From c6045d59565b559cbfc710c10fb8a8153e8abb03 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Tue, 28 Jan 2025 10:16:24 +0000 Subject: [PATCH 01/15] ENH: Refactor metadata and setup - Remove setup.cfg - Move as much information as possible to pyproject.toml - Keep versioning dynamic using versioneer. --- MANIFEST.in | 2 +- pyproject.toml | 13 ++++++++++--- setup.cfg | 31 ------------------------------- setup.py | 4 ++-- 4 files changed, 13 insertions(+), 37 deletions(-) delete mode 100644 setup.cfg diff --git a/MANIFEST.in b/MANIFEST.in index f50e20be..a7856aa6 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -6,7 +6,7 @@ include requirements-dev.txt include requirements-setup.txt include versioneer.py -recursive-include src/radiomics * +recursive-include radiomics * recursive-include data/baseline * recursive-include data *_image.nrrd diff --git a/pyproject.toml b/pyproject.toml index 8183359a..30c0ce46 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,10 @@ [build-system] -requires = ["setuptools>=61.0", "numpy", "versioneer"] +requires = ["setuptools>=61.0", "numpy", "versioneer[toml]"] build-backend = "setuptools.build_meta" [project] name = "pyradiomics" -version = "3.1.1" +dynamic = ["version"] authors = [ { name = "PyRadiomics Community", email = "pyradiomics@googlegroups.com"} ] @@ -40,8 +40,15 @@ dependencies = [ pyradiomics = "radiomics.scripts.__init__:parse_args" [project.urls] -"Homepaget" = "http://github.com/AIM-Harvard/pyradiomics#readme" +"Homepage" = "https://github.com/AIM-Harvard/pyradiomics#readme" "Radiomics.io" = "https://www.radiomics.io/" "Documentation" = "https://pyradiomics.readthedocs.io/en/latest/index.html" "Docker" = "https://hub.docker.com/r/radiomics/pyradiomics/" "Github" = "https://github.com/AIM-Harvard/pyradiomics" + +[tool.versioneer] +VCS = "git" +versionfile_source = "radiomics/_version.py" +versionfile_build = "radiomics/_version.py" +style = "pep440-post" +tag_prefix = "" diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index d4b47dff..00000000 --- a/setup.cfg +++ /dev/null @@ -1,31 +0,0 @@ -[metadata] -description = Radiomics features library for python -long_description = file: README.md -long_description_content_type = text/markdown -license = 3-Clause BSD - -[options] -install_requires = - numpy - SimpleITK - PyWavelets - pykwalify - six -include_package_data=False - -[options.packages.find] -include=radiomics* -exclude=radiomics.schemas - -[options.package_data] -radiomics = - schemas/paramSchema.yaml - schemas/schemaFuncs.py - -[versioneer] -VCS = git -versionfile_source = radiomics/_version.py -versionfile_build = radiomics/_version.py -style = pep440-post -tag_prefix = '' - diff --git a/setup.py b/setup.py index 300c1be6..4a1f81ef 100644 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ #!/usr/bin/env python -from distutils import sysconfig import platform +from sysconfig import get_paths import numpy from setuptools import Extension, setup @@ -11,7 +11,7 @@ raise Exception('PyRadiomics requires 64 bits python') commands = versioneer.get_cmdclass() -incDirs = [sysconfig.get_python_inc(), numpy.get_include()] +incDirs = [get_paths()['include'], numpy.get_include()] ext = [Extension("radiomics._cmatrices", ["radiomics/src/_cmatrices.c", "radiomics/src/cmatrices.c"], include_dirs=incDirs), From 1e2f8c31087bcf05a2e8e1023d8a0ae181aa7366 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Tue, 28 Jan 2025 11:28:09 +0000 Subject: [PATCH 02/15] ENH: Refactor project structure Follows suggestions obtained by running cookiecutter from https://learn.scientific-python.org/development/. --- .copier-answers.yml | 12 + .git_archival.txt | 3 + .gitattributes | 2 +- .github/CONTRIBUTING.md | 89 ++ .github/dependabot.yml | 11 + .github/release.yml | 5 + .github/workflows/cd.yml | 85 ++ .github/workflows/ci.yml | 71 ++ .gitignore | 107 +- .pre-commit-config.yaml | 100 ++ .readthedocs.yaml | 17 + CMakeLists.txt | 7 + MANIFEST.in | 26 - noxfile.py | 107 ++ pyproject.toml | 150 ++- radiomics/__init__.py | 5 +- radiomics/_version.py | 525 +--------- radiomics/src/CMakeLists.txt | 7 + setup.py | 30 - tests/test_package.py | 9 + versioneer.py | 1817 ---------------------------------- 21 files changed, 771 insertions(+), 2414 deletions(-) create mode 100644 .copier-answers.yml create mode 100644 .git_archival.txt create mode 100644 .github/CONTRIBUTING.md create mode 100644 .github/dependabot.yml create mode 100644 .github/release.yml create mode 100644 .github/workflows/cd.yml create mode 100644 .github/workflows/ci.yml create mode 100644 .pre-commit-config.yaml create mode 100644 .readthedocs.yaml create mode 100644 CMakeLists.txt delete mode 100644 MANIFEST.in create mode 100644 noxfile.py create mode 100644 radiomics/src/CMakeLists.txt delete mode 100644 setup.py create mode 100644 tests/test_package.py delete mode 100644 versioneer.py diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 00000000..4b42025f --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,12 @@ +# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY +_commit: 2025.01.22-2-g6a4b022 +_src_path: gh:scientific-python/cookie +backend: skbuild +email: pyradiomics@googlegroups.com +full_name: Pyradiomics Community +license: BSD +org: AIM-Harvard +project_name: pyradiomics +project_short_description: Radiomics features library for python +url: https://github.com/AIM-Harvard/pyradiomics +vcs: true diff --git a/.git_archival.txt b/.git_archival.txt new file mode 100644 index 00000000..7c510094 --- /dev/null +++ b/.git_archival.txt @@ -0,0 +1,3 @@ +node: $Format:%H$ +node-date: $Format:%cI$ +describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$ diff --git a/.gitattributes b/.gitattributes index 16ff9a76..00a7b00c 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -radiomics/_version.py export-subst +.git_archival.txt export-subst diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 00000000..875ca6dd --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,89 @@ +See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed +description of best practices for developing scientific packages. + +[spc-dev-intro]: https://learn.scientific-python.org/development/ + +# Quick development + +The fastest way to start with development is to use nox. If you don't have nox, +you can use `pipx run nox` to run it without installing, or `pipx install nox`. +If you don't have pipx (pip for applications), then you can install with +`pip install pipx` (the only case were installing an application with regular +pip is reasonable). If you use macOS, then pipx and nox are both in brew, use +`brew install pipx nox`. + +To use, run `nox`. This will lint and test using every installed version of +Python on your system, skipping ones that are not installed. You can also run +specific jobs: + +```console +$ nox -s lint # Lint only +$ nox -s tests # Python tests +$ nox -s docs # Build and serve the docs +$ nox -s build # Make an SDist and wheel +``` + +Nox handles everything for you, including setting up an temporary virtual +environment for each run. + +# Setting up a development environment manually + +You can set up a development environment by running: + +```bash +python3 -m venv .venv +source ./.venv/bin/activate +pip install -v -e .[dev] +``` + +If you have the +[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you +can instead do: + +```bash +py -m venv .venv +py -m install -v -e .[dev] +``` + +# Pre-commit + +You should prepare pre-commit, which will help you by checking that commits pass +required checks: + +```bash +pip install pre-commit # or brew install pre-commit on macOS +pre-commit install # Will install a pre-commit hook into the git repo +``` + +You can also/alternatively run `pre-commit run` (changes only) or +`pre-commit run --all-files` to check even without installing the hook. + +# Testing + +Use pytest to run the unit checks: + +```bash +pytest +``` + +# Coverage + +Use pytest-cov to generate coverage reports: + +```bash +pytest --cov=radiomics +``` + +# Building docs + +You can build and serve the docs using: + +```bash +nox -s docs +``` + +You can build the docs only with: + +```bash +nox -s docs --non-interactive +``` diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..6c4b3695 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,11 @@ +version: 2 +updates: + # Maintain dependencies for GitHub Actions + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" + groups: + actions: + patterns: + - "*" diff --git a/.github/release.yml b/.github/release.yml new file mode 100644 index 00000000..9d1e0987 --- /dev/null +++ b/.github/release.yml @@ -0,0 +1,5 @@ +changelog: + exclude: + authors: + - dependabot + - pre-commit-ci diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml new file mode 100644 index 00000000..8d531bbc --- /dev/null +++ b/.github/workflows/cd.yml @@ -0,0 +1,85 @@ +name: wheels + +on: + workflow_dispatch: + release: + types: + - published + pull_request: + paths: + - .github/workflows/cd.yml + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +env: + # Many color libraries just need this