        traitlets           5.3.0
+        wcwidth             0.2.5
+        zmq                 23.1.0
+        -----
+        IPython             8.4.0
+        jupyter_client      7.3.4
+        jupyter_core        4.10.0
+        -----
+        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+        -----
+        Session information updated at 2022-07-07 17:55

cellflow_tools-0.0.2/.github/ISSUE_TEMPLATE/config.yml

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+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.

cellflow_tools-0.0.2/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new feature for cell_flow_perturbation
+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

cellflow_tools-0.0.2/.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
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl

cellflow_tools-0.0.2/.github/workflows/lint.yml

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+name: Lint
+
+on:
+  schedule:
+    - cron: 00 00 * * 1
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint ${{ matrix.lint-kind }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        lint-kind: [code]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Cache pre-commit
+        uses: actions/cache@v3
+        if: ${{ matrix.lint-kind == 'code' }}
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox
+
+      - name: Install PyEnchant
+        if: ${{ matrix.lint-kind == 'docs' }}
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install libenchant-2-dev
+          python -m pip install pyenchant
+
+      - name: Lint ${{ matrix.lint-kind }}
+        run: |
+          tox -e lint-${{ matrix.lint-kind }}

cellflow_tools-0.0.2/.github/workflows/release.yml

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+name: Release
+
+on:
+  release:
+    types: [published]
+
+# 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/cellflow
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

cellflow_tools-0.0.2/.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
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.11"
+          - os: ubuntu-latest
+            python: "3.12"
+          - os: macos-latest
+            python: "3.12"
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+      - name: Install dependencies
+        run: |
+          pip install tox
+          pip install ${{ matrix.pip-flags }} ".[optional-dependencies.dev,optional-dependencies.test,optional-dependencies.external,optional-dependencies.docs,optional-dependencies.embedding]"
+          pip install wandb omegaconf
+      - name: Test
+        run: |
+          tox -e py-${{ matrix.python }}
+        env:
+          PYTEST_ADDOPTS: -vv -n 2
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: theislab/cell_flow_perturbation

cellflow_tools-0.0.2/.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/
+pip-wheel-metadata/
+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/
+*test_save_load_Problem.pkl
+*test_plot.png
+
+# 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/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# editors
+.idea
+
+# docs
+docs/**/genapi
+
+# macOS
+*.DS_Store
+
+# benchmarks
+notebooks/*.pdf
+*.pickle
+*.h5ad
+*.p
+
+# UML generation
+classes.dot
+packages.dot
+
+# vscode
+.vscode
+
+# plotting tests
+tests/plotting/actual_figures/
+
+# huggingface
+hub/

cellflow_tools-0.0.2/.pre-commit-config.yaml

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+repos:
+  # Hooks that are run everywhere
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
+    hooks:
+      - id: biome-format
+  # Hooks that are run for scripts
+  - 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: v0.9.9
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        files: ^(src|tests)/
+      - id: ruff-format
+        files: ^(src|tests)/

cellflow_tools-0.0.2/.readthedocs.yaml

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+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-22.04
+  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: [docs, external, embedding, dev]
+
+submodules:
+  include: [docs/notebooks]
+  recursive: true

cellflow_tools-0.0.2/CHANGELOG.md

@@ -0,0 +1,15 @@
+# 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

cellflow_tools-0.0.2/LICENSE

@@ -0,0 +1,71 @@
+# PolyForm Noncommercial License 1.0.0
+
+<https://polyformproject.org/licenses/noncommercial/1.0.0>
+
+## Acceptance
+
+In order to get any license under these terms, you must agree to them as both strict obligations and conditions to all your licenses.
+
+## Copyright License
+
+The licensor grants you a copyright license for the software to do everything you might do with the software that would otherwise infringe the licensor's copyright in it for any permitted purpose. However, you may only distribute the software according to [Distribution License](#distribution-license) and make changes or new works based on the software according to [Changes and New Works License](#changes-and-new-works-license).
+
+## Distribution License
+
+The licensor grants you an additional copyright license to distribute copies of the software. Your license to distribute covers distributing the software with changes and new works permitted by [Changes and New Works License](#changes-and-new-works-license).
+
+## Required Notices
+
+Copyright © Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
+
+## Changes and New Works License
+
+The licensor grants you an additional copyright license to make changes and new works based on the software for any permitted purpose.
+
+## Patent License
+
+The licensor grants you a patent license for the software that covers patent claims the licensor can license, or becomes able to license, that you would infringe by using the software.
+
+## Noncommercial Purposes
+
+Any noncommercial purpose is a permitted purpose.
+
+## Personal Uses
+
+Personal use for research, experiment, and testing for the benefit of public knowledge, personal study, private entertainment, hobby projects, amateur pursuits, or religious observance, without any anticipated commercial application, is use for a permitted purpose.
+
+## Noncommercial Organizations
+
+Use by any charitable organization, educational institution, public research organization, public safety or health organization, environmental protection organization, or government institution is use for a permitted purpose regardless of the source of funding or obligations resulting from the funding.
+
+## Fair Use
+
+You may have "fair use" rights for the software under the law. These terms do not limit them.
+
+## No Other Rights
+
+These terms do not allow you to sublicense or transfer any of your licenses to anyone else, or prevent the licensor from granting licenses to anyone else. These terms do not imply any other licenses.
+
+## Patent Defense
+
+If you make any written claim that the software infringes or contributes to infringement of any patent, your patent license for the software granted under these terms ends immediately. If your company makes such a claim, your patent license ends immediately for work on behalf of your company.
+
+## Violations
+
+The first time you are notified in writing that you have violated any of these terms, or done anything with the software not covered by your licenses, your licenses can nonetheless continue if you come into full compliance with these terms, and take practical steps to correct past violations, within 32 days of receiving notice. Otherwise, all your licenses end immediately.
+
+## No Liability
+
+**_As far as the law allows, the software comes as is, without any warranty or condition, and the licensor will not be liable to you for any damages arising out of these terms or the use or nature of the software, under any kind of legal claim._**
+
+## Definitions
+
+The **licensor** is the individual or entity offering these terms, and the **software** is the software the licensor makes available under these terms.
+
+**You** refers to the individual or entity agreeing to these terms.
+
+**Your company** is any legal entity, sole proprietorship, or other kind of organization that you work for, plus all organizations that have control over, are under the control of, or are under common control with that organization. **Control** means ownership of substantially all the assets of an entity, or the power to direct its management and policies by vote, contract, or otherwise. Control can be direct or indirect.
+
+**Your licenses** are all the licenses granted to you for the software under these terms.
+
+**Use** means anything you do with the software requiring one of your licenses.