Modernise the python package and testing infrastructure

.github/workflows/build-wheels.yml

@@ -10,66 +10,87 @@ on:
   release:
     types:
       - published
-
-env:
-  CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
-  CIBW_SKIP: cp3*-musllinux_*
-  CIBW_ARCHS_MACOS: x86_64
-  CIBW_ARCHS_LINUX: auto64
-  CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-  CIBW_BEFORE_ALL_LINUX: yum -y install boost-devel zlib-devel
-  CIBW_BEFORE_ALL_MACOS: brew install boost zlib gsl
-  CIBW_BEFORE_BUILD: pip install --upgrade pip setuptools wheel ninja numpy cython
-  CIBW_ENVIRONMENT_MACOS: CXX="$(brew --prefix llvm@15)/bin/clang++"
-  MACOSX_DEPLOYMENT_TARGET: 10.15
+  workflow_dispatch:
 
 jobs:
-  build_wheels:
+  build_wheels_cloud:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        include:
+          - os: ubuntu-24.04
+            arch: x86_64
+            py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            py-vers-pr: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            before-all: dnf -y install boost-devel zlib
+            extra-env: ""
+            mdt: ""
+          - os: ubuntu-24.04-arm
+            arch: aarch64
+            py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            py-vers-pr: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            before-all: dnf -y install boost-devel zlib
+            extra-env: ""
+            mdt: ""
+          - os: macos-15-intel
+            arch: x86_64
+            py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            py-vers-pr: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            before-all: brew install boost zlib
+            extra-env: CC=clang CXX=clang++
+            mdt: 15
+          - os: macos-14
+            arch: arm64
+            py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            py-vers-pr: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+            before-all: brew install boost zlib
+            extra-env: CC=clang CXX=clang++
+            mdt: 14
+
+    env:
+      CIBW_BUILD: ${{ github.event_name != 'pull_request' && matrix.py-vers-full || matrix.py-vers-pr }}
+      CIBW_SKIP: cp3*-musllinux_*
+      CIBW_ARCHS: ${{ matrix.arch }}
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+      CIBW_BEFORE_ALL: ${{ matrix.before-all }}
+      CIBW_BEFORE_BUILD: pip install --upgrade pip setuptools wheel ninja numpy cython
+      CIBW_ENVIRONMENT: ${{ matrix.extra-env }}
+      MACOSX_DEPLOYMENT_TARGET: ${{ matrix.mdt }}
 
     steps:
 
       - name: checkout repo & submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
+          submodules: true
           fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v3
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.12.0
-
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
+        uses: pypa/cibuildwheel@v3.2.0
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-cloud-${{ matrix.os }}
           path: ./wheelhouse/*.whl
           retention-days: 1
 
   upload_all:
     name: Upload to PyPI
-    needs: build_wheels
+    needs: [build_wheels_cloud]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: ${{ github.event_name == 'release' && github.event.action == 'published' }}
 
     steps:
-      - uses: actions/setup-python@v3
-
-      - name: Download wheels
-        uses: actions/download-artifact@v3
+      - name: Download wheels from cloud runners
+        uses: actions/download-artifact@v5
         with:
-          name: wheels
+          pattern: wheels-cloud-*
+          merge-multiple: true
           path: wheels
 
-      - uses: pypa/gh-action-pypi-publish@v1.6.4
+      - uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/cpp_tests.yml

@@ -0,0 +1,64 @@
+name: C++ unit tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - '**'
+  workflow_dispatch:
+
+jobs:
+
+  build-and-test:
+    name: C++ unit tests
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-24.04
+            cxx: "clang++-18"
+            sys_install: "sudo apt -y update && sudo apt -y install libboost-iostreams-dev"
+          - os: ubuntu-24.04-arm
+            cxx: "g++-12"
+            sys_install: "sudo apt -y update && sudo apt -y install libboost-iostreams-dev"
+          - os: macos-15
+            cxx: ""
+            sys_install: "brew install boost"
+          - os: macos-15
+            cxx: "$(brew --prefix llvm@18)/bin/clang"
+            sys_install: "brew install boost"
+
+    steps:
+      - name: checkout repo & submodules
+        uses: actions/checkout@v5
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - name: install deps
+        run: |
+          ${{ matrix.sys_install }}
+
+      - name: make build dir
+        run: |
+          mkdir build
+
+      - name: cmake configure
+        run: |
+          cmake ..
+        working-directory: build
+
+      - name: cmake build
+        run: |
+          cmake --build . --target cpp_tests --parallel 4
+        working-directory: build
+
+      - name: ctest
+        run: |
+          ctest --output-on-failure
+        working-directory: build

.github/workflows/python_examples.yml

@@ -0,0 +1,77 @@
+name: Python examples
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - '**'
+  workflow_dispatch:
+
+jobs:
+
+  build-and-test:
+    name: Python examples
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-24.04
+            py: "3.10"
+            sys_install: "sudo apt -y update && sudo apt -y install libboost-iostreams-dev"
+          - os: macos-15
+            py: "3.13"
+            sys_install: "brew install boost"
+
+    steps:
+      - name: checkout repo & submodules
+        uses: actions/checkout@v5
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - name: install deps
+        run: |
+          ${{ matrix.sys_install }}
+
+      - name: Set up Python ${{ matrix.py }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.py }}
+
+      - name: install python bindings
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install .
+
+      - name: prepare example
+        run: |
+          prepare_example
+
+      - name: regular ARG-Needle
+        run: |
+          infer_args
+
+      - name: ARG-Needle with ASMC-clust
+        run: |
+          infer_args --asmc_clust 1
+
+      - name: ARG-Needle without ARG normalization
+        run: |
+          infer_args --normalize 0
+
+      - name: ARG-Needle (sequence mode)
+        run: |
+          prepare_example --mode sequence --length 5e5
+          infer_args --mode sequence
+
+      - name: ARG-Needle advanced mode (multistep)
+        run: |
+          prepare_example
+          infer_args_advanced --step 1 --num_snp_samples 200
+          infer_args_advanced --step 2
+          infer_args_advanced --step 3 --trim_num_snps 0,50