to be set to any value, but at least + # one distinguishes color depth, where "3" -> "256-bit color". + FORCE_COLOR: 3 + +jobs: + make_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 + + - uses: actions/upload-artifact@v4 + with: + name: cibw-sdist + path: dist/*.tar.gz + + build_wheels: + name: Wheel on ${{ matrix.os }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, windows-latest, macos-13, macos-14] + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - uses: pypa/cibuildwheel@v2.22 + + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }} + path: wheelhouse/*.whl + + upload_all: + needs: [build_wheels, make_sdist] + environment: pypi + permissions: + id-token: write + attestations: write + contents: read + runs-on: ubuntu-latest + if: github.event_name == 'release' && github.event.action == 'published' + + steps: + - uses: actions/download-artifact@v4 + with: + pattern: cibw-* + path: dist + merge-multiple: true + + - name: Generate artifact attestations + uses: actions/attest-build-provenance@v2.1.0 + with: + subject-path: "dist/*" + + - uses: pypa/gh-action-pypi-publish@release/v1 + with: + # Remember to tell (test-)pypi about this repo before publishing + # Remove this line to publish to PyPI + repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 00000000..f6286d2c --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,71 @@ +name: CI + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +env: + # Many color libraries just need this to be set to any value, but at least + # one distinguishes color depth, where "3" -> "256-bit color". + FORCE_COLOR: 3 + +jobs: + pre-commit: + name: Format + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + - uses: actions/setup-python@v5 + with: + python-version: "3.x" + - uses: pre-commit/action@v3.0.1 + with: + extra_args: --hook-stage manual --all-files + - name: Run PyLint + run: pipx run nox -s pylint -- --output-format=github + + checks: + name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} + runs-on: ${{ matrix.runs-on }} + needs: [pre-commit] + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.13"] + runs-on: [ubuntu-latest, windows-latest, macos-14] + + include: + - python-version: "pypy-3.10" + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + allow-prereleases: true + + - name: Install package + run: python -m pip install .[test] + + - name: Test package + run: >- + python -m pytest -ra --cov --cov-report=xml --cov-report=term + --durations=20 + + - name: Upload coverage report + uses: codecov/codecov-action@v5.1.2 + with: + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore index 32ee5c3e..aa0ed637 100644 --- a/.gitignore +++ b/.gitignore @@ -8,7 +8,6 @@ __pycache__/ # Distribution / packaging .Python -env/ build/ develop-eggs/ dist/ @@ -20,9 +19,12 @@ 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 @@ -37,15 +39,17 @@ pip-delete-this-directory.txt # Unit test / coverage reports htmlcov/ .tox/ +.nox/ .coverage .coverage.* .cache - -# Temp editor files -*~ nosetests.xml coverage.xml -*,cover +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ # Translations *.mo @@ -53,6 +57,16 @@ coverage.xml # Django stuff: *.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy # Sphinx documentation docs/_build/ @@ -62,4 +76,87 @@ docs/_build/ *.swp # 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 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..ea65b8cf --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,100 @@ +ci: + autoupdate_commit_msg: "chore: update pre-commit hooks" + autofix_commit_msg: "style: pre-commit fixes" + +exclude: ^.cruft.json|.copier-answers.yml$ + +repos: + - repo: https://github.com/adamchainz/blacken-docs + rev: "1.19.1" + hooks: + - id: blacken-docs + additional_dependencies: [black==24.*] + + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: "v5.0.0" + 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/rbubley/mirrors-prettier + rev: "v3.4.2" + hooks: + - id: prettier + types_or: [yaml, markdown, html, css, scss, javascript, json] + args: [--prose-wrap=always] + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.9.2" + hooks: + - id: ruff + args: ["--fix", "--show-fixes"] + - id: ruff-format + + - repo: https://github.com/pre-commit/mirrors-clang-format + rev: "v19.1.7" + hooks: + - id: clang-format + types_or: [c++, c, cuda] + + - repo: https://github.com/pre-commit/mirrors-mypy + rev: "v1.14.1" + hooks: + - id: mypy + files: src|tests + args: [] + additional_dependencies: + - pytest + + - repo: https://github.com/codespell-project/codespell + rev: "v2.3.0" + hooks: + - id: codespell + + - repo: https://github.com/shellcheck-py/shellcheck-py + rev: "v0.10.0.1" + 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: "v0.23" + hooks: + - id: validate-pyproject + additional_dependencies: ["validate-pyproject-schema-store[all]"] + + - repo: https://github.com/python-jsonschema/check-jsonschema + rev: "0.31.0" + hooks: + - id: check-dependabot + - id: check-github-workflows + - id: check-readthedocs diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..67c194c8 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,17 @@ +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.12" + commands: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv venv + - uv pip install .[docs] + - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D + language=en docs $READTHEDOCS_OUTPUT/html diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 00000000..55bb14c8 --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,7 @@ +cmake_minimum_required(VERSION 3.15...3.26) + +project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C) + +find_package(Python COMPONENTS Interpreter Development.Module NumPy REQUIRED) + +add_subdirectory(radiomics/src) diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index a7856aa6..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,26 +0,0 @@ -include CONTRIBUTING.rst -include LICENSE.txt -include README.md -include requirements.txt -include requirements-dev.txt -include requirements-setup.txt -include versioneer.py - -recursive-include radiomics * - -recursive-include data/baseline * -recursive-include data *_image.nrrd -recursive-include data *_label.nrrd -include data/README.md - -recursive-include examples/exampleSettings *.yaml -recursive-include examples batch*.py -recursive-include examples hello*.py -include examples/testCases.csv - -recursive-include tests * - -recursive-include bin *.py - -recursive-exclude * __pycache__ -recursive-exclude * *.py[cod] diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 00000000..414a839f --- /dev/null +++ b/noxfile.py @@ -0,0 +1,107 @@ +from __future__ import annotations + +import argparse +import shutil +from pathlib import Path + +import nox + +DIR = Path(__file__).parent.resolve() + +nox.needs_version = ">=2024.3.2" +nox.options.sessions = ["lint", "pylint", "tests"] +nox.options.default_venv_backend = "uv|virtualenv" + + +@nox.session +def lint(session: nox.Session) -> None: + """ + Run the linter. + """ + session.install("pre-commit") + session.run( + "pre-commit", "run", "--all-files", "--show-diff-on-failure", *session.posargs + ) + + +@nox.session +def pylint(session: nox.Session) -> None: + """ + Run PyLint. + """ + # This needs to be installed into the package environment, and is slower + # than a pre-commit check + session.install(".", "pylint>=3.2") + session.run("pylint", "pyradiomics", *session.posargs) + + +@nox.session +def tests(session: nox.Session) -> None: + """ + Run the unit and regular tests. + """ + session.install(".[test]") + session.run("pytest", *session.posargs) + + +@nox.session(reuse_venv=True) +def docs(session: nox.Session) -> None: + """ + Build the docs. Pass --non-interactive to avoid serving. First positional argument is the target directory. + """ + + parser = argparse.ArgumentParser() + parser.add_argument( + "-b", dest="builder", default="html", help="Build target (default: html)" + ) + parser.add_argument("output", nargs="?", help="Output directory") + args, posargs = parser.parse_known_args(session.posargs) + serve = args.builder == "html" and session.interactive + + session.install("-e.