Merge branch 'main' into fix-symmetric-log-uniform

.github/workflows/basic-install.yml

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+name: Clean install
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # disable windows build test as bilby_cython is currently broken there
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install
+        run: python -m pip install .
+      - name: List environment
+        run: python -m pip list installed
+      - name: Test imports
+        run: |
+          python -c "import bilby"
+          python -c "import bilby.bilby_mcmc"
+          python -c "import bilby.core"
+          python -c "import bilby.core.prior"
+          python -c "import bilby.core.sampler"
+          python -c "import bilby.core.utils"
+          python -c "import bilby.gw"
+          python -c "import bilby.gw.detector"
+          python -c "import bilby.gw.eos"
+          python -c "import bilby.gw.likelihood"
+          python -c "import bilby.gw.sampler"
+          python -c "import bilby.hyper"
+          python -c "import cli_bilby"
+          python test/import_test.py
+      # - if: ${{ matrix.os != "windows-latest" }}
+      #   run: |
+      #     for script in $(pip show -f bilby | grep "bin\/" | xargs -I {} basename {}); do
+      #         ${script} --help;
+      #     done

.github/workflows/build-containers.yml

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+name: Build images
+
+on:
+  schedule:
+    - cron: "15 0 * * *" 
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-container:
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["310", "311", "312"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup dockerfile
+        run: |
+          cp containers/v3-dockerfile-test-suite-python${{ matrix.python-version }} Dockerfile
+          cp containers/env-template.yml .
+
+      - name: Login to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          tags: type=raw,value=latest
+          images: ghcr.io/${{ env.IMAGE_NAME }}-python${{ matrix.python-version }}
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          tags: ${{ steps.meta.outputs.tags }}
+          push: true
+          labels: ${{ steps.meta.outputs.labels }}
+
+      # FIXME: disabled as it is not working well but should probably be added in later
+      # https://docs.github.com/en/actions/security-for-github-actions/using-artifact-attestations/using-artifact-attestations-to-establish-provenance-for-builds
+      # - name: Generate artifact attestation
+      #   uses: actions/attest-build-provenance@v1
+      #   with:
+      #     subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+      #     subject-digest: ${{ steps.push.outputs.digest }}
+      #     push-to-registry: true

.github/workflows/pages.yml

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+name: GitHub Pages
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+  packages: read
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: ghcr.io/bilby-dev/bilby-python311:latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+      - name: install
+        run: python -m pip install .
+      - name: Run jupyter notebooks
+        run: |
+          python -m ipykernel install
+          cd examples/tutorials
+          jupyter nbconvert --to notebook --execute *.ipynb --output-dir ../../docs
+          cd -
+      - name: Build docs
+        run: |
+          cd docs
+          make clean
+          make html
+          cd -
+      # Upload the build docs as an artifact until we expose the pages
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html/
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main'
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/pre-commit.yml

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+name: pre-commit
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+    - name: Install jupyter
+      run: |
+        python -m pip install jupyterlab
+    - uses: pre-commit/[email protected]
+    - uses: pre-commit-ci/[email protected]
+      if: always()

.github/workflows/publish.yml

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+name: Publish Python distribution to PyPI
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/unit-tests.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Unit testing
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    container: ghcr.io/bilby-dev/bilby-python311:latest
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install package
+      run: |
+        python -m pip install .
+        conda list --show-channel-urls
+    # - name: Run precommits
+    #   run: |
+    #     pre-commit run --all-files --verbose --show-diff-on-failure
+    - name: Run unit tests
+      run: |
+        pytest --cov=bilby --durations 10
+    - name: Run sampler tests
+      run: |
+        pytest test/integration/sampler_run_test.py --durations 10 -v