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/.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-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
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..629db822
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,68 @@
+name: CI
+
+on:
+ workflow_dispatch:
+ pull_request:
+ push:
+ branches:
+ - master
+ - refactor-build-system
+
+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", "3.10"]
+ runs-on: [ubuntu-latest, windows-latest, macos-14]
+
+ 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 -e .[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..b26e91d2 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
+radiomics/_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..0ac21ab2
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,102 @@
+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 # 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 # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
+ # args: ["--pytest-test-first"]
+ - id: requirements-txt-fixer
+ #- 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 # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
+ - id: rst-directive-colons
+ - id: rst-inline-touching-normal
+
+ # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
+
+ #- 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 f50e20be..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 src/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/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/data/baseline/brain1_glcm.npy b/data/baseline/brain1_glcm.npy
index 3954e738..4a9cc1e3 100644
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diff --git a/data/baseline/brain1_gldm.npy b/data/baseline/brain1_gldm.npy
index 3bc14ef5..4f31ccff 100644
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diff --git a/data/baseline/brain1_glrlm.npy b/data/baseline/brain1_glrlm.npy
index 62dc52e8..e7c012ec 100644
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diff --git a/data/baseline/brain1_glszm.npy b/data/baseline/brain1_glszm.npy
index a4a6cfe2..bf3ffa79 100644
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index 261465ce..63ccbe61 100644
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diff --git a/data/baseline/wavelet.npy b/data/baseline/wavelet.npy
index f5aa82df..118941bf 100644
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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 8183359a..3d648c10 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,16 +1,16 @@
[build-system]
-requires = ["setuptools>=61.0", "numpy", "versioneer"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core>=0.10", "numpy"]
+build-backend = "scikit_build_core.build"
+
[project]
name = "pyradiomics"
-version = "3.1.1"
authors = [
{ name = "PyRadiomics Community", email = "pyradiomics@googlegroups.com"}
]
description = "Radiomics features library for python"
readme = "README.md"
-requires-python =">=3.5"
+requires-python =">=3.9"
license = { file = "LICENSE.txt"}
keywords = [ "radiomics", "cancerimaging", "medicalresearch", "computationalimaging" ]
classifiers = [
@@ -21,13 +21,12 @@ 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"]
dependencies = [
"numpy",
"SimpleITK",
@@ -36,12 +35,150 @@ 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]
-"Homepaget" = "http://github.com/AIM-Harvard/pyradiomics#readme"
+"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.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"]
+sdist.exclude = [".github", '.*']
+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",
+ "ignore:the load_module\\(\\) method is deprecated:DeprecationWarning",
+]
+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
deleted file mode 100644
index e518ec05..00000000
--- a/radiomics/_version.py
+++ /dev/null
@@ -1,523 +0,0 @@
-# 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."""
-
-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}
diff --git a/radiomics/_version.pyi b/radiomics/_version.pyi
new file mode 100644
index 00000000..91744f98
--- /dev/null
+++ b/radiomics/_version.pyi
@@ -0,0 +1,4 @@
+from __future__ import annotations
+
+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/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
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
deleted file mode 100644
index 300c1be6..00000000
--- a/setup.py
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-
-from distutils import sysconfig
-import platform
-
-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 = [sysconfig.get_python_inc(), 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)