[docs]", "sphinx-autobuild") + + shared_args = ( + "-n", # nitpicky mode + "-T", # full tracebacks + f"-b={args.builder}", + "docs", + args.output or f"docs/_build/{args.builder}", + *posargs, + ) + + if serve: + session.run("sphinx-autobuild", "--open-browser", *shared_args) + else: + session.run("sphinx-build", "--keep-going", *shared_args) + + +@nox.session +def build_api_docs(session: nox.Session) -> None: + """ + Build (regenerate) API docs. + """ + + session.install("sphinx") + session.run( + "sphinx-apidoc", + "-o", + "docs/api/", + "--module-first", + "--no-toc", + "--force", + "src/pyradiomics", + ) + + +@nox.session +def build(session: nox.Session) -> None: + """ + Build an SDist and wheel. + """ + + build_path = DIR.joinpath("build") + if build_path.exists(): + shutil.rmtree(build_path) + + session.install("build") + session.run("python", "-m", "build") diff --git a/pyproject.toml b/pyproject.toml index 30c0ce46..3fd67f92 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,16 +1,16 @@ [build-system] -requires = ["setuptools>=61.0", "numpy", "versioneer[toml]"] -build-backend = "setuptools.build_meta" +requires = ["scikit-build-core>=0.10", "numpy"] +build-backend = "scikit_build_core.build" + [project] name = "pyradiomics" -dynamic = ["version"] authors = [ { name = "PyRadiomics Community", email = "pyradiomics@googlegroups.com"} ] description = "Radiomics features library for python" readme = "README.md" -requires-python =">=3.5" +requires-python =">=3.8" license = { file = "LICENSE.txt"} keywords = [ "radiomics", "cancerimaging", "medicalresearch", "computationalimaging" ] classifiers = [ @@ -28,6 +28,7 @@ classifiers = [ 'Programming Language :: Python :: 3.9', 'Topic :: Scientific/Engineering :: Bio-Informatics' ] +dynamic = ["version"] dependencies = [ "numpy", "SimpleITK", @@ -36,19 +37,148 @@ dependencies = [ "six" ] +[project.optional-dependencies] +test = [ + "pytest >=6", + "pytest-cov >=3", +] +dev = [ + "pytest >=6", + "pytest-cov >=3", +] +docs = [ + "sphinx>=7.0", + "myst_parser>=0.13", + "sphinx_copybutton", + "sphinx_autodoc_typehints", + "furo>=2023.08.17", +] + [project.scripts] pyradiomics = "radiomics.scripts.__init__:parse_args" [project.urls] "Homepage" = "https://github.com/AIM-Harvard/pyradiomics#readme" +"Bug Tracker" = "https://github.com/AIM-Harvard/pyradiomics/issues" +Discussions = "https://github.com/AIM-Harvard/pyradiomics/discussions" +Changelog = "https://github.com/AIM-Harvard/pyradiomics/changes.rst" "Radiomics.io" = "https://www.radiomics.io/" "Documentation" = "https://pyradiomics.readthedocs.io/en/latest/index.html" "Docker" = "https://hub.docker.com/r/radiomics/pyradiomics/" "Github" = "https://github.com/AIM-Harvard/pyradiomics" -[tool.versioneer] -VCS = "git" -versionfile_source = "radiomics/_version.py" -versionfile_build = "radiomics/_version.py" -style = "pep440-post" -tag_prefix = "" + +[tool.scikit-build] +minimum-version = "build-system.requires" +build-dir = "build/{wheel_tag}" +metadata.version.provider = "scikit_build_core.metadata.setuptools_scm" +sdist.include = ["radiomics/_version.py"] +wheel.packages = ['radiomics', 'radiomics.scripts'] +wheel.exclude = ['radiomics/src'] + + +[tool.setuptools_scm] +write_to = "radiomics/_version.py" + + +[tool.uv] +dev-dependencies = [ + "pyradiomics[test]", +] + + +[tool.cibuildwheel] +test-command = "pytest tests" +test-extras = ["test"] + + +[tool.pytest.ini_options] +minversion = "6.0" +addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"] +xfail_strict = true +filterwarnings = [ + "error", +] +log_cli_level = "INFO" +testpaths = [ + "tests", +] + + +[tool.coverage] +run.source = ["radiomics"] +report.exclude_also = [ + '\.\.\.', + 'if typing.TYPE_CHECKING:', +] + + +[tool.mypy] +files = ["radiomics", "tests"] +python_version = "3.9" +warn_unused_configs = true +strict = true +enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] +warn_unreachable = true +disallow_untyped_defs = false +disallow_incomplete_defs = false + +[[tool.mypy.overrides]] +module = "radiomics.*" +disallow_untyped_defs = true +disallow_incomplete_defs = true + + +[tool.ruff] + +[tool.ruff.lint] +extend-select = [ + "ARG", # flake8-unused-arguments + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "EM", # flake8-errmsg + "EXE", # flake8-executable + "G", # flake8-logging-format + "I", # isort + "ICN", # flake8-import-conventions + "NPY", # NumPy specific rules + "PD", # pandas-vet + "PGH", # pygrep-hooks + "PIE", # flake8-pie + "PL", # pylint + "PT", # flake8-pytest-style + "PTH", # flake8-use-pathlib + "RET", # flake8-return + "RUF", # Ruff-specific + "SIM", # flake8-simplify + "T20", # flake8-print + "UP", # pyupgrade + "YTT", # flake8-2020 +] +ignore = [ + "PLR09", # Too many <...> + "PLR2004", # Magic value used in comparison + "ISC001", # Conflicts with formatter +] +isort.required-imports = ["from __future__ import annotations"] +# Uncomment if using a _compat.typing backport +# typing-modules = ["pyradiomics._compat.typing"] + +[tool.ruff.lint.per-file-ignores] +"tests/**" = ["T20"] +"noxfile.py" = ["T20"] + + +[tool.pylint] +py-version = "3.9" +ignore-paths = [".*/_version.py"] +reports.output-format = "colorized" +similarities.ignore-imports = "yes" +messages_control.disable = [ + "design", + "fixme", + "line-too-long", + "missing-module-docstring", + "missing-function-docstring", + "wrong-import-position", +] diff --git a/radiomics/__init__.py b/radiomics/__init__.py index 1c68c162..7b1864b3 100644 --- a/radiomics/__init__.py +++ b/radiomics/__init__.py @@ -303,7 +303,6 @@ def getProgressReporter(*args, **kwargs): getImageTypes() # 5. Set the version using the versioneer scripts -from ._version import get_versions # noqa: I202 +from ._version import version as __version__ -__version__ = get_versions()['version'] -del get_versions +__all__ = ["__version__"] diff --git a/radiomics/_version.py b/radiomics/_version.py index e518ec05..91744f98 100644 --- a/radiomics/_version.py +++ b/radiomics/_version.py @@ -1,523 +1,4 @@ -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. +from __future__ import annotations -# This file is released into the public domain. Generated by -# versioneer-0.17 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -from __future__ import print_function - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440-post" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "None" - cfg.versionfile_source = "radiomics/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} +version: str +version_tuple: tuple[int, int, int] | tuple[int, int, int, str, str] diff --git a/radiomics/src/CMakeLists.txt b/radiomics/src/CMakeLists.txt new file mode 100644 index 00000000..e0e7dbcf --- /dev/null +++ b/radiomics/src/CMakeLists.txt @@ -0,0 +1,7 @@ +Python_add_library(_cmatrices MODULE _cmatrices.c cmatrices.c) +target_link_libraries(_cmatrices PRIVATE Python::NumPy) + +Python_add_library(_cshape MODULE _cshape.c cshape.c) +target_link_libraries(_cshape PRIVATE Python::NumPy) + +install(TARGETS _cmatrices _cshape DESTINATION radiomics) diff --git a/setup.py b/setup.py deleted file mode 100644 index 4a1f81ef..00000000 --- a/setup.py +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env python - -import platform -from sysconfig import get_paths - -import numpy -from setuptools import Extension, setup -import versioneer - -if platform.architecture()[0].startswith('32'): - raise Exception('PyRadiomics requires 64 bits python') - -commands = versioneer.get_cmdclass() -incDirs = [get_paths()['include'], numpy.get_include()] - -ext = [Extension("radiomics._cmatrices", ["radiomics/src/_cmatrices.c", "radiomics/src/cmatrices.c"], - include_dirs=incDirs), - Extension("radiomics._cshape", ["radiomics/src/_cshape.c", "radiomics/src/cshape.c"], - include_dirs=incDirs)] - -setup( - name='pyradiomics', - - version=versioneer.get_version(), - cmdclass=commands, - - packages=['radiomics', 'radiomics.scripts'], - ext_modules=ext, - zip_safe=False -) diff --git a/tests/test_package.py b/tests/test_package.py new file mode 100644 index 00000000..f4fa093f --- /dev/null +++ b/tests/test_package.py @@ -0,0 +1,9 @@ +from __future__ import annotations + +import importlib.metadata + +import radiomics as m + + +def test_version(): + assert importlib.metadata.version("pyradiomics") == m.__version__ diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index f250cde5..00000000 --- a/versioneer.py +++ /dev/null @@ -1,1817 +0,0 @@ - -# Version: 0.17 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/warner/python-versioneer -* Brian Warner -* License: Public Domain -* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, and pypy -* [![Latest Version] -(https://pypip.in/version/versioneer/badge.svg?style=flat) -](https://pypi.python.org/pypi/versioneer/) -* [![Build Status] -(https://travis-ci.org/warner/python-versioneer.png?branch=master) -](https://travis-ci.org/warner/python-versioneer) - -This is a tool for managing a recorded version number in distutils-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -* `pip install versioneer` to somewhere to your $PATH -* add a `[versioneer]` section to your setup.cfg (see below) -* run `versioneer install` in your source tree, commit the results - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes. - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See details.md in the Versioneer source tree for -descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/warner/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other langauges) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - -### Unicode version strings - -While Versioneer works (and is continually tested) with both Python 2 and -Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. -Newer releases probably generate unicode version strings on py2. It's not -clear that this is wrong, but it may be surprising for applications when then -write these strings to a network connection or include them in bytes-oriented -APIs like cryptographic checksums. - -[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates -this question. