ENH: Multiple CI changes

* Main one is a new script to quickly test python-only changes using cached wheels
* Duplicate wheels.yml because I can't figure out how to set matrix dynamically, and
  build a subset of wheels on push to master
* Set main wheels.yml to build the full matrix nightly, or upon release creation

.github/workflows/ci-pytest.yml

@@ -0,0 +1,104 @@
+name: ci-pytest
+
+# Fast tests with cached antspy build designed to test changes in the python code
+# Builds on Linux only, with a single python version
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
+env:
+  # Updates or changes to this, or the runner OS or arch will invalidate the cache
+  python_version: '3.10' # Python version to use for testing - update when needed
+
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+    # Default shell needs to be bash for conda
+    # https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#important
+    defaults:
+        run:
+          shell: bash -el {0}
+    steps:
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # v3.0.3, devs recommend using hash
+      with:
+        miniconda-version: "latest"
+        python-version: ${{ env.python_version }}
+        auto-update-conda: true
+        activate-environment: "test-env"
+
+    - name: Configure Conda to use only .tar.bz2
+      run: |
+        conda config --set use_only_tar_bz2 true
+
+    - name: Checkout code
+      uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr'
+      with:
+        path: antspy-pr
+
+    - name: Load conda environment from cache if available
+      id: cache-env
+      uses: actions/cache@v4
+      with:
+        path: ~/conda-env.tar.bz2
+        key: >-
+            ${{ runner.os }}-conda-${{ env.python_version }}-
+            ${{ hashFiles('antspy-pr/ants/environment.yml', 'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py',
+            'antspy-pr/ants/scripts/configure_ITK.sh', 'antspy-pr/ants/scripts/configure_ANTsPy.sh',
+            'antspy-pr/ants/lib/*') }}
+
+    - name: Unpack cached environment
+      if: steps.cache-env.outputs.cache-hit == 'true'
+      run: |
+        mkdir -p ${CONDA}/envs/antspy-env
+        tar -xjf ~/conda-env.tar.bz2 -C ${CONDA}/envs/antspy-env
+        conda activate antspy-env
+        conda-unpack
+
+    - name: Install dependencies and ANTsPy from PR
+      if: steps.cache-env.outputs.cache-hit != 'true'
+      run: |
+        conda create -n antspy-env python=${{ env.python_version }} -y
+        conda activate antspy-env
+        conda install -c conda-forge conda-pack
+        conda info
+        pip install ./antspy-pr
+        conda list
+        antspy-pr/tests/run_tests.sh
+        conda pack -n antspy-env -o ~/conda-env.tar.bz2
+
+    - name: Cache Conda environment
+      if: steps.cache-env.outputs.cache-hit != 'true'
+      uses: actions/cache@v4
+      with:
+        path: ~/conda-env.tar.bz2
+        key: >-
+            ${{ runner.os }}-conda-${{ env.python_version }}-
+                ${{ hashFiles('antspy-pr/ants/environment.yml', 'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py',
+                'antspy-pr/ants/scripts/configure_ITK.sh', 'antspy-pr/ants/scripts/configure_ANTsPy.sh',
+                'antspy-pr/ants/lib/*') }}) }}
+
+    - name: Replace installed ANTsPy with PR code
+      if: steps.cache-env.outputs.cache-hit == 'true'
+      run: |
+        conda activate antspy-env
+        echo "List of installed packages in cached env:"
+        conda list
+        ANTS_SITE_PACKAGES="${CONDA}/envs/antspy-env/lib/python${{ env.python_version }}/site-packages/ants"
+        for d in contrib core learn registration segmentation utils viz; do
+          rm -rf $ANTS_SITE_PACKAGES/$d;
+          cp -r antspy-pr/ants/$d $ANTS_SITE_PACKAGES/$d;
+          done
+        find $ANTS_SITE_PACKAGES -name '__pycache__' -exec rm -rf {} +
+
+    - name: Run tests
+      if: steps.cache-env.outputs.cache-hit == 'true'
+      run: |
+        conda activate antspy-env
+        bash antspy-pr/tests/run_tests.sh

.github/workflows/wheels.yml

@@ -1,12 +1,8 @@
 name: Build
 
 on:
-  push:
-    branches:
-    - master
-  pull_request:
-    branches:
-    - master
+  schedule:
+    - cron: "0 2 * * *"
   release:
     types: [created]
   workflow_dispatch:
@@ -204,7 +200,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Publish prep
-        if: ${{ (github.event_name == 'push') && (runner.os == 'Linux') }}
+        if: ${{ (github.event_name == 'release') && (runner.os == 'Linux') }}
         run: |
           mywhl=`find ~/ -name "antspyx*.whl"`
           extrawheeldir=`dirname $mywhl`
@@ -218,7 +214,7 @@ jobs:
 
