sphysics 2.0.3__tar.gz

sphysics-2.0.3/.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

sphysics-2.0.3/.gitattributes

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+.git_archival.txt  export-subst

sphysics-2.0.3/.gitignore

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+# 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/
+
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp

sphysics-2.0.3/.gitlab-ci.yml

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+stages:
+  - prepare
+  - installable
+  - check
+  - build
+  - release-test
+  - deploy
+
+
+variables:
+  # image with all dependencies preinstalled, built from ci/Dockerfile by the ci-image job
+  CI_IMAGE: "$CI_REGISTRY_IMAGE/ci"
+  PYTHONFAULTHANDLER: "1"
+  TF_ENABLE_ONEDNN_OPTS: "0"
+  # compiler warnings are errors in the CI builds (off by default, see CMakeLists.txt);
+  # scikit-build-core passes this on to CMake as -DWERROR=ON
+  SKBUILD_CMAKE_DEFINE: "WERROR=ON"
+
+# The build requirements are part of the CI image. Hence, all builds use
+# --no-build-isolation; otherwise pip downloads them again into a temporary
+# build environment for every build. The exception is the
+# install-from-testpypi job, which installs sphysics the way a user does.
+
+default:
+  image: "$CI_IMAGE:latest"
+
+ci-image:
+  stage: prepare
+  image:
+    name: gcr.io/kaniko-project/executor:debug
+    entrypoint: [""]
+  tags:
+    - kubernetes-executor
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push" && $CI_COMMIT_TAG == null
+      changes:
+        - ci/Dockerfile
+        - pyproject.toml
+    # a rule without `if` would also create merge-request pipelines
+    - if: $CI_PIPELINE_SOURCE != "merge_request_event"
+      when: manual
+      allow_failure: true
+  script:
+    - echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
+    # the layer cache keeps the digests of unchanged layers, such that runner
+    # nodes only download the layers that changed; cached layers expire after
+    # 90 days (default: 2 weeks), afterwards unpinned packages get updated
+    - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/ci/Dockerfile
+      --build-arg=CI_JOB_TOKEN --cache=true --cache-repo=$CI_IMAGE/cache --cache-ttl=2160h
+      --destination $CI_IMAGE:$CI_COMMIT_SHORT_SHA --destination $CI_IMAGE:latest
+
+installable-static:
+  stage: installable
+  script:
+    - python -m pip wheel --no-build-isolation --no-deps --wheel-dir wheelhouse .
+    - python -m pip install wheelhouse/*.whl
+    - python -c "import sphysics"
+  # the wheel is reused by the jobs of the later stages
+  artifacts:
+    paths:
+      - wheelhouse/
+    expire_in: 1 day
+
+installable-editable:
+  stage: installable
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - python -m pip install --no-build-isolation --editable .
+    - python -c "import sphysics"
+
+build_pages:
+  stage: build
+  script:
+    - python -m pip install wheelhouse/*.whl
+    - cd docs
+    - python -c 'import sphysics'
+    - make clean
+    - make html
+    - mkdir -p ../public
+    - cp -r _build/html/* ../public/
+  artifacts:
+    paths:
+      - public
+
+pages:
+  stage: deploy
+  dependencies:
+    - build_pages
+  script:
+    - test -d public
+    - ls -la public | head -n 20
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+$/
+
+readthedocs:
+  stage: deploy
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+$/
+  # `needs` replaces the stage ordering, hence the release test is listed as well,
+  # such that the documentation is published only if it succeeds; the artifacts
+  # themselves are not needed here
+  needs:
+    - job: build_pages
+      artifacts: false
+    - job: install-from-testpypi
+      artifacts: false
+  script:
+    # Read the Docs serves the artifacts of build_pages instead of building the documentation
+    # itself (see .readthedocs.yaml and ci/readthedocs.py); READTHEDOCS_TOKEN is a masked CI/CD
+    # variable of the project (if it is protected, the version tags must be protected tags too,
+    # otherwise the variable is not available in tag pipelines)
+    - python ci/readthedocs.py trigger
+
+
+pre-commit:
+  stage: check
+  variables:
+    PRE_COMMIT_HOME: "$CI_PROJECT_DIR/.cache/pre-commit"
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - pre-commit run --hook-stage manual --all-files
+  cache:
+    key:
+      files:
+        - .pre-commit-config.yaml
+    paths:
