c-spikes 0.2.0rc1__tar.gz

c_spikes-0.2.0rc1/.github/actionlint.yaml

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+self-hosted-runner:
+  labels: [c-spikes-cuda]

c_spikes-0.2.0rc1/.github/workflows/build.yml

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+name: Build and test
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  workflow_dispatch:
+  workflow_call:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: build-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+env:
+  UV_LINK_MODE: copy
+
+jobs:
+  native:
+    name: Native CPU / ${{ matrix.os }} / Python 3.14
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, ubuntu-24.04-arm, windows-2022, macos-14]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          version: 0.12.1
+          python-version: "3.14"
+          enable-cache: true
+      - name: Linux prerequisites
+        if: runner.os == 'Linux'
+        run: sudo apt-get update && sudo apt-get install -y gfortran pkg-config zip unzip
+      - name: macOS prerequisites
+        if: runner.os == 'macOS'
+        run: |
+          brew install gcc@14 pkgconf
+          echo "FC=$(brew --prefix gcc@14)/bin/gfortran-14" >> "$GITHUB_ENV"
+          echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> "$GITHUB_ENV"
+      - uses: actions/cache@caa296126883cff596d87d8935842f9db880ef25 # v5
+        with:
+          path: build/vcpkg-installed
+          key: native-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('vcpkg.json', 'cmake/triplets/*', 'cmake/ports/**', 'scripts/build_native.py') }}
+      - name: Install the development package
+        run: uv sync --locked
+      - name: Test Windows wheel repair
+        if: runner.os == 'Windows'
+        run: uv run --no-sync python -m pytest tests/packaging/test_windows_wheel_repair.py --csp-profile all
+      - name: Test the editable installation
+        run: |
+          uv run --no-sync python tests/packaging/wheel_smoke.py --backend cpu --import-order numpy-first
+          uv run --no-sync python tests/packaging/wheel_smoke.py --backend cpu --import-order native-first
+      - name: Build, repair, and test installed wheel
+        run: uv run --no-sync python scripts/build_native.py --backend cpu --test --output-dir dist/native-cpu
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
+        if: always()
+        with:
+          name: native-cpu-${{ runner.os }}-${{ runner.arch }}
+          path: |
+            dist/native-cpu
+            build/*/Testing/Temporary/LastTest.log
+          if-no-files-found: warn
+
+  packaging:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          version: 0.12.1
+          python-version: "3.12"
+      - run: uv sync --locked --no-install-project
+      - run: uv run --no-sync python -m pytest tests/packaging/test_release_validation.py tests/packaging/test_build_platforms.py --csp-profile all
+
+  wheels:
+    uses: ./.github/workflows/wheels.yml
+
+  sdist:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          version: 0.12.1
+          python-version: "3.12"
+          enable-cache: true
+      - run: uv sync --locked --no-install-project
+      - run: uv run --no-sync python -m build --sdist --outdir dist/sdist
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
+        with:
+          name: sdist
+          path: dist/sdist/*.tar.gz
+          if-no-files-found: error

c_spikes-0.2.0rc1/.github/workflows/cuda-hardware.yml

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+name: CUDA hardware validation
+
+# Opt-in only: never execute pull-request code on a private GPU runner.
+on:
+  workflow_dispatch:
+    inputs:
+      os:
+        description: Registered GPU runner operating system
+        type: choice
+        options: [Linux, Windows]
+        required: true
+      host_architecture:
+        description: Registered GPU runner CPU architecture (ARM64 requires Linux)
+        type: choice
+        options: [x64, ARM64]
+        default: x64
+        required: true
+      architecture:
+        description: GPU architecture of the selected runner
+        type: choice
+        options: [PORTABLE, TURING75, AMPERE80, AMPERE86, ADA89, HOPPER90, BLACKWELL100, BLACKWELL103, BLACKWELL120, BLACKWELL121]
+        default: PORTABLE
+        required: true
+
+permissions:
+  contents: read
+
+jobs:
+  hardware:
+    if: inputs.os == 'Linux' || inputs.host_architecture == 'x64'
+    runs-on: [self-hosted, "${{ inputs.os }}", "${{ inputs.host_architecture }}", c-spikes-cuda]
+    timeout-minutes: 90
+    env:
+      UV_LINK_MODE: copy
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          version: 0.12.1
+          python-version: "3.12"
+      - run: uv sync --locked --no-install-project
+      - run: uv run --no-sync python scripts/prepare_cuda.py
+      - run: uv run --no-sync python scripts/build_native.py --backend cuda --cuda-root build/tools/cuda-12.9.1 --cuda-arch ${{ inputs.architecture }} --test --output-dir dist/cuda-hardware
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
+        if: always()
+        with:
+          name: cuda-hardware-${{ runner.os }}-${{ runner.arch }}-${{ inputs.architecture }}
+          path: |
+            dist/cuda-hardware
+            build/*/Testing/Temporary/LastTest.log
+          if-no-files-found: warn

