Refactor project for PyPI distribution and wheel packaging

[pyomp]
- Move to a src layout
- Remove dependency on LLVM binaries in pyomp
- Add versioning
- Try-except without error for CUDALegalization (removed in recent numba) for
  CUDA lowering
- Remove deprecated compile_isolated usage and update tests
- Remove static libnrt building to avoid numba version dependency and use
  trampolines to link numba symbols to openmp target cpu modules
- Add hello world examples
- Update README

[ci]
- Create pypi workflow
- Add test pipelines for multiple platforms, numba, and python versions
- Simplify conda pipeline

[openmp libraries]
- Build openmp libraries through setup.py using LLVM static libraries from
  conda env
- Add patches for missing includes and link statically with LLVM libs

[pyomp pass]
- Export entry point function to interface with python for running the pass
- Link pass plugin with LLVM static libraries from conda env

[packaging]
- Extend range of supported numba (0.57-0.60) and python versions (3.9-3.12)
- Make target offloading mandatory in tests
- Remove building the static library in setup.py

[packaging.wheel]
- Add cibuildwheel scripts
- Add MANIFEST.in
- Add license files
- Upload pre-release to testpypi, full release to pyp
- Build and publish sdist

[packaging.conda]
- Remove llvm-openmp-dev recipe
- Add missing deps in meta.yaml
- Upload as a separate command to detect errors
- Use "main" tag for full release for conda packages, "test" for pre-release,
  "dev" for PR

[container]
- Update dockerfile to avoid TOS issues
- Add pyomp's version to the container

Author: ggeorgakoudis

.github/workflows/build-containers.yml

@@ -9,22 +9,24 @@ jobs:
     steps:
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
- 
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
- 
+
       - name: Login to GitHub Container Registry
         uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
- 
+
       - name: Build and push pyomp container
         uses: docker/build-push-action@v6
         with:
           platforms: linux/amd64,linux/arm64
           file: buildscripts/containers/Dockerfile
           push: true
           provenance: false
-          tags: ghcr.io/python-for-hpc/pyomp:latest
+          tags: |
+            ghcr.io/python-for-hpc/pyomp:latest
+            ghcr.io/python-for-hpc/pyomp:${{ github.event.release.tag_name }}

.github/workflows/build-upload-conda-base.yml

@@ -1,18 +1,81 @@
-name: Deploy conda pkgs (main)
+name: conda
 
 on:
   release:
     types: [published]
+  pull_request:
+    paths:
+      - "buildscripts/conda-recipes/**"
+      - ".github/workflows/build-upload-conda.yml"
+      - "src/**"
+      - setup.py
+      - MANIFEST.in
+      - pyproject.toml
   workflow_dispatch:
 
 jobs:
+  # Job to deploy pyomp conda matrixed on os and python version.
   deploy-conda:
-    uses: ./.github/workflows/build-upload-conda-base.yml
-    with:
-      label: main
-      env: .github/workflows/envs/env.yml
-    secrets: inherit
+    name: ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    env:
+      CONDA_LABEL: dev
+    strategy:
+      matrix:
+        # TODO: Add windows.
+        os: [ubuntu-latest, macos-latest, ubuntu-24.04-arm]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - name: Determine conda label
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
+            echo "CONDA_LABEL=dev" >> $GITHUB_ENV
+          elif [[ "${{ github.event_name }}" == "release" && "${{ github.event.release.prerelease }}" == "true" ]]; then
+            echo "CONDA_LABEL=test" >> $GITHUB_ENV
+          else
+            echo "CONDA_LABEL=main" >> $GITHUB_ENV
+          fi
+
+      - uses: actions/checkout@v4
+        # Checkout the repo with history to get the commit hash for the build
+        # string.
+        with:
+          fetch-depth: 0
+
+      - name: Create and activate conda env
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: "3.10"
+          auto-update-conda: false
+          show-channel-urls: true
+
+      - name: Build and upload pyomp
+        # This ensures conda env is active.
+        shell: bash -l {0}
+        run: |
+          # Setup the anaconda environment.
+          conda remove --name base conda-anaconda-telemetry
+          conda install -q -y -c conda-forge conda-build conda-verify anaconda-client
+          conda config --set anaconda_upload no
+
+          # Build the package.
+          conda build \
+            -c conda-forge \
+            --python ${{ matrix.python-version }} \
+            buildscripts/conda-recipes/pyomp
+
+          # Get the output file path.
+          OUTPUT=$(conda build -c conda-forge --output \
+            --python ${{ matrix.python-version }} \
+            buildscripts/conda-recipes/pyomp)
+
+          # Upload the package.
+          anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload \
+            --user python-for-hpc --label ${{ env.CONDA_LABEL}} \
+            --force "$OUTPUT"
+
   deploy-containers:
     needs: deploy-conda
+    if: github.event_name == 'release' && !github.event.release.prerelease
     uses: ./.github/workflows/build-containers.yml
     secrets: inherit

