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Update to pyproject.toml specification, update workflows (#76)
* Add pyproject.toml * Remove old specs from setup.py * Add dependabot * Update build and deploy github workflow * Add ripser.py as an optional dependency * Update testing workflow, rename to test * Remove dist specification from action * Allow for python 3.7 * Remove python requirement; remove build, wheel, and toml setuptool requires * Bump version * Add Abe as maintainer
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‎.github/dependabot.yml‎

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# Set update schedule for GitHub Actions
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions every week
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interval: "weekly"

‎.github/workflows/build_and_deploy.yml‎

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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: Build and Upload Python Package
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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release:
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types:
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- published
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jobs:
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build_wheel_and_sdist:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Build SDist and wheel
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run: pipx run build
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- uses: actions/upload-artifact@v4
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with:
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name: Packages
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path: dist/*
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- name: Check metadata
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run: pipx run twine check dist/*
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upload_pypi:
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name: Upload release to PyPI
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needs: [build_wheel_and_sdist]
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/persim
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permissions:
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id-token: write
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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steps:
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- uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/python-app.yml‎

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‎.github/workflows/python-publish.yml‎

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‎.github/workflows/python-test.yml‎

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python application
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8
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pip install -e ".[testing]"
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pytest --cov persim
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- name: Upload coverage results
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run: |
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bash <(curl -s https://codecov.io/bash)

‎RELEASE.txt‎

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0.3.6
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- Update to pyproject.toml specification.
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- Update github workflows.
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0.3.5
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- Fix broken notebook, Issue #77 (https://github.com/scikit-tda/persim/issues/77).
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‎persim/_version.py‎

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__version__ = "0.3.5"
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__version__ = "0.3.6"

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools >= 61.0"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "persim"
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dynamic = ["version"]
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description = "Distances and representations of persistence diagrams"
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readme = "README.md"
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authors = [
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{ name = "Nathaniel Saul", email = "[email protected]" },
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{ name = "Chris Tralie", email = "[email protected]" },
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{ name = "Francis Motta", email = "[email protected]" },
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{ name = "Michael Catanzaro", email = "[email protected]" },
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{ name = "Gabrielle Angeloro", email = "[email protected]" },
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{ name = "Calder Sheagren", email = "[email protected]" },
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]
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maintainers = [
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{ name = "Nathaniel Saul", email = "[email protected]" },
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{ name = "Chris Tralie", email = "[email protected]" },
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{ name = "Michael Catanzaro", email = "[email protected]" },
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{ name = "Abraham Smith", email = "[email protected]" },
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]
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dependencies = [
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"deprecated",
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"hopcroftkarp",
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"joblib",
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"matplotlib",
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"numpy",
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"scikit-learn",
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Science/Research",
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"Intended Audience :: Education",
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"Intended Audience :: Financial and Insurance Industry",
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"Intended Audience :: Healthcare Industry",
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"Topic :: Scientific/Engineering :: Information Analysis",
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"Topic :: Scientific/Engineering :: Mathematics",
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"License :: OSI Approved :: MIT License",
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"Programming Language :: Python",
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]
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keywords = [
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"persistent homology",
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"persistence images",
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"persistence diagrams",
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"topological data analysis",
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"algebraic topology",
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"unsupervised learning",
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"supervised learning",
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"machine learning",
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"sliced wasserstein distance",
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"bottleneck distance",
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]
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[project.optional-dependencies]
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testing = ["pytest", "pytest-cov"]
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docs = ["ripser", "sktda_docs_config"]
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[project.urls]
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Homepage = "https://persim.scikit-tda.org"
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Documentation = "https://persim.scikit-tda.org"
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Repository = "https://github.com/scikit-tda/persim"
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Issues = "https://github.com/scikit-tda/persim/issues"
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Changelog = "https://github.com/scikit-tda/persim/blob/master/RELEASE.txt"

‎setup.py‎

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#!/usr/bin/env python
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from setuptools import setup
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import setuptools
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import re
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VERSIONFILE = "persim/_version.py"
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verstrline = open(VERSIONFILE, "rt").read()
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VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
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mo = re.search(VSRE, verstrline, re.M)
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if mo:
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verstr = mo.group(1)
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else:
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raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
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with open("README.md") as f:
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long_description = f.read()
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def get_version():
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VERSIONFILE = "persim/_version.py"
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verstrline = open(VERSIONFILE, "rt").read()
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VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
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mo = re.search(VSRE, verstrline, re.M)
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if mo:
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return mo.group(1)
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else:
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raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
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setup(
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name="persim",
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version=verstr,
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description="Distances and representations of persistence diagrams",
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long_description=long_description,
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long_description_content_type="text/markdown",
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author="Nathaniel Saul, Chris Tralie, Francis Motta, Michael Catanzaro, Gabrielle Angeloro, Calder Sheagren",
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author_email="[email protected], [email protected], [email protected], [email protected], [email protected], [email protected]",
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url="https://persim.scikit-tda.org",
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license="MIT",
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packages=["persim"],
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include_package_data=True,
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install_requires=[
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"scikit-learn",
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"numpy",
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"matplotlib",
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"scipy",
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"hopcroftkarp",
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"deprecated",
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"joblib",
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],
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extras_require={ # use `pip install -e ".[testing]"``
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"testing": ["pytest", "pytest-cov"],
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"docs": [ # `pip install -e ".[docs]"``
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"sktda_docs_config"
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],
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},
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python_requires=">=3.6",
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classifiers=[
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Science/Research",
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"Intended Audience :: Education",
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"Intended Audience :: Financial and Insurance Industry",
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"Intended Audience :: Healthcare Industry",
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"Topic :: Scientific/Engineering :: Information Analysis",
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"Topic :: Scientific/Engineering :: Mathematics",
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"License :: OSI Approved :: MIT License",
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"Programming Language :: Python :: 3.6",
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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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],
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keywords="persistent homology, persistence images, persistence diagrams, topological data analysis, algebraic topology, unsupervised learning, supervised learning, machine learning, sliced wasserstein distance, bottleneck distance",
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setuptools.setup(
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version=get_version(),
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)

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