c_spikes-0.2.0rc1/.github/workflows/release.yml

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+name: Publish tagged release to PyPI
+
+on:
+  push:
+    tags: ["v*"]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: pypi-release-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  version:
+    if: github.repository == 'gerardjb/C-SPIKES'
+    runs-on: ubuntu-24.04
+    timeout-minutes: 5
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Validate release tag and source
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          python3 scripts/validate_release.py version --tag "$RELEASE_TAG"
+          git merge-base --is-ancestor HEAD origin/main
+
+  build:
+    needs: version
+    uses: ./.github/workflows/build.yml
+
+  prepare:
+    needs: build
+    runs-on: ubuntu-24.04
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          persist-credentials: false
+      # Select combined Linux/Windows wheels and CPU-only Apple Silicon wheels.
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8
+        with:
+          name: wheels-Linux-X64-cuda
+          path: dist/release
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8
+        with:
+          name: wheels-Windows-X64-cuda
+          path: dist/release
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8
+        with:
+          name: wheels-macOS-ARM64-cpu
+          path: dist/release
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8
+        with:
+          name: wheels-Linux-ARM64-cuda
+          path: dist/release
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8
+        with:
+          name: sdist
+          path: dist/release
+      - name: Validate the full matrix and record distribution hashes
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          python3 scripts/validate_release.py bundle --tag "$RELEASE_TAG" --directory dist/release
+          echo '### Validated release artifacts' >> "$GITHUB_STEP_SUMMARY"
+          echo '```json' >> "$GITHUB_STEP_SUMMARY"
+          cat release-manifest.json >> "$GITHUB_STEP_SUMMARY"
+          echo '```' >> "$GITHUB_STEP_SUMMARY"
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
+        with:
+          name: pypi-distributions
+          path: |
+            dist/release/*.whl
+            dist/release/*.tar.gz
+            release-manifest.json
+          if-no-files-found: error
+
+  publish:
+    needs: prepare
+    runs-on: ubuntu-24.04
+    timeout-minutes: 10
+    environment:
+      name: pypi
+      url: https://pypi.org/p/c-spikes
+    permissions:
+      id-token: write
+    steps:
+      # No package checkout or build in the job holding the publishing identity.
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8
+        with:
+          name: pypi-distributions
+          path: prepared
+      - name: Verify the prepared bytes
+        run: |
+          python3 - <<'PY'
+          import hashlib, json
+          from pathlib import Path
+          root = Path('prepared')
+          manifest = json.loads((root / 'release-manifest.json').read_text())
+          files = list((root / 'dist/release').iterdir())
+          assert {p.name for p in files} == set(manifest['files']), 'Distribution set changed'
+          for path in files:
+              with path.open('rb') as stream:
+                  assert hashlib.file_digest(stream, 'sha256').hexdigest() == manifest['files'][path.name], path.name
+          PY
+      - name: Publish platform wheels and sdist using Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0
+        with:
+          packages-dir: prepared/dist/release/
+          attestations: true
+          skip-existing: false
+          print-hash: true

