diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
deleted file mode 100644
index 6dac22f0..00000000
--- a/.github/workflows/pythonpackage.yml
+++ /dev/null
@@ -1,96 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python package
-
-on:
- push:
- branches: [ '*' ]
- tags: [ '*' ]
- pull_request:
- branches: [ master, 'maint/*' ]
-
-jobs:
- build:
- if: "!contains(github.event.head_commit.message, '[skip ci]')"
- runs-on: ubuntu-latest
- strategy:
- matrix:
- python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-
- steps:
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v5
- with:
- python-version: ${{ matrix.python-version }}
- - uses: actions/checkout@v4
- with:
- fetch-depth: 0
- - name: Build package
- run: |
- pipx run build
- - name: Determine expected version
- run: |
- python -m venv /tmp/getversion
- source /tmp/getversion/bin/activate
- python -m pip install setuptools_scm
-
- # Interpolate version
- if [[ "$GITHUB_REF" == refs/tags/* ]]; then
- TAG=${GITHUB_REF##*/}
- fi
- THISVERSION=$( python -m setuptools_scm )
- THISVERSION=${TAG:-$THISVERSION}
- echo "Expected VERSION: \"${THISVERSION}\""
- echo "THISVERSION=${THISVERSION}" >> ${GITHUB_ENV}
-
- - name: Install in confined environment [sdist]
- run: |
- python -m venv /tmp/install_sdist
- source /tmp/install_sdist/bin/activate
- python -m pip install --upgrade pip
- python -m pip install dist/nitransforms*.tar.gz
- INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
- echo "VERSION: \"${THISVERSION}\""
- echo "INSTALLED: \"${INSTALLED_VERSION}\""
- test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
- - name: Install in confined environment [wheel]
- run: |
- python -m venv /tmp/install_wheel
- source /tmp/install_wheel/bin/activate
- python -m pip install --upgrade pip
- python -m pip install dist/nitransforms*.whl
- INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
- echo "INSTALLED: \"${INSTALLED_VERSION}\""
- test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
- - name: Install in confined environment [pip install .]
- run: |
- python -m venv /tmp/setup_install
- source /tmp/setup_install/bin/activate
- python -m pip install --upgrade pip wheel
- python -m pip install .
- INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
- echo "INSTALLED: \"${INSTALLED_VERSION}\""
- test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
- - name: Install in confined environment [pip install -e .]
- run: |
- python -m venv /tmp/setup_develop
- source /tmp/setup_develop/bin/activate
- python -m pip install pip
- python -m pip install --upgrade pip wheel
- python -m pip install -e .
- INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
- echo "INSTALLED: \"${INSTALLED_VERSION}\""
- test "${INSTALLED_VERSION}" = "${THISVERSION}"
-
- flake8:
- if: "!contains(github.event.head_commit.message, '[skip ci]')"
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v4
- - name: Set up Python 3
- uses: actions/setup-python@v5
- - run: pipx run flake8 nitransforms
diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml
new file mode 100644
index 00000000..49e8211a
--- /dev/null
+++ b/.github/workflows/tox.yml
@@ -0,0 +1,130 @@
+name: Tox
+
+on:
+ push:
+ branches: [ master, main, 'maint/*' ]
+ tags: [ '*' ]
+ pull_request:
+ branches: [ master, main, 'maint/*' ]
+ schedule:
+ - cron: '0 0 * * *'
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
+
+permissions:
+ contents: read
+
+env:
+ # Force tox and pytest to use color
+ FORCE_COLOR: true
+ TEST_DATA_HOME: /home/runner/testdata/nitransforms-tests
+
+jobs:
+ cache-test-data:
+ if: "!contains(github.event.head_commit.message, '[skip ci]')"
+ runs-on: ubuntu-latest
+ outputs:
+ SHA: ${{ steps.test-head.outputs.SHA }}
+ steps:
+ - name: Install the latest version of uv
+ uses: astral-sh/setup-uv@v3
+ - name: Git settings (pacify DataLad)
+ run: |
+ git config --global user.name 'NiPreps Bot'
+ git config --global user.email 'nipreps@gmail.com'
+ - name: Install DataLad
+ run: |
+ $CONDA/bin/conda install -c conda-forge git-annex
+ uv tool install --with=datalad-next --with=datalad-osf datalad
+ - name: Check remote HEAD
+ id: test-head
+ run: |
+ git ls-remote https://gin.g-node.org/oesteban/nitransforms-tests \
+ | awk '/HEAD/{ print "SHA=" $1 }' >> $GITHUB_OUTPUT
+
+ - uses: actions/cache@v4
+ with:
+ path: ${{ env.TEST_DATA_HOME }}
+ key: data-cache-v2-${{ steps.test-head.outputs.SHA }}
+ restore-keys: |
+ data-cache-v2-${{ steps.test-head.outputs.SHA }}
+ data-cache-v2
+
+ - name: Install test data
+ run: |
+ export PATH=$CONDA/bin:$PATH
+ mkdir -p /home/runner/testdata
+
+ datalad install -s https://gin.g-node.org/oesteban/nitransforms-tests $TEST_DATA_HOME
