Add @MonkeyBreaker's GitHub action for wheel building (#646)

* Merge with latest master, do not delete Azure CI, remove Py36, add Py310 and Apple Silicon

* Enable cross-compilation on macOS as done by @MonkeyBreaker in pyflagser and giotto-ph

* Linting in test_rips_complex

* Bump install-boost version to 2.3.1 (latest)

* Bumping cibuildwheel version to 2.9.0 (latest)

Co-authored-by: julian <monkeybreaker@protonmail.com>

.github/workflows/wheels.yml

@@ -0,0 +1,97 @@
+name: Build Wheels
+
+# https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions#onworkflow_dispatchinputs
+on :
+  workflow_dispatch:
+    inputs:
+      nightlyRelease:
+        description: 'Generates wheels for the nightly release'
+        type: boolean
+        required: true
+        default: false
+
+jobs:
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        include:
+          - os: ubuntu-latest
+            boost_install_dir: /home/runner/work
+          - os: macos-latest
+            boost_install_dir: /Users/runner/work
+          - os: windows-latest
+            boost_install_dir: D:\
+    env:
+      BOOST_VERSION: 1.76.0
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Change name to giotto-tda-nightly
+        if: ${{ github.event.inputs.nightlyRelease == true }}
+        run: |
+          set -e
+          sed -i "s/'giotto-tda'/'giotto-tda-nightly'/1" setup.py
+          sed -i 's/"giotto-tda"/"giotto-tda-nightly"/1' setup.py
+          sed -i "s/__version__.*/__version__ = '$(Build.BuildNumber)'/1" gtda/_version.py
+        shell: bash
+
+      - name: Create directories boost
+        run: |
+          cd ${{ matrix.boost_install_dir }}
+          mkdir -p boost/boost
+          cd -
+
+      - name: Cache boost ${{env.BOOST_VERSION}} in ${{ matrix.boost_install_dir }}
+        # FIXME For an unknown reason on windows runner, when the cache is hit
+        # The compilation fails because it doesn't find some headers
+        # I don't know if the cache is corrupted, for the moment hard to debug
+        if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }}
+        uses: actions/cache@v2
+        id: cache-boost
+        with:
+          # Set the default path as the path to cache
+          path: ${{ matrix.boost_install_dir }}/boost/boost
+            # Use the version as the key to only cache the correct version
+          key: 1-boost-${{env.BOOST_VERSION}}
+
+      - name: Install boost ${{env.BOOST_VERSION}}
+        uses: MarkusJx/install-boost@v2.3.1
+        id: install-boost
+        if: steps.cache-boost.outputs.cache-hit != 'true'
+        with:
+          boost_version: ${{env.BOOST_VERSION}}
+          boost_install_dir: ${{ matrix.boost_install_dir }}
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.9.0
+        env:
+          # Specify which Python versions to build wheels
+          # https://cibuildwheel.readthedocs.io/en/stable/options/#build-skip
+          CIBW_BUILD: "cp37-* cp38-* cp39-* cp310-*"
+          # Skip 32 bit architectures, musllinux, and i686, and macOS x86_64 wheels for CP3.8 -- CP3.10
+          CIBW_SKIP: "*-win32 *-musllinux_x86_64 *_i686 cp38-macosx_x86_64 cp39-macosx_x86_64 cp310-macosx_x86_64"
+          CIBW_BEFORE_BUILD_WINDOWS: python -m pip install cmake && python -m pip install --upgrade pip setuptools && sed -i $'s/\r$//' README.rst && python -m pip install delvewheel
+          CIBW_BEFORE_BUILD_LINUX: python -m pip install cmake && python -m pip install --upgrade pip setuptools
+          CIBW_BEFORE_BUILD_MACOS: python -m pip install cmake && python -m pip install --upgrade pip setuptools
+          CIBW_TEST_COMMAND: python -m pytest --pyargs gtda
+          # nbformat is needed by plotly: https://github.com/plotly/plotly.py/issues/2159
+          CIBW_TEST_REQUIRES: pytest hypothesis pandas nbformat
+          CIBW_ENVIRONMENT_WINDOWS: BOOST_ROOT='${{ matrix.boost_install_dir }}boost\boost'
+          CIBW_ENVIRONMENT_MACOS: BOOST_ROOT='${{ matrix.boost_install_dir }}/boost'
+          CIBW_ENVIRONMENT_LINUX: BOOST_ROOT=/host${{ matrix.boost_install_dir }}/boost
+          CIBW_ENVIRONMENT_PASS_LINUX: BOOST_ROOT
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -vv -w {dest_dir} {wheel}"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          # Should generate universal2 wheels for CP3.8 -- CP3.10
+          CIBW_ARCHS_MACOS: x86_64 universal2
+
+      - uses: actions/upload-artifact@v2
+        name: Upload wheels
+        with:
+          path: ./wheelhouse/*.whl

doc/contributing/index.rst

@@ -6,8 +6,7 @@ Contributing
 
 This page contains a summary of what one needs to do to contribute.
 
-..
-   toctree::
+.. toctree::
    :maxdepth: 2
    :hidden:
 

gtda/externals/__init__.py

@@ -3,12 +3,14 @@
 
 from .modules.gtda_bottleneck import bottleneck_distance
 from .modules.gtda_wasserstein import wasserstein_distance
-from .python import SparseRipsComplex, CechComplex, CubicalComplex, \
-    PeriodicCubicalComplex, SimplexTree, WitnessComplex, StrongWitnessComplex
+from .python import RipsComplex, SparseRipsComplex, CechComplex, \
+    CubicalComplex, PeriodicCubicalComplex, SimplexTree, WitnessComplex, \
+    StrongWitnessComplex
 
 __all__ = [
     'bottleneck_distance',
     'wasserstein_distance',
+    'RipsComplex',
     'SparseRipsComplex',
     'CechComplex',
     'CubicalComplex',

gtda/externals/python/tests/test_rips_complex.py

@@ -1,14 +1,13 @@
 from .. import RipsComplex, SparseRipsComplex
 
-""" Test comes from
+"""Test comes from
 https://github.com/GUDHI/gudhi-devel/blob/master/src/python/test/test_rips_complex.py
-
 """
 
 
 def test_empty_rips():
     rips_complex = RipsComplex()
-    del(rips_complex)
+    del rips_complex
 
 
 def test_sparse_filtered_rips_from_points():

setup.py

@@ -129,6 +129,13 @@ def build_extension(self, ext):
             cmake_args += [f"-DCMAKE_BUILD_TYPE={cfg}"]
             build_args += ["--", "-j2"]
 
+        if sys.platform.startswith("darwin"):
+            # Cross-compile support for macOS - respect ARCHFLAGS if set
+            archs = re.findall(r"-arch (\S+)", os.environ.get("ARCHFLAGS", ""))
+            if archs:
+                cmake_args += \
+                    ["-DCMAKE_OSX_ARCHITECTURES={}".format(";".join(archs))]
+
         env = os.environ.copy()
         env["CXXFLAGS"] = f"{env.get('CXXFLAGS', '')} -DVERSION_INFO="\
                           f"\\'{self.distribution.get_version()}\\'"