simind-python-connector 1.2.0__tar.gz → 2.0.1__tar.gz

simind_python_connector-2.0.1/.github/workflows/containers.yml

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+name: Container tests
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 3 * * 1"
+  pull_request:
+    paths:
+      - "simind_python_connector/recon/**"
+      - "simind_python_connector/connectors/**"
+      - "simind_python_connector/builders/**"
+      - "simind_python_connector/utils/interfile.py"
+      - "docker/**"
+
+jobs:
+  sirf:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-buildx-action@v3
+      - uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: docker/sirf/Dockerfile
+          tags: simind-python-connector/sirf:ci
+          load: true
+          cache-from: type=gha,scope=sirf
+          cache-to: type=gha,mode=max,scope=sirf
+      - name: SIRF and CIL tests
+        run: >
+          docker run --rm -e CI=true -v "$PWD:/workspace" -w /workspace
+          simind-python-connector/sirf:ci
+          python -m pytest -q -m "(requires_sirf or requires_cil) and not requires_simind"
+
+  stir:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-buildx-action@v3
+      - uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: docker/stir/Dockerfile
+          tags: simind-python-connector/stir:ci
+          load: true
+          cache-from: type=gha,scope=stir
+          cache-to: type=gha,mode=max,scope=stir
+      - name: STIR tests
+        run: >
+          docker run --rm -e CI=true -v "$PWD:/workspace" -w /workspace
+          simind-python-connector/stir:ci
+          python -m pytest -q -m "requires_stir and not requires_simind"

simind_python_connector-2.0.1/.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches: [ main, develop, "release/**" ]
+  pull_request:
+    branches: [ main, develop, "release/**" ]
+  workflow_call:
+    inputs:
+      ref:
+        description: Ref (for example a release tag) to check out and document
+        required: false
+        type: string
+        default: ""
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+      - name: Check the tag matches the documented version
+        run: |
+          # Python 3.10 (matched to Read the Docs) predates the TOML parser in
+          # the standard library, so read [project] version with pathlib/re.
+          version=$(python -c 'import pathlib, re; text = pathlib.Path("pyproject.toml").read_text(encoding="utf-8"); project = re.search(r"(?ms)^\[project\].*?(?=^\[|\Z)", text).group(0); print(re.search(r"(?m)^version\s*=\s*\"([^\"]+)\"", project).group(1))')
+          if [[ "$GITHUB_REF_NAME" == v* ]] && [ "$GITHUB_REF_NAME" != "v${version}" ]; then
+            echo "Tag $GITHUB_REF_NAME does not match version v${version}"
+            exit 1
+          fi
+      - name: Build the documentation without executing examples
+        env:
+          SIMIND_GALLERY_BACKEND: ""
+        run: |
+          python -m sphinx -b html -W --keep-going docs docs/_build/html
+      - name: Check the generated gallery indexes are committed
+        run: |
+          git status --porcelain -- docs/auto_examples
+          test -z "$(git status --porcelain -- docs/auto_examples)"
+      - name: Upload the built documentation
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/_build/html

simind_python_connector-2.0.1/.github/workflows/publish.yml

@@ -0,0 +1,47 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  tests:
+    uses: ./.github/workflows/tests.yml
+    with:
+      ref: ${{ github.event.release.tag_name }}
+
+  docs:
+    uses: ./.github/workflows/docs.yml
+    with:
+      ref: ${{ github.event.release.tag_name }}
+
+  publish:
+    needs: [tests, docs]
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.release.tag_name }}
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Check the tag matches the package version
+        run: |
+          version=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])")
+          if [ "$GITHUB_REF_NAME" != "v${version}" ]; then
+            echo "Tag $GITHUB_REF_NAME does not match version v${version}"
+            exit 1
+          fi
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check dist/*
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

simind_python_connector-2.0.1/.github/workflows/tests.yml

@@ -0,0 +1,91 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, develop, "release/**" ]
+  pull_request:
+    branches: [ main, develop, "release/**" ]
+  workflow_call:
+    inputs:
+      ref:
+        description: Ref (for example a release tag) to check out and test
+        required: false
+        type: string
+        default: ""
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+      - name: Lint and format check with ruff
+        run: |
+          ruff check .
+          ruff format --check .
+      - name: Check gallery outputs are current
+        run: python scripts/check_gallery_current.py
+      - name: Run CI-friendly tests
+        run: |
+          python -m pytest -m "not integration and not requires_sirf and not requires_stir and not requires_simind and not requires_pytomography and not requires_cil and not ci_skip and not validation and not macos_v9" --cov=simind_python_connector --cov-report=xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+      - name: Build package
+        run: |
+          python -m build
+      - name: Check package
+        run: |
+          twine check dist/*
+      - name: Smoke-test wheel resources outside the checkout
+        run: |
+          repo="$GITHUB_WORKSPACE"
+          venv="$(mktemp -d)/wheel-env"
+          python -m venv "$venv"
+          "$venv/bin/python" -m pip install --quiet dist/*.whl
+          workdir="$(mktemp -d)"
+          cd "$workdir"
+          "$venv/bin/python" "$repo/scripts/check_wheel_resources.py" --repo "$repo"
+
+  container-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+      - name: Core container validation
+        run: bash scripts/run_container_validation.sh --only-core
+
+      - name: Core container examples (SIMIND optional)
+        run: bash scripts/run_container_examples.sh --only-core

simind_python_connector-2.0.1/.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: ubuntu-22.04         
+  tools:
+    python: "3.10"        
+
+sphinx:
+  configuration: docs/conf.py
+  # Fail the public deployment on any warning (including a duplicate object
+  # description) so it matches the docs job in .github/workflows/docs.yml.
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev

simind_python_connector-2.0.1/.zenodo.json

@@ -0,0 +1,35 @@
+{
+  "title": "simind-python-connector: Python SIMIND Monte Carlo connector with STIR/SIRF/PyTomography adaptors",
+  "upload_type": "software",
+  "description": "A Python package providing SIMIND Monte Carlo simulation connector with adaptors for STIR/SIRF and PyTomography reconstruction frameworks. Enables Python-driven SIMIND simulations and data processing workflows.",
+  "creators": [
+    {
+      "name": "Porter, Sam",
+      "affiliation": "University College London",
+      "orcid": "0000-0002-1815-4716"
+    },
+    {
+      "name": "Varzakis, Efstathios (Stahis)",
+      "affiliation": "University College London",
+      "orcid": "0000-0003-3503-7754"
+    },
+    {
+      "name": "Thielemans, Kris",
+      "affiliation": "University College London",
+      "orcid": "0000-0001-6353-9538"
+    }
+  ],
+  "keywords": [
+    "SPECT",
+    "Monte Carlo",
+    "medical imaging",
+    "SIMIND",
+    "SIRF",
+    "STIR",
+    "PyTomography",
+    "Python"
+  ],
+  "access_right": "open",
+  "license": "apache-2.0",
+  "version": "2.0.1"
+}