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

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/build_and_deploy.yml

@@ -0,0 +1,52 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Build and Upload Python Package
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheel_and_sdist:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist and wheel
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: Packages
+          path: dist/*
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+  upload_pypi:
+    name: Upload release to PyPI
+    needs: [build_wheel_and_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/persim
+    permissions:
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/python-test.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8
+          pip install -e ".[testing]"
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest --cov persim
+      - name: Upload coverage results
+        run: |
+          bash <(curl -s https://codecov.io/bash)

RELEASE.txt

@@ -1,3 +1,7 @@
+0.3.6
+    - Update to pyproject.toml specification.
+    - Update github workflows.
+
 0.3.5
     - Fix broken notebook, Issue #77 (https://github.com/scikit-tda/persim/issues/77).
 

persim/_version.py

@@ -1 +1 @@
-__version__ = "0.3.5"
+__version__ = "0.3.6"

pyproject.toml

@@ -0,0 +1,69 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "persim"
+dynamic = ["version"]
+description = "Distances and representations of persistence diagrams"
+readme = "README.md"
+authors = [
+  { name = "Nathaniel Saul", email = "[email protected]" },
+  { name = "Chris Tralie", email = "[email protected]" },
+  { name = "Francis Motta", email = "[email protected]" },
+  { name = "Michael Catanzaro", email = "[email protected]" },
+  { name = "Gabrielle Angeloro", email = "[email protected]" },
+  { name = "Calder Sheagren", email = "[email protected]" },
+]
+maintainers = [
+  { name = "Nathaniel Saul", email = "[email protected]" },
+  { name = "Chris Tralie", email = "[email protected]" },
+  { name = "Michael Catanzaro", email = "[email protected]" },
+  { name = "Abraham Smith", email = "[email protected]" },
+]
+
+dependencies = [
+  "deprecated",
+  "hopcroftkarp",
+  "joblib",
+  "matplotlib",
+  "numpy",
+  "scikit-learn",
+]
+
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Education",
+  "Intended Audience :: Financial and Insurance Industry",
+  "Intended Audience :: Healthcare Industry",
+  "Topic :: Scientific/Engineering :: Information Analysis",
+  "Topic :: Scientific/Engineering :: Mathematics",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python",
+]
+
+
+keywords = [
+  "persistent homology",
+  "persistence images",
+  "persistence diagrams",
+  "topological data analysis",
+  "algebraic topology",
+  "unsupervised learning",
+  "supervised learning",
+  "machine learning",
+  "sliced wasserstein distance",
+  "bottleneck distance",
+]
+[project.optional-dependencies]
+testing = ["pytest", "pytest-cov"]
+
+docs = ["ripser", "sktda_docs_config"]
+
+[project.urls]
+Homepage = "https://persim.scikit-tda.org"
+Documentation = "https://persim.scikit-tda.org"
+Repository = "https://github.com/scikit-tda/persim"
+Issues = "https://github.com/scikit-tda/persim/issues"
+Changelog = "https://github.com/scikit-tda/persim/blob/master/RELEASE.txt"

setup.py

@@ -1,62 +1,18 @@
-#!/usr/bin/env python
-
-from setuptools import setup
-
-
+import setuptools
 import re
 
-VERSIONFILE = "persim/_version.py"
-verstrline = open(VERSIONFILE, "rt").read()
-VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
-mo = re.search(VSRE, verstrline, re.M)
-if mo:
-    verstr = mo.group(1)
-else:
-    raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
 
-with open("README.md") as f:
-    long_description = f.read()
+def get_version():
+    VERSIONFILE = "persim/_version.py"
+    verstrline = open(VERSIONFILE, "rt").read()
+    VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
+    mo = re.search(VSRE, verstrline, re.M)
+    if mo:
+        return mo.group(1)
+    else:
+        raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
+
 
-setup(
-    name="persim",
-    version=verstr,
-    description="Distances and representations of persistence diagrams",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author="Nathaniel Saul, Chris Tralie, Francis Motta, Michael Catanzaro, Gabrielle Angeloro, Calder Sheagren",
-    author_email="[email protected], [email protected], [email protected], [email protected], [email protected], [email protected]",
-    url="https://persim.scikit-tda.org",
-    license="MIT",
-    packages=["persim"],
-    include_package_data=True,
-    install_requires=[
-        "scikit-learn",
-        "numpy",
-        "matplotlib",
-        "scipy",
-        "hopcroftkarp",
-        "deprecated",
-        "joblib",
-    ],
-    extras_require={  # use `pip install -e ".[testing]"``
-        "testing": ["pytest", "pytest-cov"],
-        "docs": [  # `pip install -e ".[docs]"``
-            "sktda_docs_config"
-        ],
-    },
-    python_requires=">=3.6",
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "Intended Audience :: Science/Research",
-        "Intended Audience :: Education",
-        "Intended Audience :: Financial and Insurance Industry",
-        "Intended Audience :: Healthcare Industry",
-        "Topic :: Scientific/Engineering :: Information Analysis",
-        "Topic :: Scientific/Engineering :: Mathematics",
-        "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-    ],
-    keywords="persistent homology, persistence images, persistence diagrams, topological data analysis, algebraic topology, unsupervised learning, supervised learning, machine learning, sliced wasserstein distance, bottleneck distance",
+setuptools.setup(
+    version=get_version(),
 )