pyg4ometry 1.1.2__tar.gz → 1.2.2__tar.gz

pyg4ometry-1.2.2/.github/bin/install-deps-fedora.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+yum -y update || exit 1
+yum -y install boost boost-devel gmp  gmp-devel  mpfr  mpfr-devel vtk-devel || exit 1
+
+# Install CGAL from source
+wget https://github.com/CGAL/cgal/releases/download/v5.6.1/CGAL-5.6.1.tar.xz
+tar xf CGAL-5.6.1.tar.xz
+cd CGAL-5.6.1 || exit 1
+cmake -DCMAKE_BUILD_TYPE=Release .
+make install || exit 1
+rm -rf cd CGAL-5.6.1
+
+# Install ROOT
+root_version="6.32.04"
+ROOTSYS="/opt/root"
+
+mkdir -p "$ROOTSYS" || exit 1
+wget -q -O- "https://root.cern/download/root_v${root_version}.Linux-fedora39-x86_64-gcc13.3.tar.gz" \
+    | tar --strip-components 1 -C "$ROOTSYS" --strip=1 -x -z || exit 1

pyg4ometry-1.2.2/.github/bin/install-deps-macos.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+brew update
+brew install --overwrite python # github's fault
+
+brew unlink python@3.11
+brew install --overwrite python@3.11 python@3.12
+brew link python@3.12
+
+brew unlink node@18
+brew install --overwrite node@18
+brew link node@18
+
+brew install boost cgal gmp mpfr opencascade vtk root numdiff
+
+# needed for cibuildwheel on macos
+export GMP_LIBRARIES=/opt/lib/
+export GMP_INCLUDE_DIR=/opt/include/

pyg4ometry-1.2.2/.github/bin/install-deps-windows.cmd

@@ -0,0 +1 @@
+conda install -c conda-forge cmake pybind11 cgal-cpp occt git

pyg4ometry-1.2.2/.github/workflows/distribution.yml

@@ -0,0 +1,153 @@
+name: distribute
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+
+jobs:
+  build_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  build_linux_wheels:
+    name: Wheel on linux
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get number of CPU cores
+        uses: SimenB/github-actions-cpu-cores@v2
+        id: cpu-cores
+
+      - uses: pypa/cibuildwheel@v2.20.0
+        env:
+          MAKEFLAGS: -j${{ steps.cpu-cores.outputs.count }}
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: linux_wheels
+          path: wheelhouse/*.whl
+
+  build_macos_wheels:
+    name: Wheel on macos
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-13, macOS-14]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install non-pip (brew) dependencies on MacOS
+        if: runner.os == 'macOS'
+        run: .github/bin/install-deps-macos.sh
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Get number of CPU cores
+        uses: SimenB/github-actions-cpu-cores@v2
+        id: cpu-cores
+
+      - name: Build MacOS wheel ${{ matrix.python-version }}
+        run: pipx run build --wheel
+
+      - name: Upload macos artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.os }}_${{ matrix.python-version }}
+          path: dist/*.whl
+
+  build_windows_wheels:
+    name: Wheel on windows
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install conda on Windows
+        if: runner.os == 'Windows'
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install non-pip (conda) dependencies on windows
+        if: runner.os == 'windows'
+        run: .github/bin/install-deps-windows.cmd
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Get number of CPU cores
+        uses: SimenB/github-actions-cpu-cores@v2
+        id: cpu-cores
+
+      - name: Build windows wheel ${{ matrix.python-version }}
+        run: |
+          ${{ steps.setup-python.outputs.python-path}} -m pip install build
+          ${{ steps.setup-python.outputs.python-path}} -m build .
+
+      - name: Upload windows artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: windows_${{ matrix.python-version }}
+          path: dist/*.whl
+
+  upload_all:
+    needs:
+      [
+        build_linux_wheels,
+        build_macos_wheels,
+        build_windows_wheels,
+        build_sdist,
+      ]
+
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