+ datalad update --merge -d $TEST_DATA_HOME
+ datalad get -J 2 -d $TEST_DATA_HOME
+
+ test:
+ runs-on: ubuntu-latest
+ needs: [cache-test-data]
+ strategy:
+ matrix:
+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+ dependencies: [latest, pre]
+ include:
+ - python-version: "3.9"
+ dependencies: min
+ exclude:
+ # Do not test pre-releases for versions out of SPEC0
+ - python-version: "3.9"
+ dependencies: pre
+ - python-version: "3.10"
+ dependencies: pre
+
+ env:
+ DEPENDS: ${{ matrix.dependencies }}
+
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ submodules: recursive
+ fetch-depth: 0
+ - name: Install the latest version of uv
+ uses: astral-sh/setup-uv@v3
+ - uses: actions/cache/restore@v4
+ with:
+ path: ${{ env.TEST_DATA_HOME }}
+ key: data-cache-v2-${{ needs.cache-test-data.outputs.SHA }}
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Display Python version
+ run: python -c "import sys; print(sys.version)"
+ - name: Install tox
+ run: |
+ uv tool install tox --with=tox-uv --with=tox-gh-actions
+ - name: Show tox config
+ run: tox c
+ - name: Run tox
+ run: tox -v --exit-and-dump-after 1200
+ - uses: codecov/codecov-action@v4
+ with:
+ file: coverage.xml
+ token: ${{ secrets.CODECOV_TOKEN }}
+ if: ${{ always() }}
+
+ checks:
+ runs-on: 'ubuntu-latest'
+ continue-on-error: true
+ strategy:
+ matrix:
+ check: ['style']
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: Install the latest version of uv
+ uses: astral-sh/setup-uv@v3
+ - name: Show tox config
+ run: uvx tox c
+ - name: Show tox config (this call)
+ run: uvx tox c -e ${{ matrix.check }}
+ - name: Run check
+ run: uvx tox -e ${{ matrix.check }}
diff --git a/.github/workflows/travis.yml b/.github/workflows/travis.yml
deleted file mode 100644
index 2a9473ed..00000000
--- a/.github/workflows/travis.yml
+++ /dev/null
@@ -1,91 +0,0 @@
-name: Deps & CI
-
-on:
- push:
- branches: [ '*' ]
- pull_request:
- branches: [ master, 'maint/*' ]
- schedule:
- - cron: '0 0 * * 1'
- # Allow job to be triggered manually from GitHub interface
- workflow_dispatch:
-
-concurrency:
- group: ${{ github.workflow }}-${{ github.ref }}
- cancel-in-progress: true
-
-permissions:
- contents: read
-
-jobs:
- cache-test-data:
- if: "!contains(github.event.head_commit.message, '[skip ci]')"
- runs-on: ubuntu-latest
- env:
- TEST_DATA_HOME: /home/runner/testdata/nitransforms-tests
- outputs:
- SHA: ${{ steps.test-head.outputs.SHA }}
- steps:
- - name: Git settings (pacify DataLad)
- run: |
- git config --global user.name 'NiPreps Bot'
- git config --global user.email 'nipreps@gmail.com'
- - name: Install DataLad
- run: |
- $CONDA/bin/conda install -c conda-forge git-annex
- python -m pip install datalad datalad-next datalad-osf
- - name: Check remote HEAD
- id: test-head
- run: |
- git ls-remote https://gin.g-node.org/oesteban/nitransforms-tests \
- | awk '/HEAD/{ print "SHA=" $1 }' >> $GITHUB_OUTPUT
-
- - uses: actions/cache@v4
- with:
- path: ${{ env.TEST_DATA_HOME }}
- key: data-cache-v2-${{ steps.test-head.outputs.SHA }}
- restore-keys: |
- data-cache-v2-${{ steps.test-head.outputs.SHA }}
- data-cache-v2
-
- - name: Install test data
- run: |
- export PATH=$CONDA/bin:$PATH
- mkdir -p /home/runner/testdata
-
- datalad install -s https://gin.g-node.org/oesteban/nitransforms-tests $TEST_DATA_HOME
- datalad update --merge -d $TEST_DATA_HOME
- datalad get -J 2 -d $TEST_DATA_HOME
-
- build-linux:
- if: "!contains(github.event.head_commit.message, '[skip ci]')"
- runs-on: ubuntu-latest
- needs: [cache-test-data]
- env:
- TEST_DATA_HOME: /home/runner/testdata/nitransforms-tests
- strategy:
- max-parallel: 5
- matrix:
- python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
- steps:
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v5
- with:
- python-version: ${{ matrix.python-version }}
- - uses: actions/cache/restore@v4
- with:
- path: ${{ env.TEST_DATA_HOME }}
- key: data-cache-v2-${{ needs.cache-test-data.outputs.SHA }}
-
- - uses: actions/checkout@v4
- - name: Install minimal dependencies
- run: |
- pip install .[tests]
- - name: Run pytest
- run: |
- pytest -v --cov nitransforms --cov-config .coveragerc --cov-report xml:cov.xml --doctest-modules nitransforms/
-
- - name: Submit code coverage
- uses: codecov/codecov-action@v4
- with:
- files: cov.xml
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 34413ca6..4cb47fff 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,19 +1,21 @@
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
version: 2
build:
- os: ubuntu-20.04
+ os: ubuntu-lts-latest
tools:
- python: "3.8"
-
-sphinx:
- configuration: docs/conf.py
+ python: latest
-python:
- install:
- - path: .