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-        if: ${{ (github.event_name == 'push') && (runner.os == 'Linux') }}
+        if: ${{ (github.event_name == 'release') && (runner.os == 'Linux') }}
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/wheels_faster.yml

@@ -0,0 +1,126 @@
+name: Cross-platform wheel test
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheel for cp${{ matrix.cibw_python }}-${{ matrix.platform_id }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # Have to specify python version twice so that the same python is used to build and test
+          # Need to quote decimal versions as string to avoid the "Norway problem"
+
+          # Windows 64-bit
+          - os: windows-latest
+            python: '3.9'
+            cibw_python: 39
+            platform_id: win_amd64
+
+            # Linux 64-bit
+          - os: ubuntu-latest
+            python: '3.9'
+            cibw_python: 39
+            platform_id: manylinux_x86_64
+
+          # macOS on Intel 64-bit
+          - os: macos-12
+            python: '3.9'
+            cibw_python: 39
+            arch: x86_64
+            platform_id: macosx_x86_64
+
+          # macOS on Apple M1 64-bit, supported for Python 3.10 and later
+          - os: macos-14
+            python: '3.10'
+            cibw_python: 310
+            arch: arm64
+            platform_id: macosx_arm64
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v5
+        name: Install Python host for cibuildwheel
+        with:
+          python-version: ${{ matrix.python }}
+
+        # Visual Studio
+      - name: Set up MSVC x64
+        if: matrix.platform_id == 'win_amd64'
+        uses: ilammy/msvc-dev-cmd@v1
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.16.2 setuptools
+
+      - name: Get package name and version (Linux / Mac)
+        if: ${{ ! startsWith(matrix.os, 'windows-') }}
+        run: |
+          echo PACKAGE_NAME=$( python setup.py --name ) >> $GITHUB_ENV
+          echo PACKAGE_VERSION=$( python setup.py --version ) >> $GITHUB_ENV
+
+      # Some shells require "-Encoding utf8" to append to GITHUB_ENV
+      # https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions?tool=powershell#environment-files
+      - name: Get package name and version (Windows)
+        if: startsWith(matrix.os, 'windows-')
+        run: |
+          echo "PACKAGE_NAME=$( python setup.py --name )" | Out-File -FilePath $env:GITHUB_ENV `
+          -Append
+          echo "PACKAGE_VERSION=$( python setup.py --version )" | Out-File -FilePath $env:GITHUB_ENV `
+          -Append
+      - name: Build wheels
+        env:
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+          CIBW_BUILD: cp${{ matrix.cibw_python }}-${{ matrix.platform_id }}
+
+          # Include latest Python beta
+          CIBW_PRERELEASE_PYTHONS: True
+
+          CIBW_BEFORE_ALL_LINUX: |
+            echo "Installing system dependencies with yum"
+            yum install -y gcc-c++ libpng-devel libpng
+            echo "pip installing cmake and ninja"
+            python -m pip install cmake ninja setuptools
+
+          CIBW_BEFORE_ALL_WINDOWS: |
+            python -m pip install cmake ninja setuptools
+
+          CIBW_ARCHS_MACOS: ${{ matrix.arch }}
+          CIBW_BEFORE_ALL_MACOS: |
+            python -m pip install cmake ninja setuptools
+            brew update
+            if ! brew list libpng &>/dev/null; then
+                HOMEBREW_NO_AUTO_UPDATE=1 brew install libpng
+            fi
+
+          CIBW_ENVIRONMENT_MACOS: |
+            CMAKE_OSX_ARCHITECTURES=${{ matrix.arch }} CMAKE_PREFIX_PATH=/usr/local
+
+        run: python -m cibuildwheel --output-dir wheelhouse/cp${{ matrix.cibw_python }}-${{matrix.platform_id }}
+
+      - name: Install and test (Linux / Mac)
+        if: ${{ ! startsWith(matrix.os, 'windows-') }}
+        run: |
+          python -m pip install wheelhouse/cp${{ matrix.cibw_python }}-${{matrix.platform_id }}/*.whl
+          tests/run_tests.sh
+
+      - name: Install and test (Windows)
+        if: startsWith(matrix.os, 'windows-')
+        run: |
+          python -m pip install --find-links=.\wheelhouse\cp${{ matrix.cibw_python }}-${{matrix.platform_id }} antspyx
+          tests\run_tests.ps1
+
+      - uses: actions/upload-artifact@v3
+        with:
+          retention-days: 3
+          name: ${{ env.PACKAGE_NAME }}-${{ env.PACKAGE_VERSION }}-cp${{ matrix.cibw_python }}-${{ matrix.platform_id }}
+          path: ./wheelhouse/cp${{ matrix.cibw_python }}-${{ matrix.platform_id }}/*.whl