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -""" - -from __future__ import print_function -try: - import configparser -except ImportError: - import ConfigParser as configparser -import errno -import json -import os -import re -import subprocess -import sys - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py)) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: - parser.readfp(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None - cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): - cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode -LONG_VERSION_PY['git'] = ''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.17 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%%d" %% pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(manifest_in, versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] - if ipy: - files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: - pass - if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.17) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except EnvironmentError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(): - """Get the custom setuptools/distutils subclasses used by Versioneer.""" - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/warner/python-versioneer/issues/52 - - cmds = {} - - # we add "version" to both distutils and setuptools - from distutils.core import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version - - # we override "build_py" in both distutils and setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # we override different "build_py" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py - else: - from distutils.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if 'py2exe' in sys.modules: # py2exe enabled? - try: - from py2exe.distutils_buildexe import py2exe as _py2exe # py3 - except ImportError: - from py2exe.build_exe import py2exe as _py2exe # py2 - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["py2exe"] = cmd_py2exe - - # we override different "sdist" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist - else: - from distutils.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -INIT_PY_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - - -def do_setup(): - """Main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (EnvironmentError, configparser.NoSectionError, - configparser.NoOptionError) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except EnvironmentError: - old = "" - if INIT_PY_SNIPPET not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print(" appending versionfile_source ('%s') to MANIFEST.in" % - cfg.versionfile_source) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1) From fc6944bf3281e90af95d69f980bb9c545bf48e00 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Tue, 28 Jan 2025 17:16:40 +0000 Subject: [PATCH 03/15] TEST: Fix failing tests - Update the matrices baseline numpy arrays to newer version. Values are unchanged, matrices were simply loaded and saved again using `arr = numpy.load(); numpy.save(, arr);`. - Ignore specific deprecation warning related to a deprecated function being used in PyKwalify. See also https://github.com/Grokzen/pykwalify/issues/202 and https://github.com/Grokzen/pykwalify/pull/203. --- data/baseline/brain1_glcm.npy | Bin 113384 -> 113384 bytes data/baseline/brain1_gldm.npy | Bin 2768 -> 2768 bytes data/baseline/brain1_glrlm.npy | Bin 24152 -> 24152 bytes data/baseline/brain1_glszm.npy | Bin 6728 -> 6728 bytes data/baseline/brain1_ngtdm.npy | Bin 920 -> 920 bytes data/baseline/brain2_glcm.npy | Bin 75944 -> 75944 bytes data/baseline/brain2_gldm.npy | Bin 1856 -> 1856 bytes data/baseline/brain2_glrlm.npy | Bin 19784 -> 19784 bytes data/baseline/brain2_glszm.npy | Bin 3152 -> 3152 bytes data/baseline/brain2_ngtdm.npy | Bin 776 -> 776 bytes data/baseline/breast1_glcm.npy | Bin 1064 -> 1064 bytes data/baseline/breast1_gldm.npy | Bin 536 -> 536 bytes data/baseline/breast1_glrlm.npy | Bin 2312 -> 2312 bytes data/baseline/breast1_glszm.npy | Bin 248 -> 248 bytes data/baseline/breast1_ngtdm.npy | Bin 200 -> 200 bytes data/baseline/lung1_glcm.npy | Bin 65128 -> 65128 bytes data/baseline/lung1_gldm.npy | Bin 4928 -> 4928 bytes data/baseline/lung1_glrlm.npy | Bin 28728 -> 28728 bytes data/baseline/lung1_glszm.npy | Bin 3128 -> 3128 bytes data/baseline/lung1_ngtdm.npy | Bin 728 -> 728 bytes data/baseline/lung2_glcm.npy | Bin 158312 -> 158312 bytes data/baseline/lung2_gldm.npy | Bin 8552 -> 8552 bytes data/baseline/lung2_glrlm.npy | Bin 158312 -> 158312 bytes data/baseline/lung2_glszm.npy | Bin 11984 -> 11984 bytes data/baseline/lung2_ngtdm.npy | Bin 1064 -> 1064 bytes data/baseline/wavelet.npy | Bin 17000 -> 17000 bytes pyproject.toml | 1 + 27 files changed, 1 insertion(+) diff --git a/data/baseline/brain1_glcm.npy b/data/baseline/brain1_glcm.npy index 3954e738b80a9a3bc6e452e7470640e00f3ed24d..4a9cc1e36e06a5e08df66b813c1ef0a61c21b8c8 100644 GIT binary patch delta 34 qcmaFymF>k>wh8t;Its?dItqrynmP)#69e@oCa^WuZ>?v{+ywyO84Ohb delta 34 ocmaFymF>k>wh8w9J~|4<#z4Z**hf=Gp>|@RUSrMH8pfPm0N~9GLI3~& diff --git a/data/baseline/brain1_gldm.npy 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ncmaFS!uXkB)+op@F53rjA1G#6Z1?3G5r|UpfK+sUQlu diff --git a/pyproject.toml b/pyproject.toml index 3fd67f92..01d03e78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -98,6 +98,7 @@ addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"] xfail_strict = true filterwarnings = [ "error", + "ignore:the load_module\\(\\) method is deprecated:DeprecationWarning", ] log_cli_level = "INFO" testpaths = [ From fd0325ea05e6d194eba65fa27e86399eecaaee2f Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Tue, 28 Jan 2025 17:30:54 +0000 Subject: [PATCH 04/15] ENH: Exclude some config files from sdist - Excludes github config from `.github`. - Excludes `.*` files in the root. --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 01d03e78..83544c78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,6 +73,7 @@ minimum-version = "build-system.requires" build-dir = "build/{wheel_tag}" metadata.version.provider = "scikit_build_core.metadata.setuptools_scm" sdist.include = ["radiomics/_version.py"] +sdist.exclude = [".github", '.*'] wheel.packages = ['radiomics', 'radiomics.scripts'] wheel.exclude = ['radiomics/src'] From a3d5b1f2186463d82ac53407fc2714991f8851d7 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Tue, 28 Jan 2025 17:57:10 +0000 Subject: [PATCH 05/15] CI: Remove CircleCI and AppVeyor workflows Also remove deprecated requirements files (now defined in `pyproject.toml`. --- .circleci/config.yml | 314 --------------------------------------- .github/workflows/ci.yml | 2 +- README.md | 181 +++++++++++++--------- appveyor.yml | 72 --------- requirements-dev.txt | 5 - requirements-setup.txt | 1 - requirements.txt | 5 - scikit-ci.yml | 52 ------- 8 files changed, 110 insertions(+), 522 deletions(-) delete mode 100644 .circleci/config.yml delete mode 100644 appveyor.yml delete mode 100644 requirements-dev.txt delete mode 100644 requirements-setup.txt delete mode 100644 requirements.txt delete mode 100644 scikit-ci.yml diff --git a/.circleci/config.yml b/.circleci/config.yml deleted file mode 100644 index 179f0312..00000000 --- a/.circleci/config.yml +++ /dev/null @@ -1,314 +0,0 @@ -# To test: -# docker pull circleci/picard -# docker run -it --rm -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):$(pwd) -v ~/.circleci/:/root/.circleci --workdir $(pwd) circleci/picard circleci build - -version: 2.1 -jobs: - test-notebooks: - working_directory: /pyradiomics - docker: - - image: jupyter/datascience-notebook - user: root - steps: - - run: - # CircleCI says we need SSH and the docker doesn't have it installed - name: Update - command: | - apt-get update - apt-get install -y openssh-client openssh-server - - run: - name: Avoid hosts unknown for github - command: echo -e "Host github.com\n\tStrictHostKeyChecking no\n" > /etc/ssh/ssh_config - - checkout - - run: - name: Install pyradiomics in Python 3 - command: | - source activate root - python -m pip install --no-cache-dir -r requirements.txt - python -m pip install --no-cache-dir -r requirements-dev.txt - python setup.py install - - run: - name: test notebooks in python 3 - command: | - jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute notebooks/helloRadiomics.ipynb notebooks/helloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb - - build-mac-37: &build_mac_template - working_directory: ~/pyradiomics - macos: - xcode: 12.5.1 - environment: - PYTHON_VERSION: 3.7.10 - PYTHON_SHORT_VERSION: 3.7 - steps: - - run: - name: Setup MAC OS environment - # Workaround the following error occurring because python installation is cached but gettext dependency is not - # dyld: Library not loaded: /usr/local/opt/gettext/lib/libintl.8.dylib - # Referenced from: /Users/travis/.pyenv/versions/3.7.2/bin/python - # Reason: Incompatible library version: python requires version 11.0.0 or later, but libintl.8.dylib provides version 10.0.0 - # See