+      - .cache/pre-commit
+
+lint:
+  stage: check
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - pylint --rcfile src/sphysics/pylintrc --reports=n
+      --output-format=text,pylint_gitlab.GitlabCodeClimateReporter:codeclimate.json src/sphysics
+  artifacts:
+    when: always
+    reports:
+      codequality: codeclimate.json
+    paths:
+      - codeclimate.json
+
+tests:
+  stage: check
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - python -m pip install wheelhouse/*.whl
+    - python -m pytest -vv -ra --junitxml=pytest-report.xml
+  artifacts:
+    when: always
+    reports:
+      junit: pytest-report.xml
+    paths:
+      - pytest-report.xml
+
+build_package:
+  stage: build
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  dependencies: []
+  script:
+    - python -m build --sdist --no-isolation
+    - python -m twine check dist/*
+    - python -m pip install --no-build-isolation dist/*.tar.gz
+    - python -c "import sphysics"
+  artifacts:
+    paths:
+      - dist/
+    expire_in: 7 days
+
+# The release-test stage runs for release tags only. It uploads the sdist to
+# TestPyPI and then installs it from there the way a user does. The deploy stage
+# (GitLab package registry, PyPI, documentation) starts only if this succeeds.
+
+# TESTPYPI_TOKEN is an API token of test.pypi.org stored as masked CI/CD
+# variable of the project (if it is protected, the version tags must be
+# protected tags too, otherwise the variable is not available in tag pipelines)
+publish_testpypi:
+  stage: release-test
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+$/
+  dependencies:
+    - build_package
+  variables:
+    TWINE_REPOSITORY_URL: "https://test.pypi.org/legacy/"
+    TWINE_USERNAME: "__token__"
+    TWINE_PASSWORD: "${TESTPYPI_TOKEN}"
+  script:
+    # --skip-existing, such that the job can be retried; a version can be uploaded only once
+    - python -m twine upload --verbose --skip-existing dist/*
+
+# Installs the sdist uploaded to TestPyPI the way a user does with `pip install
+# sphysics`: in a plain Python image with only a compiler, with pip build
+# isolation (i.e. the build requirements come from pyproject.toml and not from
+# the CI image), and with the default compiler flags (no -Werror).
+install-from-testpypi:
+  stage: release-test
+  image: python:3.11-slim-trixie
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+$/
+  needs:
+    - job: publish_testpypi
+      artifacts: false
+  variables:
+    # the repository is not needed
+    GIT_STRATEGY: none
+    SKBUILD_CMAKE_DEFINE: "WERROR=OFF"
+    PIP_NO_CACHE_DIR: "1"
+    PIP_DISABLE_PIP_VERSION_CHECK: "1"
+    PIP_ROOT_USER_ACTION: "ignore"
+  script:
+    - apt-get update
+    - apt-get install -y --no-install-recommends g++ make
+    - cd /tmp
+    # Only the sdist of sphysics is taken from TestPyPI, by its URL; the build
+    # requirements and dependencies are taken from PyPI. TestPyPI is not used
+    # as package index, because anyone can upload packages with the names of
+    # the dependencies there. The upload may take a moment to become available.
+    - |
+      for i in $(seq 1 30); do
+        SDIST_URL=$(python -c "import json, urllib.request; r = json.load(urllib.request.urlopen('https://test.pypi.org/pypi/sphysics/${CI_COMMIT_TAG}/json')); print(next(u['url'] for u in r['urls'] if u['packagetype'] == 'sdist'))") && break
+        echo "sphysics ${CI_COMMIT_TAG} is not yet available on TestPyPI, trying again in 10 s"
+        sleep 10
+      done
+    - test -n "$SDIST_URL"
+    - python -m pip install "$SDIST_URL"
+    - python -c "import sphysics; print(sphysics.__file__)"
+
+publish_package:
+  stage: deploy
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+$/
+  dependencies:
+    - build_package
+  variables:
+    TWINE_REPOSITORY_URL: "https://gitlab.desy.de/api/v4/projects/${CI_PROJECT_ID}/packages/pypi"
+    TWINE_USERNAME: "gitlab-ci-token"
+    TWINE_PASSWORD: "${CI_JOB_TOKEN}"
+  script:
+    - python -m twine upload --verbose dist/*
+
+# PYPI_TOKEN is an API token of pypi.org stored as masked CI/CD variable of the
+# project (see the comment on TESTPYPI_TOKEN)
+publish_pypi:
+  stage: deploy
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+$/
+  dependencies:
+    - build_package
+  variables:
+    TWINE_USERNAME: "__token__"
+    TWINE_PASSWORD: "${PYPI_TOKEN}"
+  script:
+    - python -m twine upload --verbose dist/*