pyg4ometry-1.2.2/.github/workflows/main.yml

@@ -0,0 +1,100 @@
+name: pyg4ometry
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - "releases/**"
+  pull_request:
+  release:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-and-test:
+    name: Test with Python
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install conda on Windows
+        if: runner.os == 'Windows'
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+      - name: Install non-pip (apt) dependencies on Ubuntu
+        if: runner.os == 'Linux'
+        run: sudo .github/bin/install-deps-ubuntu.sh
+      - name: Install non-pip (brew) dependencies on MacOS
+        if: runner.os == 'macOS'
+        run: .github/bin/install-deps-macos.sh
+      - name: Install non-pip (conda) dependencies on Windows
+        if: runner.os == 'Windows'
+        run: .github/bin/install-deps-windows.cmd
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get number of CPU cores
+        uses: SimenB/github-actions-cpu-cores@v2
+        id: cpu-cores
+      - name: Get dependencies and install pyg4ometry
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          python -m pip install --upgrade --verbose .[test]
+      - name: Run unit tests
+        if: runner.os != 'Windows'
+        run: |
+          python -m pytest
+
+  test-in-container:
+    name: Test in Docker container
+    runs-on: ubuntu-latest
+    container: docker://g4edge/ubuntu:latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get number of CPU cores
+        uses: SimenB/github-actions-cpu-cores@v2
+        id: cpu-cores
+      - name: Get dependencies and install pyg4ometry
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          MAKEFLAGS=-j${{ steps.cpu-cores.outputs.count }} python -m pip install --upgrade --verbose .[test]
+      - name: Run unit tests
+        run: |
+          python -m pytest --runxfail
+
+  test-coverage:
+    name: Calculate and upload test coverage
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - name: Install non-pip dependencies on Ubuntu
+        run: |
+          sudo .github/bin/install-deps-ubuntu.sh
+          .github/bin/setenv-ubuntu.sh
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Get number of CPU cores
+        uses: SimenB/github-actions-cpu-cores@v2
+        id: cpu-cores
+      - name: Generate Report
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          MAKEFLAGS=-j${{ steps.cpu-cores.outputs.count }} python -m pip install --upgrade --verbose .[test]
+          python -m pytest --runxfail --cov=pyg4ometry --cov-report=xml
+      - name: Upload Coverage to codecov.io
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

pyg4ometry-1.2.2/.gitignore

@@ -0,0 +1,185 @@
+*.swp
+.DS_Store
+/src/pyg4ometry/_version.py
+
+# CMake
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Testing
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# 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/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+/docs/source/autoapi
+
+# 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
+
+# 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/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__packages__/
+
+# 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/
+
+run-fluka
+fluka-run
+flair_autosave.pickle
+
+*interp
+*tokens

pyg4ometry-1.2.2/.pre-commit-config.yaml

@@ -0,0 +1,93 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autoupdate_schedule: "quarterly"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: forbid-new-submodules
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black
+    rev: "24.4.2"
+    hooks:
+      - id: black-jupyter
+        args: ["--line-length", "100"]
+
+  - repo: https://github.com/asottile/blacken-docs
+    rev: "1.18.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==23.3.0]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.5.0"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.49"
+    hooks:
+      - id: check-manifest
+        stages: [manual]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+        args: ["-L", "commun,precess"]
+        types_or: [rst]
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
+      - id: python-no-log-warn
+      # - id: python-no-eval
+      # - id: python-use-type-annotations
+      # - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v4.0.0-alpha.8"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: "0.7.1"
+    hooks:
+      - id: nbstripout
+        args:
+          [
+            "--drop-empty-cells",
+            "--extra-keys",
+            "metadata.kernelspec metadata.language_info",
+          ]
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: "v18.1.8"
+    hooks:
+      - id: clang-format
+        types_or: [c++, c, cuda]

pyg4ometry-1.2.2/CITATION.cff

@@ -0,0 +1,64 @@
+cff-version: 1.2.0
+title: pyg4ometry
+doi: 10.5281/zenodo.10449301
+date-released: 2024-01-01
+url: https://github.com/github-linguist/linguist
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Boogert
+    given-names: Stewart
+    orcid: https://orcid.org/0000-0002-7742-4237
+  - family-names: Abramov
+    given-names: Andrey
+    orcid: https://orcid.org/0000-0003-4764-771X
+  - family-names: Nevay
+    given-names: Laurence
+    orcid: https://orcid.org/0000-0001-7225-9327
+  - family-names: Shields
+    given-names: William
+    orcid: https://orcid.org/0000-0002-4825-0303
+  - family-names: Walker
+    given-names: Stuart
+    orcid: https://orcid.org/0000-0003-1301-2724
+  - family-names: Butcher
+    given-names: Alistar
+    affiliation: "Royal Holloway, University of London"
+  - family-names: Hernalsteens
+    given-names: Cedric
+    orcid: https://orcid.org/0000-0003-4038-6246
+  - family-names: Shellswell
+    given-names: Benjamin
+    affiliation: "Royal Holloway, University of London"
+  - family-names: Ramoisiaux
+    given-names: Eliott
+    orcid: https://orcid.org/0000-0001-6523-2337
+  - family-names: Pertoldi
+    given-names: Luigi
+    orcid: https://orcid.org/0000-0002-0467-2571
+  - family-names: Huber
+    given-names: Manuel
+    email: info@manuelhu.de
+
+preferred-citation:
+  type: article
+  authors:
+  - family-names: Boogert
+    given-names: Stewart
+    orcid: https://orcid.org/0000-0002-7742-4237
+  - family-names: Abramov
+    given-names: Andrey
+    orcid: https://orcid.org/0000-0003-4764-771X
+  - family-names: Nevay
+    given-names: Laurence
+    orcid: https://orcid.org/0000-0001-7225-9327
+  - family-names: Shields
+    given-names: William
+    orcid: https://orcid.org/0000-0002-4825-0303
+  - family-names: Walker
+    given-names: Stuart
+    orcid: https://orcid.org/0000-0003-1301-2724
+  doi: 10.1016/j.cpc.2021.108228
+  journal: "Comput. Phys. Commun."
+  title: "Pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries"
+  volume: 272
+  year: 2022