https://github.com/scikit-build/cmake-python-distributions/issues/112 and - # https://github.com/scikit-build/cmake-python-distributions/pull/113 - command: | - echo "HOMEBREW_NO_AUTO_UPDATE=1" >> $BASH_ENV - brew install gettext - brew install pyenv - echo 'export PATH=$HOME/.pyenv/versions/$PYTHON_VERSION/bin:$HOME/bin:$PATH' >> $BASH_ENV - mkdir -p $HOME/bin - ln -s $(which pip3) $HOME/bin/pip - ln -s $(which python3) $HOME/bin/python - pyenv install --list - pyenv install $PYTHON_VERSION - - run: - name: Setup SciKit-CI - command: | - pip install scikit-ci scikit-ci-addons - ci_addons --install ../addons - - run: - name: Setup PyEnv - command: python ../addons/travis/install_pyenv.py - - checkout - - attach_workspace: - at: ~/pyradiomics - - run: - name: Install - command: ci install - - run: - name: Test - command: ci test - - run: - name: Build Distribution - command: ci after_test - - persist_to_workspace: - root: . - paths: [dist] - - build-mac-38: - <<: *build_mac_template - environment: - PYTHON_VERSION: 3.8.10 - PYTHON_SHORT_VERSION: 3.7 - - build-mac-39: - <<: *build_mac_template - environment: - PYTHON_VERSION: 3.9.5 - PYTHON_SHORT_VERSION: 3.9 - - build-37: &build_template - working_directory: /pyradiomics - docker: - - image: cimg/python:3.7 - user: root - steps: - - checkout - - attach_workspace: - at: /pyradiomics - - run: - name: Setup SciKit-CI - command: | - pip install scikit-ci==0.13.0 scikit-ci-addons==0.11.0 - ci_addons --install ../addons - - run: - name: Install - command: ci install - - run: - name: Test - command: ci test - - run: - name: Build Distribution - command: ci after_test - - persist_to_workspace: - root: . - paths: [dist] - - build-38: - <<: *build_template - docker: - - image: cimg/python:3.8 - user: root - - build-39: - <<: *build_template - docker: - - image: cimg/python:3.9 - user: root - - test_deploy: - working_directory: /pyradiomics - docker: - - image: cimg/python:3.8 - user: root - steps: - - run: - name: Check Repo User - command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi - - checkout - - run: - name: Setup SciKit-CI - command: | - pip install scikit-ci scikit-ci-addons - ci_addons --install ../addons - - run: - name: Install - command: ci install - - run: - name: Install patchelf auditwheel, twine - command: | - apt update - apt-get install patchelf # needed to run auditwheel - python -m pip install "auditwheel<3.2.0" - python -m pip install twine - # only attach the workspace at this point to prevent the removal of source distributions - - attach_workspace: - at: /pyradiomics - - run: - name: Create sdist - command: python setup.py sdist - - run: - name: Fix Distribution Wheels - command: | - ls ./dist/*-linux_$(uname -m).whl # This will prevent further deployment if no wheels are found - # Since there are no external shared libraries to bundle into the wheels - # this step will fixup the wheel switching from 'linux' to 'manylinux1' tag - for whl in $(ls ./dist/*-linux_$(uname -m).whl); do - python -m auditwheel repair $whl -w ./dist/ - rm $whl - done - - run: - name: Deploy source and linux wheels - command: python -m twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_TEST_USER -p $PYPI_TEST_PASSWORD -r testpypi - - deploy: - working_directory: /pyradiomics - docker: - - image: cimg/python:3.6 - user: root - steps: - - run: - name: Check Repo User - command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi - - checkout - - run: - name: Setup SciKit-CI - command: | - pip install scikit-ci scikit-ci-addons - ci_addons --install ../addons - - run: - name: Install - command: ci install - - run: - name: Install patchelf auditwheel, twine - command: | - apt update - apt-get install patchelf # needed to run auditwheel - python -m pip install "auditwheel<3.2.0" - python -m pip install twine - # only attach the workspace at this point to prevent the removal of source distributions - - attach_workspace: - at: /pyradiomics - - run: - name: Create sdist - command: python setup.py sdist - - run: - name: Fix Distribution Wheels - command: | - ls ./dist/*-linux_$(uname -m).whl # This will prevent further deployment if no wheels are found - # Since there are no external shared libraries to bundle into the wheels - # this step will fixup the wheel switching from 'linux' to 'manylinux1' tag - for whl in $(ls ./dist/*-linux_$(uname -m).whl); do - python -m auditwheel repair $whl -w ./dist/ - rm $whl - done - - run: - name: Deploy source and linux wheels - command: python -m twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_USER -p $PYPI_PASSWORD - - deploy_conda: - working_directory: /pyradiomics - docker: - - image: cimg/python:3.8 - user: root - steps: - - run: - name: Check Repo User - command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi - - checkout - - run: - name: Install Miniconda - command: | - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; - bash miniconda.sh -b -p $HOME/miniconda - hash -r - echo 'export PATH=$HOME/miniconda/bin:$PATH' >> $BASH_ENV - - run: - name: Configure Miniconda - command: | - conda install gcc_linux-64 libgcc - bash ./conda/configure_conda.sh - - run: - name: Build Conda packages - command: | - mkdir /conda-bld - conda build ./conda --python=3.6 --croot /conda-bld - conda build ./conda --python=3.7 --croot /conda-bld - conda build ./conda --python=3.8 --croot /conda-bld - conda build ./conda --python=3.9 --croot /conda-bld - - run: - name: Deploy Conda packages - command: | - anaconda -t $ANACONDA_TOKEN upload -u Radiomics /conda-bld/linux-64/pyradiomics-*.tar.bz2 --force - -workflows: - version: 2 - build_and_deploy: - jobs: - - build-mac-37: &build_job_template - filters: - tags: - only: - - /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?/ - - build-mac-38: - <<: *build_job_template - - build-mac-39: - <<: *build_job_template - - build-37: - <<: *build_job_template - - build-38: - <<: *build_job_template - - build-39: - <<: *build_job_template - - test-notebooks: &requires_template - requires: - - build-37 - - build-38 - - build-39 - - build-mac-37 - - build-mac-38 - - build-mac-39 - - test_deploy: - <<: *requires_template - filters: - branches: - ignore: - - /.*/ - tags: - only: - - /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)/ - - deploy: - <<: *requires_template - filters: - branches: - ignore: - - /.*/ - tags: - only: - - /^v?[0-9]+(\.[0-9]+)*/ - - deploy_conda: - <<: *requires_template - filters: - branches: - ignore: - - /.*/ - tags: - only: - - /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?/ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f6286d2c..6d34beaf 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,7 +5,7 @@ on: pull_request: push: branches: - - main + - master concurrency: group: ${{ github.workflow }}-${{ github.ref }} diff --git a/README.md b/README.md index 02795f2b..f0aa41e0 100644 --- a/README.md +++ b/README.md @@ -6,46 +6,55 @@ | ----------------------------- | ----------------------------- | | [![][circleci]][circleci-lnk] | [![][appveyor]][appveyor-lnk] | - -[appveyor]: https://ci.appveyor.com/api/projects/status/kvu7897q0v4imwdc?svg=true +[appveyor]: + https://ci.appveyor.com/api/projects/status/kvu7897q0v4imwdc?svg=true [appveyor-lnk]: https://ci.appveyor.com/project/AIM-Harvard/pyradiomics-k4sto - -[circleci]: https://dl.circleci.com/status-badge/img/gh/AIM-Harvard/pyradiomics/tree/master.svg?style=shield +[circleci]: + https://dl.circleci.com/status-badge/img/gh/AIM-Harvard/pyradiomics/tree/master.svg?style=shield [circleci-lnk]: https://circleci.com/gh/AIM-Harvard/pyradiomics ## Radiomics feature extraction in Python -This is an open-source python package for the extraction of Radiomics features from medical imaging. -With this package we aim to establish a reference standard for Radiomic Analysis, and provide a tested and maintained -open-source platform for easy and reproducible Radiomic Feature extraction. By doing so, we hope to increase awareness -of radiomic capabilities and expand the community. +This is an open-source python package for the extraction of Radiomics features +from medical imaging. -The platform supports both the feature extraction in 2D and 3D and can be used to calculate single values per feature -for a region of interest ("segment-based") or to generate feature maps ("voxel-based"). +With this package we aim to establish a reference standard for Radiomic +Analysis, and provide a tested and maintained open-source platform for easy and +reproducible Radiomic Feature extraction. By doing so, we hope to increase +awareness of radiomic capabilities and expand the community. + +The platform supports both the feature extraction in 2D and 3D and can be used +to calculate single values per feature for a region of interest +("segment-based") or to generate feature maps ("voxel-based"). **Not intended for clinical use.