Update code cov (#210)

* Bump action versions

* Suppress no array bound warnings on windows

* Only get test coverage for source files

* Skipping py314 free-threaded builds for now

* Update CI to use ruff instead of flake8

* Update README

* Update dependabot message prefix

* Update changelog

* Explicitly add macos14 for testing

* Fix incorrect specification for os in test-conda job

* try removing libpython for conda tests for windows

* drop py3.14 for conda; sklearn not supp yet

* Add plotting test

Author: catanzaromj

.github/dependabot.yml

@@ -7,3 +7,5 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+    commit-message:
+      prefix: "chore(deps): "

.github/workflows/build_and_deploy.yml

@@ -19,6 +19,7 @@ jobs:
             ubuntu-24.04-arm,
             windows-latest,
             macos-13,
+            macos-14,
             macos-latest,
           ]
 
@@ -38,7 +39,7 @@ jobs:
           CIBW_TEST_COMMAND: "pytest {project}/tests"
           CIBW_TEST_SKIP: "*win32 *musllinux* cp314t-*"
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
@@ -56,7 +57,7 @@ jobs:
       - name: Build sdist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           name: cibw-sdist
           path: dist/*.tar.gz
@@ -72,7 +73,7 @@ jobs:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v6
         with:
           # unpacks all CIBW artifacts into dist/
           pattern: cibw-*

.github/workflows/python-tests.yml

@@ -11,11 +11,30 @@ on:
   workflow_dispatch:
 
 jobs:
+  lint_and_format_check_with_ruff:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - uses: astral-sh/ruff-action@v3
+        with:
+          args: "format --check"
+
+      - uses: astral-sh/ruff-action@v3
+        with:
+          args: "check"
+
   test:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        os: ["ubuntu-latest", "macos-latest", "macos-14"]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -30,45 +49,49 @@ jobs:
           python -m pip install --upgrade pip
           pip install flake8 pytest-cov Cython
           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-report=xml --cov-report=term --cov=src/ripser
+
       - name: Upload coverage results
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
         uses: codecov/codecov-action@v5
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           name: ripser
           verbose: true
-          fail_ci_if_error: true
+          fail_ci_if_error: false
 
   test-conda:
-    runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] # 3.14 not supported by conda yet
+        os: ["macos-latest", "macos-14"]
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v5
-      - uses: conda-incubator/setup-miniconda@v3
+
+      - name: Set up miniconda
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           activate-environment: test
-      - name: Set up conda
+
+      - name: Install conda dependencies
         shell: bash -l {0}
         run: |
-          conda install git numpy pandas scipy matplotlib pytest cython
+          conda install numpy scipy scikit-learn matplotlib pytest cython
           git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
-          python -m pip install .
+
+      - name: Install ripser with pip in conda environment
+        shell: bash -l {0}
+        run: |
+          pip install -e ".[testing]"
+
       - name: Test with pytest
         shell: bash -l {0}
         run: |
@@ -79,7 +102,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - uses: actions/checkout@v5
@@ -92,7 +115,7 @@ jobs:
         shell: bash -l {0}
         run: |
           echo -e "[build]\ncompiler=msvc\n" >> setup.cfg
-          conda install git numpy pandas scipy matplotlib pytest libpython cython
+          conda install git numpy pandas scipy matplotlib pytest cython
           git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
           python -m pip install .
       - name: Test with pytest

CHANGELOG.md

@@ -1,126 +1,140 @@
-# 0.6.11
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.6.13] - 2025-11-26 
+
+### Fixed
+
+    - Fix broken wheel and conda builds for macos. Include python 3.14. Use ruff for linting and formatting. Update CI actions.
+    - No code changes.
+
+## [0.6.11]  
 
     - Update cocycle notebook (fix #83).
 
-# 0.6.10
+## [0.6.10]
 
     - Update build process to include python code and wheels. No code change.
 
-# 0.6.9
+## [0.6.9]
 
     - Convert package to `src` style.
     - Fix build command not including python source files.
 
-# 0.6.8
+## [0.6.8]
 
     - Update CD commands for newer build system.
 
-# 0.6.7
+## [0.6.7]
 
     - Failed to build wheels. This version does not exist.
 
-# 0.6.6
+## [0.6.6]
 
     - Failed to build wheels. This version does not exist.
 
-# 0.6.5
+## [0.6.5]
 
     - Bugfix for lower star filtrations with edges that come in at exactly 0 (courtesy of Riccardo Ceccaroni)
 
-# 0.6.4
+## [0.6.4]
 
     - Add some includes to ripser.cpp for newer Ubuntu/C++ environments
 
-# 0.6.3
+## [0.6.3]
 
     - Update numpy header
 
-# 0.6.2
+## [0.6.2]
 
     - Prevent simplex assembly in last dimension for improved memory usage (courtesy of Umberto Lupo)
 
-# 0.6.1
+## [0.6.1]
 
     - Lazy import plotting dependencies
 
-# 0.6.0
+## [0.6.0]
 
     - Update C++ backend to commit 286d369 of [ripser](https://github.com/Ripser/ripser) but keeping same functionalities
     - Add support to robinhood hashmap into the C++ Backend
     - Update CI in order to compile C++ with robinhood enable
     - Enable Enclosing radius when threshold is set to infinity
 
-# 0.5.5
+## [0.5.5]
 
     - Updating CI/CD pipeline.
 