sphysics-2.0.3/.pre-commit-config.yaml

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+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+exclude: ^src/cppLib/|^data/|README.md|LICENSE|.gitlab-ci.yml
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==23.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: "v17.0.6"
+    hooks:
+      - id: clang-format
+        types_or: [c++, c, cuda]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.6"
+    hooks:
+      - id: shellcheck
+
+  #  - repo: local
+  #    hooks:
+  #      - id: disallow-caps
+  #        name: Disallow improper capitalization
+  #        language: pygrep
+  #        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+  #        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: "v0.6.13"
+    hooks:
+      - id: cmake-format
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.25"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.27.3"
+    hooks:
+      - id: check-gitlab-ci
+      - id: check-readthedocs
+#   - repo: https://github.com/astral-sh/ruff-pre-commit
+#     rev: "v0.1.14"
+#     hooks:
+#       - id: ruff
+#         args: ["--fix", "--show-fixes"]
+#       - id: ruff-format

sphysics-2.0.3/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.com/platform/stable/config-file/v2.html for details
+#
+# Read the Docs does not build the documentation itself. Instead, ci/readthedocs.py downloads
+# the HTML that the build_pages job of the GitLab CI built for the same commit, such that Read
+# the Docs serves exactly the files that the pages job deploys to GitLab Pages. See the script
+# for details and for the required environment variable GITLAB_TOKEN.
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  commands:
+    - python ci/readthedocs.py fetch

sphysics-2.0.3/AUTHORS.md

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+# Authors
+
+sphysics is developed by Stefan Wallner (main author), with contributions by
+Martin Bartl, Julien Beckers, Yannik Fausch, Godo Kurten, Fabian Krinner,
+Claudia Perez-Orive, Markus Reif, Xavier Simo, Oskar Tittel, and Miriam
+Weiskopf.
+
+## Code from other authors and projects
+
+- [ROOTPWA](https://github.com/ROOTPWA-Maintainers/ROOTPWA) (GNU GPL version 3
+  or later): the build system (`CMakeLists.txt` files and `cmakeModules/`), the
+  particleData library and the particle data tables (`src/cppLib/particleData/`,
+  `data/particleDatatable/`), and the Python bindings of the particle data
+  (`particleProperties_py.cc` and `particleDataTable_py.cc` in
+  `src/cppLib/pyBindings/constants/`), which are based on ROOTPWA's boost.python
+  bindings. Their authors are named in the file headers.
+- [basf2](https://github.com/belle2/basf2) (GNU LGPL version 3 or later): the
+  particle names and PDG codes in `src/sphysics/_constants/_pdgcodes.py`.
+
+## Data
+
+- The particle properties in the particle data tables are taken from the Review
+  of Particle Physics of the Particle Data Group.
+- `data/amplitudes/K0K0barspinnolam.csv` and `KplusKminusspinnolam.csv`:
+  triangle amplitude of the a1(1420), provided by the COMPASS Collaboration and
+  published with permission, see Phys. Rev. Lett. 127, 082501 (2021).
+- `data/amplitudes/kpiS_Pelaez-Rodas_2010.11222.csv`: Kπ S-wave amplitude
+  provided by J. R. Peláez and A. Rodas, Phys. Rept. 969 (2022) 1
+  (arXiv:2010.11222). Code:
+  https://github.com/Hadron-Madrid-HadMad/HadMad.github

sphysics-2.0.3/CITATION.cff

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+cff-version: 1.2.0
+message: If you use sphysics, please cite it using the metadata from this file.
+type: software
+title: sphysics
+abstract: Tools for amplitude analysis, event selection, kinematic calculations, machine learning, and more
+authors:
+  - family-names: Wallner
+    given-names: Stefan
+    orcid: https://orcid.org/0000-0002-9105-1625
+  - family-names: Bartl
+    given-names: Martin
+    orcid: https://orcid.org/0009-0002-7835-0855
+  - family-names: Beckers
+    given-names: Julien
+  - family-names: Fausch
+    given-names: Yannik
+  - family-names: Kurten
+    given-names: Godo
+    orcid: https://orcid.org/0009-0000-0553-7964
+  - family-names: Krinner
+    given-names: Fabian
+  - family-names: Perez-Orive
+    given-names: Claudia
+  - family-names: Reif
+    given-names: Markus
+    orcid: https://orcid.org/0000-0002-0706-0247
+  - family-names: Simo
+    given-names: Xavier
+  - family-names: Tittel
+    given-names: Oskar
+    orcid: https://orcid.org/0000-0001-9128-6240
+  - family-names: Weiskopf
+    given-names: Miriam
+doi: 10.5281/zenodo.23214121
+repository-code: https://github.com/sAmplitudes/sphysics
+url: https://sphysics.readthedocs.io
+license: GPL-3.0-or-later
+keywords:
+  - amplitude analyses
+  - PWA
+  - partial-wave analyses
+  - particle physics