ci: Update codecov, update compilation flags

Swap out Ofast for O3 in compile args

Ofast is deprecated, and it defaults to `-O3 -ffast-math`. `ffast-math`
does not handle infinities correctly, which lead to failures on all the
macos runners and wheel builds.

Bump action versions

Suppress no array bound warnings on windows

Only get test coverage for source files

Try skipping py314 free-threaded builds for now

Author: catanzaromj

.github/workflows/build_and_deploy.yml

@@ -23,20 +23,20 @@ jobs:
           ]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Clone robinhood
         run: |
           git clone https://github.com/martinus/robin-hood-hashing robinhood
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.3
+        uses: pypa/cibuildwheel@v3.2.0
         env:
-          CIBW_SKIP: "pp* cp36-* cp37-* *win_arm64 *_i686"
+          CIBW_SKIP: "*win_arm64 *_i686"
           CIBW_BUILD_VERBOSITY: 1
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: "pytest {project}/tests"
-          CIBW_TEST_SKIP: "*win32 *musllinux*"
+          CIBW_TEST_SKIP: "*win32 *musllinux* cp314t-*"
 
       - uses: actions/upload-artifact@v4
         with:
@@ -47,7 +47,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Clone robinhood
         run: |
@@ -72,7 +72,7 @@ jobs:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           # unpacks all CIBW artifacts into dist/
           pattern: cibw-*

.github/workflows/python-tests.yml

@@ -19,9 +19,9 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -38,7 +38,7 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          pytest --cov-report=xml --cov=./
+          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
@@ -57,7 +57,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
@@ -82,7 +82,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true

setup.py

@@ -41,7 +41,7 @@ def run(self):
         build_ext.run(self)
 
 
-extra_compile_args = ["-Ofast", "-D_hypot=hypot"]
+extra_compile_args = ["-O3", "-D_hypot=hypot"]
 extra_link_args = []
 
 if platform.system() == "Windows":