** -**If you publish any work which uses this package, please cite the following publication:** -*van Griethuysen, J. J. M., Fedorov, A., Parmar, C., Hosny, A., Aucoin, N., Narayan, V., Beets-Tan, R. G. H., -Fillion-Robin, J. C., Pieper, S., Aerts, H. J. W. L. (2017). Computational Radiomics System to Decode the Radiographic -Phenotype. Cancer Research, 77(21), e104–e107. https://doi.org/10.1158/0008-5472.CAN-17-0339* +**If you publish any work which uses this package, please cite the following +publication:** _van Griethuysen, J. J. M., Fedorov, A., Parmar, C., Hosny, A., +Aucoin, N., Narayan, V., Beets-Tan, R. G. H., Fillion-Robin, J. C., Pieper, S., +Aerts, H. J. W. L. (2017). Computational Radiomics System to Decode the +Radiographic Phenotype. Cancer Research, 77(21), e104–e107. +https://doi.org/10.1158/0008-5472.CAN-17-0339_ ### Join the Community! -Please join the [Radiomics community section of the 3D Slicer Discourse](https://discourse.slicer.org/c/community/radiomics/23). +Please join the +[Radiomics community section of the 3D Slicer Discourse](https://discourse.slicer.org/c/community/radiomics/23). ### Feature Classes + Currently supports the following feature classes: - - First Order Statistics - - Shape-based (2D and 3D) - - Gray Level Co-occurrence Matrix (GLCM) - - Gray Level Run Length Matrix (GLRLM) - - Gray Level Size Zone Matrix (GLSZM) - - Gray Level Dependece Matrix (GLDM) - - Neighboring Gray Tone Difference Matrix (NGTDM) +- First Order Statistics +- Shape-based (2D and 3D) +- Gray Level Co-occurrence Matrix (GLCM) +- Gray Level Run Length Matrix (GLRLM) +- Gray Level Size Zone Matrix (GLSZM) +- Gray Level Dependece Matrix (GLDM) +- Neighboring Gray Tone Difference Matrix (NGTDM) ### Filter Classes + Aside from the feature classes, there are also some built-in optional filters: - Laplacian of Gaussian (LoG, based on SimpleITK functionality) @@ -58,41 +67,55 @@ Aside from the feature classes, there are also some built-in optional filters: - Local Binary Pattern (LBP) 2D / 3D ### Supporting reproducible extraction -Aside from calculating features, the pyradiomics package includes provenance information in the -output. This information contains information on used image and mask, as well as applied settings -and filters, thereby enabling fully reproducible feature extraction. + +Aside from calculating features, the pyradiomics package includes provenance +information in the output. This information contains information on used image +and mask, as well as applied settings and filters, thereby enabling fully +reproducible feature extraction. ### Documentation -For more information, see the sphinx generated documentation available [here](http://pyradiomics.readthedocs.io/). -Alternatively, you can generate the documentation by checking out the master branch and running from the root directory: +For more information, see the sphinx generated documentation available +[here](http://pyradiomics.readthedocs.io/). + +Alternatively, you can generate the documentation by checking out the master +branch and running from the root directory: python setup.py build_sphinx -The documentation can then be viewed in a browser by opening `PACKAGE_ROOT\build\sphinx\html\index.html`. +The documentation can then be viewed in a browser by opening +`PACKAGE_ROOT\build\sphinx\html\index.html`. -Furthermore, an instruction video is available [here](http://radiomics.io/pyradiomics.html). +Furthermore, an instruction video is available +[here](http://radiomics.io/pyradiomics.html). ### Installation -PyRadiomics is OS independent and compatible with Python >= 3.5. Pre-built binaries are available on -PyPi and Conda. To install PyRadiomics, ensure you have python -installed and run: + +PyRadiomics is OS independent and compatible with Python >= 3.5. Pre-built +binaries are available on PyPi and Conda. To install PyRadiomics, ensure you +have python installed and run: `python -m pip install pyradiomics` -Detailed installation instructions, as well as instructions for building PyRadiomics from source, are available in the +Detailed installation instructions, as well as instructions for building +PyRadiomics from source, are available in the [documentation](http://pyradiomics.readthedocs.io/en/latest/installation.html). ### Docker -PyRadiomics also supports [Dockers](https://www.docker.com/). Currently, 2 dockers are available: -The first one is a [Jupyter notebook](http://jupyter.org/) with PyRadiomics pre-installed with example Notebooks. +PyRadiomics also supports [Dockers](https://www.docker.com/). Currently, 2 +dockers are available: + +The first one is a [Jupyter notebook](http://jupyter.org/) with PyRadiomics +pre-installed with example Notebooks. To get the Docker: docker pull radiomics/pyradiomics:latest -The `radiomics/notebook` Docker has an exposed volume (`/data`) that can be mapped to the host system directory. For example, to mount the current directory: +The `radiomics/notebook` Docker has an exposed volume (`/data`) that can be +mapped to the host system directory. For example, to mount the current +directory: docker run --rm -it --publish 8888:8888 -v `pwd`:/data radiomics/notebook @@ -100,9 +123,11 @@ or for a less secure notebook, skip the randomly generated token docker run --rm -it --publish 8888:8888 -v `pwd`:/data radiomics/notebook start-notebook.sh --NotebookApp.token='' -and open the local webpage at http://localhost:8888/ with the current directory at http://localhost:8888/tree/data. +and open the local webpage at http://localhost:8888/ with the current directory +at http://localhost:8888/tree/data. -The second is a docker which exposes the PyRadiomics CLI interface. To get the CLI-Docker: +The second is a docker which exposes the PyRadiomics CLI interface. To get the +CLI-Docker: docker pull radiomics/pyradiomics:CLI @@ -114,52 +139,64 @@ For more information on using docker, see [here](https://pyradiomics.readthedocs.io/en/latest/installation.html#use-pyradiomics-docker) ### Usage + PyRadiomics can be easily used in a Python script through the `featureextractor` -module. Furthermore, PyRadiomics provides a commandline script, `pyradiomics`, for both single image extraction and -batchprocessing. Finally, a convenient front-end interface is provided as the 'Radiomics' -extension for 3D Slicer, available [here](https://github.com/AIM-Harvard/SlicerRadiomics). +module. Furthermore, PyRadiomics provides a commandline script, `pyradiomics`, +for both single image extraction and batchprocessing. Finally, a convenient +front-end interface is provided as the 'Radiomics' extension for 3D Slicer, +available [here](https://github.com/AIM-Harvard/SlicerRadiomics). ### 3rd-party packages used in pyradiomics: - - SimpleITK (Image loading and preprocessing) - - numpy (Feature calculation) - - PyWavelets (Wavelet filter) - - pykwalify (Enabling yaml parameters file checking) - - six (Python 3 Compatibility) - - scipy (Only for LBP filter, install separately to enable this filter) - - scikit-image (Only for LBP filter, install separately to enable this filter) - - trimesh (Only for LBP filter, install separately to enable this filter) -See also the [requirements file](requirements.txt). +- SimpleITK (Image loading and preprocessing) +- numpy (Feature calculation) +- PyWavelets (Wavelet filter) +- pykwalify (Enabling yaml parameters file checking) +- six (Python 3 Compatibility) +- scipy (Only for LBP filter, install separately to enable this filter) +- scikit-image (Only for LBP filter, install separately to enable this filter) +- trimesh (Only for LBP filter, install separately to enable this filter) + +See also the requirements section of the [pyproject file](pyproject.toml). ### 3D Slicer -PyRadiomics is also available as an [extension](https://github.com/AIM-Harvard/SlicerRadiomics) to [3D Slicer](slicer.org). -Download and install the 3D slicer [nightly build](http://download.slicer.org/), the extension is then available in the -extension manager under "SlicerRadiomics". + +PyRadiomics is also available as an +[extension](https://github.com/AIM-Harvard/SlicerRadiomics) to +[3D Slicer](slicer.org). Download and install the 3D slicer +[nightly build](http://download.slicer.org/), the extension is then available in +the extension manager under "SlicerRadiomics". ### License + This package is covered by the open source [3-clause BSD License](LICENSE.txt). ### Developers - - [Joost van Griethuysen](https://github.com/JoostJM)1,3,4 - - [Andriy Fedorov](https://github.com/fedorov)2 - - [Nicole Aucoin](https://github.com/naucoin)2 - - [Jean-Christophe Fillion-Robin](https://github.com/jcfr)5 - - [Ahmed Hosny](https://github.com/ahmedhosny)1 - - [Steve Pieper](https://github.com/pieper)6 - - [Hugo Aerts (PI)](https://github.com/hugoaerts)1,2 - -1Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, -2Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, -3Department of Radiology, Netherlands Cancer Institute, Amsterdam, The Netherlands, -4GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands, -5Kitware, -6Isomics + +- [Joost van Griethuysen](https://github.com/JoostJM)1,3,4 +- [Andriy Fedorov](https://github.com/fedorov)2 +- [Nicole Aucoin](https://github.com/naucoin)2 +- [Jean-Christophe Fillion-Robin](https://github.com/jcfr)5 +- [Ahmed Hosny](https://github.com/ahmedhosny)1 +- [Steve