c_spikes-0.2.0rc1/.github/workflows/wheels.yml

@@ -0,0 +1,66 @@
+name: Build wheel artifacts
+
+on:
+  workflow_call:
+    inputs:
+      backend:
+        type: string
+        default: cuda
+
+permissions:
+  contents: read
+
+env:
+  UV_LINK_MODE: copy
+
+jobs:
+  build:
+    name: Wheels / ${{ matrix.os }} / ${{ matrix.backend }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-24.04
+            backend: ${{ inputs.backend }}
+          - os: ubuntu-24.04-arm
+            backend: ${{ inputs.backend }}
+          - os: windows-2022
+            backend: ${{ inputs.backend }}
+          - os: macos-14
+            backend: cpu
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 180
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          version: 0.12.1
+          python-version: "3.12"
+          enable-cache: true
+      - run: uv sync --locked --no-install-project --group ci
+      - name: macOS prerequisites
+        if: runner.os == 'macOS'
+        run: |
+          brew install gcc@14 pkgconf
+          echo "FC=$(brew --prefix gcc@14)/bin/gfortran-14" >> "$GITHUB_ENV"
+          echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> "$GITHUB_ENV"
+      - uses: actions/cache@caa296126883cff596d87d8935842f9db880ef25 # v5
+        if: runner.os != 'Linux'
+        with:
+          path: build/vcpkg-installed
+          key: native-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('vcpkg.json', 'cmake/triplets/*', 'cmake/ports/**', 'scripts/build_native.py') }}
+      - name: Build repaired CPython 3.11–3.14 wheels
+        env:
+          WHEEL_BACKEND: ${{ matrix.backend }}
+        shell: bash
+        run: uv run --no-sync python scripts/build_wheels.py --backend "$WHEEL_BACKEND" --output-dir "dist/wheels-$WHEEL_BACKEND"
+      # Hosted runners cannot execute CUDA kernels. The separate hardware
+      # workflow and build_native.py --test qualify CUDA runtime behavior.
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
+        with:
+          name: wheels-${{ runner.os }}-${{ runner.arch }}-${{ matrix.backend }}
+          path: dist/wheels-${{ matrix.backend }}/*.whl
+          if-no-files-found: error

c_spikes-0.2.0rc1/.gitignore

@@ -0,0 +1,261 @@
+# python dev stuff
+__pycache__
+*.py[cod]
+*bin/
+*build/
+*dist/
+*env/
+
+# C
+*.so
+*.o
+*.a
+*.dylib
+*.dSYM/
+.DS_Store
+
+# Windows native build outputs
+*.obj
+*.dll
+*.lib
+*.exp
+*.pdb
+*.ilk
+*.exe
+
+# Local CMake/Ninja builds and IDE settings
+/build-*/
+/cmake-build-*/
+CMakeFiles/
+CMakeCache.txt
+cmake_install.cmake
+CTestTestfile.cmake
+build.ninja
+.ninja_deps
+.ninja_log
+CMakeUserPresets.json
+.vs/
+/vcpkg_installed/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Data
+Ground_truth/*
+data/
+
+# Gui output dirs
+spike_inference/
+biophys_ml/
+!src/c_spikes/biophys_ml/
+!src/c_spikes/biophys_ml/**
+edges/
+
+# Misc in codebase
+vcpkg/
+.vscode/
+src/c_spikes/_version.py
+profiles/
+results/
+gt_noise_dir/
+!src/c_spikes/syn_gen/gt_noise_dir/
+!src/c_spikes/syn_gen/gt_noise_dir/**
+gt_data/
+logs/
+tmp/
+core*
+
+# kokkos tools
+kokkos-tools/
+
+# slurm stuff
+slurm-*.out
+
+# Outputs for syn_gen and cascade
+Ground_truth/*
+
+# Outputs for pgas test, when run outside of pytest.
+tests/sample_data/output/
+
+# Ignore slurm output files if any of those get made
+slurm-*.out
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+wheelhouse/
+*.whl
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+/release-manifest.json
+src/c_spikes/_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+# Commit uv.lock to pin development and CI dependencies.
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# codex things
+.codex/
+.codex_temp/

c_spikes-0.2.0rc1/.python-version

@@ -0,0 +1 @@
+3.14