-# 0.5.4
+## [0.5.4]
 
     - Fixing issue with inconsistent answers from different scipy.sparse formats, courtesy of Umberto Lupo
 
-# 0.5.3
+## [0.5.3]
 
     - Adding link to ripser++ GPU version by Simon Zhang
 
-# 0.5.2:
+## [0.5.2]2]
 
     - Cocycle indices now correspond to point cloud indices, even
       when a greedy permutation is in use
 
-# 0.4.1:
+## [0.4.1]
 
     - Fixed packing so C++ is MSVC compatible.
 
-# 0.4.0:
+## [0.4.0]
 
     - Added license to distributed packages.
 
-# 0.3.2:
+## [0.3.2]2]
 
     - Added support for greedy permutations.
     - Outsourced plotting to persim.
     - Outsourced data construction in examples to tadasets.
     - Revamped documentation.
 
-# 0.3.0:
+## [0.3.0]
 
     - Completed JOSS review, thanks @lmcinnes and @arokem!!
     - Documentation details updated.
 
-# 0.2.7:
+## [0.2.7]
 
     - Updating home url
 
-# 0.2.6:
+## [0.2.6]6]
 
     - Update license to MIT.
 
-# 0.2.5:
+## [0.2.5]
 
     - Docs and notebooks revamp.
     - Support for Windows.
 
-# 0.2.4:
+## [0.2.4]
 
     - Interface redesign
 
-# 0.2.3:
+## [0.2.3]
 
     - Support for lower star filtrations
     - Notebook on lower star filtrations
 
-# 0.2.1:
+## [0.2.1]1]
 
     - Sparse distance matrix support
     - Two additional notebooks about sparsity
     - Language agnostic bindings support
     - Bug fixes (filtrations with low number of points)
 
-# 0.2.0:
+## [0.2.0]
 
     - Bug fixes (int rounding error for small magnitude threshold)
 
-# 0.1.7:
+## [0.1.7]
 
     - Generation of cocycles.
     - Handle inf in C code and in plotting.

README.md

@@ -7,6 +7,7 @@
 [![Build status](https://ci.appveyor.com/api/projects/status/020nrvrq2rdg2iu1?svg=true)](https://ci.appveyor.com/project/sauln/ripser-py)
 [![codecov](https://codecov.io/gh/scikit-tda/ripser.py/branch/master/graph/badge.svg)](https://codecov.io/gh/scikit-tda/ripser.py)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 # Ripser.py
 
@@ -111,10 +112,16 @@ rips.plot(diagrams)
 
 # Contributions
 
-We welcome all kinds of contributions! Please get in touch if you would like to help out. Everything from code to notebooks to examples and documentation are all equally valuable so please don't feel you can't contribute. To contribute please fork the project make your changes and submit a pull request. We will do our best to work through any issues with you and get your code merged into the main branch.
+We welcome all kinds of contributions! Please get in touch if you would like to
+help out. Everything from code to notebooks to examples and documentation are
+all equally valuable so please don't feel you can't contribute.
+To contribute please fork the project make your changes and submit a pull request. See scikit-tda's
+[contributing docs](https://github.com/scikit-tda/scikit-tda/blob/master/CONTRIBUTING.md) for more
+detailed information. We will do our best to work through any issues with you and get your code merged into the main branch.
 
 If you found a bug, have questions, or are just having trouble with the library, please open an issue in our [issue tracker](https://github.com/scikit-tda/ripser.py/issues/new) and we'll try to help resolve the concern.
 
+
 # License
 
 Ripser.py is available under an MIT license! The core C++ code is derived from Ripser, which is also available under an MIT license and copyright to Ulrich Bauer. The modifications, Python code, and documentation is copyright to Christopher Tralie and Nathaniel Saul.

docs/conf.py

@@ -1,26 +1,29 @@
 # -*- coding: utf-8 -*-
 import os
 import sys
-sys.path.insert(0, os.path.abspath('.'))
+
+sys.path.insert(0, os.path.abspath("."))
 from ripser import __version__
 from sktda_docs_config import *
 
-project = u'Ripser.py'
-copyright = u'2019, Christopher Tralie and Nathaniel Saul'
-author = u'Christopher Tralie and Nathaniel Saul'
+project = "Ripser.py"
+copyright = "2019, Christopher Tralie and Nathaniel Saul"
+author = "Christopher Tralie and Nathaniel Saul"
 version = __version__
 release = __version__
-language = 'en'
+language = "en"
 
-html_theme_options.update({
-  # Google Analytics info
-  'ga_ua': 'UA-124965309-2',
-  'ga_domain': '',
-  'gh_url': 'scikit-tda/ripser.py'
-})
+html_theme_options.update(
+    {
+        # Google Analytics info
+        "ga_ua": "UA-124965309-2",
+        "ga_domain": "",
+        "gh_url": "scikit-tda/ripser.py",
+    }
+)
 
 html_short_title = project
-htmlhelp_basename = 'ripserdoc'
+htmlhelp_basename = "ripserdoc"
 
 # Set canonical URL from the Read the Docs Domain
 html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")