.github/workflows/build-upload-conda-test.yml

@@ -0,0 +1,150 @@
+name: pypi
+
+on:
+  release:
+    types: [published]
+  pull_request:
+    paths:
+      - "buildscripts/cibuildwheel/**"
+      - ".github/workflows/build-upload-wheels.yml"
+      - "src/**"
+      - setup.py
+      - MANIFEST.in
+      - pyproject.toml
+  workflow_dispatch:
+
+jobs:
+  # Always runs: Build wheels for all platforms and upload artifacts.
+  build-wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # TODO: Add windows.
+        os: [ubuntu-latest, macos-latest, ubuntu-24.04-arm]
+    steps:
+      - uses: actions/checkout@v4
+        # Checkout the repo with history to get the commit hash for the build
+        # string.
+        with:
+          fetch-depth: 0
+
+       # Used to host cibuildwheel.
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==3.1.4
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build-sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  # Always runs: Test wheels across OS/Python/Numba matrix.
+  test-wheels:
+    needs: build-wheels
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, ubuntu-24.04-arm]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        numba-version: ['0.57.0', '0.57.1', '0.58.0', '0.58.1', '0.59.0', '0.59.1', '0.60.0']
+        exclude:
+        # Known incompatibilities based on numba's official support
+        # Numba 0.57 supports Python 3.8-3.11
+        - python-version: '3.12'
+          numba-version: '0.57.0'
+        - python-version: '3.12'
+          numba-version: '0.57.1'
+
+        # Numba 0.58 supports Python 3.8-3.11
+        - python-version: '3.12'
+          numba-version: '0.58.0'
+        - python-version: '3.12'
+          numba-version: '0.58.1'
+    steps:
+      - name: Download built wheels
+        uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install and test wheel
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "numba==${{ matrix.numba-version }}" lark cffi setuptools
+          python -m pip install --pre --no-deps --no-index --find-links dist/ pyomp
+
+          # Verify the numba version.
+          python -c "import numba; assert numba.__version__ == '${{ matrix.numba-version }}'"
+
+          # Run host OpenMP tests.
+          TEST_DEVICES=0 RUN_TARGET=0 python -m numba.runtests -v -- numba.openmp.tests.test_openmp
+
+          # Run device (cpu target) OpenMP tests.
+          OMP_TARGET_OFFLOAD=mandatory TEST_DEVICES=1 RUN_TARGET=1 \
+            python -m numba.runtests -v -- numba.openmp.tests.test_openmp.TestOpenmpTarget
+
+  # Only on pre-release: Publish to TestPyPI for testing.
+  publish-testpypi:
+    needs: [build-wheels, test-wheels, build-sdist]
+    if: github.event.release.prerelease
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Publish testpypi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+  # Only on full release: Publish to production PyPI.
+  publish-pypi:
+    needs: [build-wheels, test-wheels, build-sdist]
+    if: github.event_name == 'release' && !github.event.release.prerelease
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Publish pypi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true