- extra_requirements:
- - all
- - requirements: docs/requirements.txt
+ jobs:
+ pre_create_environment:
+ - asdf plugin add uv
+ - asdf install uv latest
+ - asdf global uv latest
+ # Turn `python -m virtualenv` into `python -c pass`
+ - truncate --size 0 $( dirname $( uv python find ) )/../lib/python3*/site-packages/virtualenv/__main__.py
+ post_create_environment:
+ - uv venv $READTHEDOCS_VIRTUALENV_PATH
+ # Turn `python -m pip` into `python -c pass`
+ - truncate --size 0 $( ls -d $READTHEDOCS_VIRTUALENV_PATH/lib/python3* )/site-packages/pip.py
+ post_install:
+ - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache .[niftiext]
+ - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache -r docs/requirements.txt
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 1d115b13..00000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,7 +0,0 @@
-recursive-exclude .circleci/ *
-recursive-exclude .github/ *
-recursive-exclude docker/ *
-recursive-exclude docs/ *
-recursive-exclude joss/ *
-recursive-exclude nitransforms/tests *
-exclude .codecov.yml .coveragerc .gitignore .pep8speaks.yml .travis.yml Dockerfile
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 18e532a1..025d649b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -76,7 +76,7 @@
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 8a932a22..d74f8faf 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -4,5 +4,5 @@ packaging
pydot>=1.2.3
pydotplus
sphinx-argparse
-sphinx ~= 4.0
-sphinx_rtd_theme
\ No newline at end of file
+sphinx~=7.0
+sphinx_rtd_theme
diff --git a/pyproject.toml b/pyproject.toml
index 45a691bb..63876722 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,6 +2,60 @@
requires = ["setuptools >= 45", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"
+[project]
+name = "nitransforms"
+authors = [{name = "The NiPy developers", email = "nipreps@gmail.com"}]
+readme = "README.md"
+classifiers = [
+ "Development Status :: 2 - Pre-Alpha",
+ "Intended Audience :: Science/Research",
+ "Topic :: Scientific/Engineering :: Image Recognition",
+ "License :: OSI Approved :: BSD License",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+ "Programming Language :: Python :: 3.12",
+ "Programming Language :: Python :: 3.13",
+]
+description = "NiTransforms -- Neuroimaging spatial transforms in Python."
+license = {text = "MIT License"}
+requires-python = ">= 3.9"
+dependencies = [
+ "numpy >= 1.21",
+ "scipy >= 1.8",
+ "nibabel >= 4.0",
+ "h5py >= 3.9",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/nipy/nitransforms"
+Manuscript = "https://doi.org/10.31219/osf.io/8aq7b"
+NiBabel = "https://github.com/nipy/nibabel/pull/656"
+
+[project.optional-dependencies]
+niftiext = ["lxml >= 4.6"]
+test = [
+ "pytest >= 6",
+ "pytest-cov >= 2.11",
+ "pytest-env",
+ "pytest-xdist >= 2.5",
+ "coverage[toml] >= 5.2.1",
+ "nitransforms[niftiext]",
+]
+# Aliases
+niftiexts = ["nitransforms[niftiext]"]
+tests = ["nitransforms[test]"]
+all = [
+ "nitransforms[test]",
+]
+
+[project.scripts]
+nb-transform = "nitransforms.cli:main"
+
+[tool.setuptools.packages.find]
+include = ["nitransforms*"]
+
[tool.setuptools_scm]
write_to = "nitransforms/_version.py"
write_to_template = """\
@@ -9,3 +63,24 @@ write_to_template = """\
__version__ = "{version}"
"""
fallback_version = "0.0"
+
+[tool.pytest.ini_options]
+minversion = "6"
+testpaths = ["nitransforms"]
+log_cli_level = "INFO"
+xfail_strict = true
+norecursedirs = [".git"]
+addopts = [
+ "-svx",
+ "-ra",
+ "--strict-config",
+ "--strict-markers",
+ "--doctest-modules",
+ "--cov=nitransforms",
+ "--cov-report=xml",
+ "--cov-config=pyproject.toml",
+]
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+junit_family = "xunit2"
diff --git a/setup.cfg b/setup.cfg
index 4607288f..f355be94 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,66 +1,3 @@
-[metadata]
-author = The NiPy developers
-author_email = nipreps@gmail.com
-classifiers =
- Development Status :: 2 - Pre-Alpha
- Intended Audience :: Science/Research
- Topic :: Scientific/Engineering :: Image Recognition
- License :: OSI Approved :: BSD License
- Programming Language :: Python :: 3.8
- Programming Language :: Python :: 3.9
- Programming Language :: Python :: 3.10
- Programming Language :: Python :: 3.11
-description = NiTransforms -- Neuroimaging spatial transforms in Python.