Pieper](https://github.com/pieper)6 +- [Hugo Aerts (PI)](https://github.com/hugoaerts)1,2 + +1Department of Radiation Oncology, Dana-Farber Cancer Institute, +Brigham and Women's Hospital, Harvard Medical School, Boston, MA, +2Department of Radiology, Brigham and Women's Hospital, Harvard +Medical School, Boston, MA, 3Department of Radiology, Netherlands +Cancer Institute, Amsterdam, The Netherlands, 4GROW-School for +Oncology and Developmental Biology, Maastricht University Medical Center, +Maastricht, The Netherlands, 5Kitware, 6Isomics ### Contact -We are happy to help you with any questions. Please contact us on the [Radiomics community section of the 3D Slicer Discourse](https://discourse.slicer.org/c/community/radiomics/23). -We welcome contributions to PyRadiomics. Please read the [contributing guidelines](CONTRIBUTING.rst) on how to -contribute to PyRadiomics. +We are happy to help you with any questions. Please contact us on the +[Radiomics community section of the 3D Slicer Discourse](https://discourse.slicer.org/c/community/radiomics/23). + +We welcome contributions to PyRadiomics. Please read the +[contributing guidelines](CONTRIBUTING.rst) on how to contribute to PyRadiomics. -**This work was supported in part by the US National Cancer Institute grants: -U24CA194354 - QUANTITATIVE RADIOMICS SYSTEM DECODING THE TUMOR PHENOTYPE and U01CA190234 - TUMOR GENOTYPE AND RADIOMIC PHENOTYPE IN LUNG CANCER** +**This work was supported in part by the US National Cancer Institute grants: +U24CA194354 - QUANTITATIVE RADIOMICS SYSTEM DECODING THE TUMOR PHENOTYPE and +U01CA190234 - TUMOR GENOTYPE AND RADIOMIC PHENOTYPE IN LUNG CANCER** diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index cfcda140..00000000 --- a/appveyor.yml +++ /dev/null @@ -1,72 +0,0 @@ -version: "3.0.{build}" - -image: Visual Studio 2019 -environment: - PYTHON_ARCH: "64" - BLOCK: "0" - - matrix: - - # Visual Studio (Python 3, 64 bit) - - - PYTHON_DIR: "C:\\Python37-x64" - PYTHON_VERSION: "3.7.x" - PYTHON_SHORT_VERSION: "3.7" - - - PYTHON_DIR: "C:\\Python38-x64" - PYTHON_VERSION: "3.8.x" - PYTHON_SHORT_VERSION: "3.8" - - - PYTHON_DIR: "C:\\Python39-x64" - PYTHON_VERSION: "3.9.x" - PYTHON_SHORT_VERSION: "3.9" - -init: - - ps: $env:PATH=$env:PYTHON_DIR + ";" + $env:PYTHON_DIR + "\\Scripts;" + $env:PATH - # - ps: iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1')) - - ps: python -c "import sys;print(sys.version, sys.executable)" - - python -m pip install scikit-ci scikit-ci-addons - - python -m ci_addons --install ../addons - - python -m pip install twine - - - ps: ../addons/appveyor/rolling-build.ps1 - -install: - - ci install - -build_script: - - ci build - -test_script: - - ci test - -after_test: - - ci after_test - -artifacts: - - path: dist/* - name: pypiartefacts - -on_finish: - - ps: ../addons/appveyor/enable-worker-remote-access.ps1 -check_for_block - -deploy_script: - - echo checking deployment - - ps: if ($env:APPVEYOR_REPO_NAME -notmatch 'AIM-Harvard/pyradiomics') { appveyor exit } - - ps: if ($env:APPVEYOR_REPO_TAG_NAME -notmatch '^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?$') { appveyor exit } - - echo starting PyPi deployment - - ps: if ($env:APPVEYOR_REPO_TAG_NAME -match '^v?[0-9]+(\.[0-9]+)*$') { twine upload dist/*.whl -u $Env:PYPI_USER -p $Env:PYPI_PASSWORD } - - ps: if ($env:APPVEYOR_REPO_TAG_NAME -match '^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)$') { twine upload dist/*.whl -u $Env:PYPI_TEST_USER -p $Env:PYPI_TEST_PASSWORD -r testpypi } - - echo starting Anaconda deployment - - CALL C:\Miniconda3-x64\condabin\conda.bat activate - - conda config --set always_yes yes --set changeps1 no --set anaconda_upload no - - conda config --add channels simpleitk --add channels conda-forge - - conda install conda-build - - conda install anaconda-client - - conda update -q conda - - conda build ./conda --python=%PYTHON_SHORT_VERSION% --croot C:/conda-bld - - anaconda -t %ANACONDA_TOKEN% upload -u Radiomics C:/conda-bld/win-64/pyradiomics-*.tar.bz2 --force - - echo finished deployment - -matrix: - fast_finish: false diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index d3315d69..00000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,5 +0,0 @@ -pytest -flake8 -flake8-import-order -sphinx>=1.4 -sphinx_rtd_theme>=0.2.2 diff --git a/requirements-setup.txt b/requirements-setup.txt deleted file mode 100644 index 2569c8a4..00000000 --- a/requirements-setup.txt +++ /dev/null @@ -1 +0,0 @@ -numpy>=1.9.2 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index e533ab68..00000000 --- a/requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -numpy -SimpleITK -PyWavelets -pykwalify -six diff --git a/scikit-ci.yml b/scikit-ci.yml deleted file mode 100644 index 8aabcda7..00000000 --- a/scikit-ci.yml +++ /dev/null @@ -1,52 +0,0 @@ -schema_version: "0.5.0" - -before_install: - - appveyor: - environment: - RUN_ENV: .\\..\\addons\\appveyor\\run-with-visual-studio.cmd - commands: - - python ../addons/appveyor/patch_vs2008.py - - $ pip install numpy>=1.9.2 - - $ pip install cython - - circle: - environment: - PATH: /opt/python/$/bin:$ - commands: - - rm -rf dist/* - - travis: - osx: - environment: - PATH: $/.pyenv/versions/$/bin:$ - commands: - - python ../addons/travis/install_pyenv.py - -install: - commands: - - python --version - - python -m pip install --disable-pip-version-check --upgrade pip - - $ pip install wheel>=0.29.0 - - $ pip install setuptools>=38.6.0 - - $ pip install numpy>=1.9.2 - - $ pip install SimpleITK>=0.9.1 - - $ python -c "import SimpleITK; print('SimpleITK Version:' + SimpleITK.Version_VersionString())" - - $ pip install -r requirements.txt - - $ pip install -r requirements-dev.txt - -before_build: - commands: - - flake8 - -build: - commands: - - $ python setup.py develop - -test: - commands: - - $ pytest - -after_test: - commands: - - $ python setup.py bdist_wheel From 182b7c7d664b042962bcd5203c8b7f60c3197df6 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 08:58:07 +0000 Subject: [PATCH 06/15] ENH: Also run ci workflow on specific branch For migration purposes, also add the `refactor-build-system` branch to the push event of the CI workflow. --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6d34beaf..4bf909a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -6,6 +6,7 @@ on: push: branches: - master + - refactor-build-system concurrency: group: ${{ github.workflow }}-${{ github.ref }} From d42a24acc4a8d36448871d679afac74e05aec150 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 09:10:02 +0000 Subject: [PATCH 07/15] CI: Disable pre-commit job for current branch Due to migration being in progress, the pre-commit job is expected to fail. Error occurring in this job are scheduled to be fixed after CI setup is up and running to catch bugs that arise due to style changes. --- .github/workflows/ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4bf909a5..3b56744e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,6 +19,7 @@ env: jobs: pre-commit: + if: ${{ github.ref_name != 'refactor-build-system' }} name: Format runs-on: ubuntu-latest steps: @@ -37,7 +38,7 @@ jobs: checks: name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} runs-on: ${{ matrix.runs-on }} - needs: [pre-commit] + #needs: [pre-commit] strategy: fail-fast: false matrix: From 2b29460494b2108bbaf7a224ff81823c10a065fc Mon Sep 17 00:00:00 2001 From: Jean-Christophe Fillion-Robin Date: Wed, 29 Jan 2025 07:55:17 -0500 Subject: [PATCH 08/15] CI: Fix wheel generation renaming _version.py to _version.pyi This commit fixes the following error: ``` $ pip install .[test] [...] *** Making wheel... 2025-01-29 09:11:34,654 - scikit_build_core - ERROR - Metadata mismatch in METADATA: b'Metadata-Version: 2.1\nName: pyradiomics\nVersion: 3.0.1a4.dev38+gf2f3c6b\nSummary: Radiomics features library for python\nKeywords: radiomics,cancerimaging,medicalresearch,computationalimaging\nAuthor-Email: PyRadiomics Community \n[...]' Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in main() File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel return _build_backend().build_wheel(wheel_directory, config_settings, File "/tmp/pip-build-env-u6dnfh2j/overlay/lib/python3.9/site-packages/scikit_build_core/build/__init__.py", line 33, in build_wheel return _build_wheel_impl( File "/tmp/pip-build-env-u6dnfh2j/overlay/lib/python3.9/site-packages/scikit_build_core/build/wheel.py", line 175, in _build_wheel_impl return _build_wheel_impl_impl( File "/tmp/pip-build-env-u6dnfh2j/overlay/lib/python3.9/site-packages/scikit_build_core/build/wheel.py", line 508, in _build_wheel_impl_impl raise AssertionError(msg) AssertionError: Metadata mismatch in METADATA [...] ``` --- .gitignore | 2 +- radiomics/{_version.py => _version.pyi} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename radiomics/{_version.py => _version.pyi} (100%) diff --git a/.gitignore b/.gitignore index aa0ed637..b26e91d2 100644 --- a/.gitignore +++ b/.gitignore @@ -142,7 +142,7 @@ dmypy.json cython_debug/ # setuptools_scm -src/*/_version.py +radiomics/_version.py # ruff diff --git a/radiomics/_version.py b/radiomics/_version.pyi similarity index 100% rename from radiomics/_version.py rename to radiomics/_version.pyi From 5d51087e0d785a91176e4bd8263e0d8846c0815a Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 13:05:34 +0000 Subject: [PATCH 09/15] CI: Install pyradiomics as editable to correctly run tests. --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3b56744e..52362184 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -60,7 +60,7 @@ jobs: allow-prereleases: true - name: Install package - run: python -m pip install .[test] + run: python -m pip install -e .[test] - name: Test package run: >- From db2d95b93d81b1ded87c4b358b03b5b1d2a9bd2b Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 14:00:38 +0000 Subject: [PATCH 10/15] CI: Update Python versions Supports Python versions 3.8-3.10. 3.11+ fails with segmentation fault, most likely due to new multithreading support. --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 52362184..a8138dd3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,7 +42,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.13"] + python-version: ["3.8", "3.9", "3.10"] runs-on: [ubuntu-latest, windows-latest, macos-14] include: From ae57151eb3bd5c467366ea2077d8b3375ed315df Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 14:15:09 +0000 Subject: [PATCH 11/15] CI: Remove pypy-3.10 Fails CI because of an error during a build of SimpleITK (apparently no appropriate wheel available). --- .github/workflows/ci.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a8138dd3..3dc6ea4f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,10 +45,6 @@ jobs: python-version: ["3.8", "3.9", "3.10"] runs-on: [ubuntu-latest, windows-latest, macos-14] - include: - - python-version: "pypy-3.10" - runs-on: ubuntu-latest - steps: - uses: actions/checkout@v4 with: From 9c52147cc7498866aea44c705993306d4d1eb9c4 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 18:04:49 +0000 Subject: [PATCH 12/15] STYL: Add .git-blame-ignore-revs Allows to exclude commits from git-blame. This should contain commits reflecting only style changes. --- .git-blame-ignore-revs | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 .git-blame-ignore-revs diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs new file mode 100644 index 00000000..ede1bf81 --- /dev/null +++ b/.git-blame-ignore-revs @@ -0,0 +1,32 @@ +# Run this command to always ignore formatting commits in `git blame` +# git config blame.ignoreRevsFile .git-blame-ignore-revs + +# Add commit hashes below to exclude them from the git blame history + +# typos +103a16df931f36199055c97a64a9f13703d7205f +73cdf13c7073a7f0d404bc04d16303a4c9b9ad87 +c1bddb96a9898d2e954a3fe065c12ac3c301c12e +df824811c0a7cb96736d18b0050517f4321b957d +aa51f3f03235bf26e1e235d982e7e9844660a1df +462f3476ca27bdc477eb1b7cec8a02104d9a4bda +70f1c4827a4dd7904c11e47e5f672884f9d6bc48 +da7321dd4d5f704ecfc92398509670b1de07360a +4ba909ab798fa1c206ab5410a441194a825d47ec +8061e7f785a99441e3f7c43136cb9309498ce0ac +b677b0dc593987d8eee2a30516148ba1d50cc8a2 +8f12a5165acfdcdf2dfe32e1e3d4b03dd5245669 +eae15efff0fe67dbe05e74876ed564cf21e87412 +c46ed88c6ed69af4c29860826624b45af05ba268 +e24a67e4f3abb6ffcfa315c3118667f94df86cf2 +bafd7e21dd97a495dd8eab01ef32dd9cb6184bb6 +896682d785dac99d13cb1abb7f1cf47f494c0064 +e100f1d014ecb9e19f2fc929323e448be70e7f3a +33f564907c484c4151a5b0052130b511cc91a036 +8bf0b05781fe4c1b3358b3048b0c3bdb9a8ff2ba +25db7e8a9a781fee9f7a5dc72f9dbe7dbe65f05e +304f73335fc781f005bd49a13b3af34807308ded +51a6d00bb4beb07d64a530f9db8bebf800c2345d + +# Style changes +be9f2b2c1e10c947f5845725152332a5ba1a2f7e From 632c739891a6360c08b15dc3a9e64c2fe6994755 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 18:24:39 +0000 Subject: [PATCH 13/15] CI: Re-enable pre-commit, disable failing checks. See issue #899 --- .github/workflows/ci.yml | 3 +- .pre-commit-config.yaml | 100 ++++++++++++++++++++------------------- 2 files changed, 52 insertions(+), 51 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3dc6ea4f..ea11356e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,6 @@ env: jobs: pre-commit: - if: ${{ github.ref_name != 'refactor-build-system' }} name: Format runs-on: ubuntu-latest steps: @@ -38,7 +37,7 @@ jobs: checks: name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} runs-on: ${{ matrix.runs-on }} - #needs: [pre-commit] + needs: [pre-commit] strategy: fail-fast: false matrix: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ea65b8cf..0ac21ab2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,73 +18,75 @@ repos: - id: check-case-conflict - id: check-merge-conflict - id: check-symlinks - - id: check-yaml + #- id: check-yaml # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899) - id: debug-statements - id: end-of-file-fixer - id: mixed-line-ending - - id: name-tests-test - args: ["--pytest-test-first"] + #- id: name-tests-test # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899) + # args: ["--pytest-test-first"] - id: requirements-txt-fixer - - id: trailing-whitespace + #- id: trailing-whitespace # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899) - repo: https://github.com/pre-commit/pygrep-hooks rev: "v1.10.0" hooks: - - id: rst-backticks + #- id: rst-backticks # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899) - id: rst-directive-colons - id: rst-inline-touching-normal - - repo: https://github.com/rbubley/mirrors-prettier - rev: "v3.4.2" - hooks: - - id: prettier - types_or: [yaml, markdown, html, css, scss, javascript, json] - args: [--prose-wrap=always] + # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899) - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.9.2" - hooks: - - id: ruff - args: ["--fix", "--show-fixes"] - - id: ruff-format + #- repo: https://github.com/rbubley/mirrors-prettier + # rev: "v3.4.2" + # 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: "v19.1.7" - hooks: - - id: clang-format - types_or: [c++, c, cuda] + #- repo: https://github.com/astral-sh/ruff-pre-commit + # rev: "v0.9.2" + # hooks: + # - id: ruff + # args: ["--fix", "--show-fixes"] + # - id: ruff-format - - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.14.1" - hooks: - - id: mypy - files: src|tests - args: [] - additional_dependencies: - - pytest + #- repo: https://github.com/pre-commit/mirrors-clang-format + # rev: "v19.1.7" + # hooks: + # - id: clang-format + # types_or: [c++, c, cuda] - - repo: https://github.com/codespell-project/codespell - rev: "v2.3.0" - hooks: - - id: codespell + #- repo: https://github.com/pre-commit/mirrors-mypy + # rev: "v1.14.1" + # hooks: + # - id: mypy + # files: src|tests + # args: [] + # additional_dependencies: + # - pytest - - repo: https://github.com/shellcheck-py/shellcheck-py - rev: "v0.10.0.1" - hooks: - - id: shellcheck + #- repo: https://github.com/codespell-project/codespell + # rev: "v2.3.0" + # hooks: + # - id: codespell - - 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/shellcheck-py/shellcheck-py + # rev: "v0.10.0.1" + # hooks: + # - id: shellcheck - - repo: https://github.com/cheshirekow/cmake-format-precommit - rev: "v0.6.13" - hooks: - - id: cmake-format + #- 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: "v0.23" From a2b18ea7e3447f60951f4089cd4affce881144a0 Mon Sep 17 00:00:00 2001 From: Joost van Griethuysen Date: Wed, 29 Jan 2025 18:37:39 +0000 Subject: [PATCH 14/15] CI: Disable failing pylint See issue #899 --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ea11356e..dd88d7ca 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,8 +31,8 @@ jobs: - uses: pre-commit/action@v3.0.1 with: extra_args: --hook-stage manual --all-files - - name: Run PyLint - run: pipx run nox -s pylint -- --output-format=github + #- name: Run PyLint + # run: pipx run nox -s pylint -- --output-format=github checks: name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} From d891113656d8cab9c7979b84d9b7b82b1d4aeb5a Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Sat, 10 May 2025 08:13:21 -0500 Subject: [PATCH 15/15] ENH: Restrict to python3.9 and above. --- .github/workflows/ci.yml | 2 +- pyproject.toml | 8 +++----- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dd88d7ca..629db822 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -41,7 +41,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.9", "3.10"] runs-on: [ubuntu-latest, windows-latest, macos-14] steps: diff --git a/pyproject.toml b/pyproject.toml index 83544c78..3d648c10 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ authors = [ ] description = "Radiomics features library for python" readme = "README.md" -requires-python =">=3.8" +requires-python =">=3.9" license = { file = "LICENSE.txt"} keywords = [ "radiomics", "cancerimaging", "medicalresearch", "computationalimaging" ] classifiers = [ @@ -21,11 +21,9 @@ classifiers = [ 'License :: OSI Approved :: BSD License', 'Operating System :: OS Independent', 'Programming Language :: C', - 'Programming Language :: Python :: 3.5', - 'Programming Language :: Python :: 3.6', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', 'Topic :: Scientific/Engineering :: Bio-Informatics' ] dynamic = ["version"]