-license = MIT License
-long_description = file:README.md
-long_description_content_type = text/markdown; charset=UTF-8
-provides = nitransforms
-project_urls =
- Manuscript=https://doi.org/10.31219/osf.io/8aq7b
- NiBabel=https://github.com/nipy/nibabel/pull/656
-url = https://github.com/nipy/nitransforms
-
-[options]
-python_requires = >= 3.8
-install_requires =
- numpy ~= 1.21
- scipy >= 1.6.0
- nibabel >= 3.0
- h5py
-test_requires =
- pytest
- pytest-cov
- pytest-env
- nose
- codecov
-setup_requires =
- setuptools_scm
- toml
-packages = find:
-include_package_data = True
-
-[options.extras_require]
-niftiext =
- lxml
-niftiexts =
- %(niftiext)s
-test =
- pytest
- pytest-cov
- pytest-env
- codecov
- lxml
-tests =
- %(test)s
-
-all =
- %(niftiext)s
- %(test)s
-
-[options.entry_points]
-console_scripts =
- nb-transform = nitransforms.cli:main
-
[flake8]
max-line-length = 99
doctests = False
@@ -68,13 +5,3 @@ ignore =
E266
E231
W503
-
-[tool:pytest]
-norecursedirs = .git
-addopts = -svx --doctest-modules
-doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS
-env =
- PYTHONHASHSEED=0
-filterwarnings =
- ignore::DeprecationWarning
-junit_family=xunit2
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 78ec8923..00000000
--- a/setup.py
+++ /dev/null
@@ -1,7 +0,0 @@
-"""Prepare package for distribution."""
-from setuptools import setup
-
-if __name__ == "__main__":
- setup(
- name="nitransforms",
- )
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 00000000..fe549039
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,110 @@
+[tox]
+requires =
+ tox>=4
+envlist =
+ py3{9,10,11,12,13}-latest
+ py39-min
+ py3{11,12,13}-pre
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+ 3.9: py39
+ 3.10: py310
+ 3.11: py311
+ 3.12: py312
+ 3.13: py313
+
+[gh-actions:env]
+DEPENDS =
+ min: min
+ latest: latest
+ pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+ pre: true
+pass_env =
+ # Overrides default location for finding test data
+ TEST_DATA_HOME
+ # getpass.getuser() sources for Windows:
+ LOGNAME
+ USER
+ LNAME
+ USERNAME
+ # Pass user color preferences through
+ PY_COLORS
+ FORCE_COLOR
+ NO_COLOR
+ CLICOLOR
+ CLICOLOR_FORCE
+ PYTHON_GIL
+extras = tests
+setenv =
+ FSLOUTPUTTYPE=NIFTI_GZ
+ pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+ pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+uv_resolution =
+ min: lowest-direct
+
+commands =
+ python -c "import nitransforms; print(nitransforms.__version__)"
+ pytest --durations=20 --durations-min=1.0 --cov-report term-missing {posargs:-n auto}
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+ flake8
+skip_install = true
+commands =
+ flake8 nitransforms
+
+[testenv:style-fix]
+description = Auto-apply style guide to the extent possible
+labels = pre-release
+deps =
+ ruff
+skip_install = true
+commands =
+ ruff check --fix
+ ruff format
+ ruff check --select ISC001
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+ codespell[toml]
+skip_install = true
+commands =
+ codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+ check
+ pre-release
+deps =
+ build
+ twine
+skip_install = true
+set_env =
+ # Ignore specific known warnings:
+ # https://github.com/pypa/pip/issues/11684
+ # https://github.com/pypa/pip/issues/12243
+ strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
+commands =
+ python -m build
+ python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+ twine
+skip_install = true
+commands =
+ python -m twine upload dist/*