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Merge pull request #112 from poldracklab/maint/travis-to-gha
MAINT: Move from TravisCI to GHA
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‎.github/workflows/pythonpackage.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python package
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on:
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push:
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branches: [ '*' ]
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tags: [ '*' ]
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pull_request:
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branches: [ master, 'maint/*' ]
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jobs:
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build:
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if: "!contains(github.event.head_commit.message, '[skip ci]')"
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Build in confined, updated environment and interpolate version
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run: |
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python -m venv /tmp/buildenv
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source /tmp/buildenv/bin/activate
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python -m pip install -U setuptools pip wheel twine docutils
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python setup.py sdist bdist_wheel
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python -m twine check dist/nitransforms*
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# Interpolate version
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if [[ "$GITHUB_REF" == refs/tags/* ]]; then
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TAG=${GITHUB_REF##*/}
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fi
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THISVERSION=$( python setup.py --version )
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THISVERSION=${TAG:-$THISVERSION}
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echo "Expected VERSION: \"${THISVERSION}\""
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echo "THISVERSION=${THISVERSION}" >> ${GITHUB_ENV}
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- name: Install in confined environment [sdist]
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run: |
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python -m venv /tmp/install_sdist
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source /tmp/install_sdist/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install dist/nitransforms*.tar.gz
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "VERSION: \"${THISVERSION}\""
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [wheel]
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run: |
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python -m venv /tmp/install_wheel
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source /tmp/install_wheel/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install dist/nitransforms*.whl
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [pip install .]
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run: |
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python -m venv /tmp/setup_install
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source /tmp/setup_install/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install .
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [pip install -e .]
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run: |
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python -m venv /tmp/setup_develop
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source /tmp/setup_develop/bin/activate
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python -m pip install pip
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python -m pip install --upgrade pip wheel
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python -m pip install -e .
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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flake8:
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if: "!contains(github.event.head_commit.message, '[skip ci]')"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- run: pip install flake8
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- run: flake8 nitransforms/

‎.github/workflows/travis.yml

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name: Deps & CI
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on: [push, pull_request]
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jobs:
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build-linux:
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if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'poldracklab/nitransforms'))"
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runs-on: ubuntu-latest
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env:
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TEST_DATA_HOME: /home/runner/testdata/nitransforms-tests
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strategy:
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max-parallel: 5
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matrix:
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python-version: [3.7, 3.8, 3.9]
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steps:
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- name: Git settings (pacify DataLad)
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run: |
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git config --global user.name 'NiPreps Bot'
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git config --global user.email '[email protected]'
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/cache@v2
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id: conda
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with:
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path: |
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/usr/share/miniconda/pkgs
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/home/runner/.cache/pip
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key: python-${{ matrix.python-version }}-v1
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restore-keys: |
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python-${{ matrix.python-version }}-
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- name: Install DataLad
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run: |
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$CONDA/bin/conda install -c conda-forge git-annex datalad pip codecov pytest
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$CONDA/bin/python -m pip install datalad-osf
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# $CONDA/bin/pip install git+https://github.com/Lykos153/AnnexRemote.git
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- uses: actions/cache@v2
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with:
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path: ${{ env.TEST_DATA_HOME }}
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key: data-cache-v1
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restore-keys: |
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data-cache-
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- name: Install test data
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run: |
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export PATH=$CONDA/bin:$PATH
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mkdir -p /home/runner/testdata
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cd /home/runner/testdata
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$CONDA/bin/datalad install https://github.com/nipreps-data/nitransforms-tests.git
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$CONDA/bin/datalad update --merge -d nitransforms-tests/
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$CONDA/bin/datalad get -d nitransforms-tests/
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- uses: actions/checkout@v2
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- name: Install minimal dependencies
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run: |
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$CONDA/bin/pip install .[tests]
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- name: Run pytest
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run: |
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$CONDA/bin/pytest -v --cov nitransforms --cov-config .coveragerc --cov-report xml:cov.xml --doctest-modules nitransforms/
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- name: Submit code coverage
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run: |
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$CONDA/bin/python -m codecov --flags travis --file cov.xml -e $GITHUB_RUN_NUMBER

‎MANIFEST.in

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recursive-exclude .circleci/ *
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recursive-exclude .github/ *
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recursive-exclude docker/ *
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recursive-exclude docs/ *
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recursive-exclude joss/ *
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recursive-exclude nitransforms/tests *
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exclude .codecov.yml .coveragerc .gitignore .pep8speaks.yml .travis.yml Dockerfile

‎nitransforms/io/afni.py

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tf = cls()
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sa = tf.structarr
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lines = [
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l
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for l in string.splitlines()
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if l.strip() and not (l.startswith("#") or "3dvolreg matrices" in l)
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line
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for line in string.splitlines()
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if line.strip() and not (line.startswith("#") or "3dvolreg matrices" in line)
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]
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if not lines:
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strings = []
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for i, xfm in enumerate(self.xforms):
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lines = [
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l.strip()
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for l in xfm.to_string(banner=(i == 0)).splitlines()
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if l.strip()
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line.strip()
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for line in xfm.to_string(banner=(i == 0)).splitlines()
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if line.strip()
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]
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strings += lines
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return "\n".join(strings)
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_self = cls()
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lines = [
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l.strip()
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for l in string.splitlines()
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if l.strip() and not l.startswith("#")
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line.strip()
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for line in string.splitlines()
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if line.strip() and not line.startswith("#")
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]
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if not lines:
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raise TransformFileError("Input string is empty.")
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_self.xforms = [cls._inner_type.from_string(l) for l in lines]
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_self.xforms = [cls._inner_type.from_string(line) for line in lines]
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return _self
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‎nitransforms/io/base.py

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"""
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template_dtype = np.dtype([("parameters", "f8", (4, 4)),])
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template_dtype = np.dtype([("parameters", "f8", (4, 4))])
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dtype = template_dtype
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def __init__(self, parameters=None):

‎nitransforms/io/fsl.py

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"""Read the struct from string."""
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tf = cls()
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sa = tf.structarr
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lines = [l.strip() for l in string.splitlines() if l.strip()]
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lines = [line.strip() for line in string.splitlines() if line.strip()]
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if not lines or len(lines) < 4:
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raise TransformFileError
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‎nitransforms/io/itk.py

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"AffineTransform_double_3_3",
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mdict.get("AffineTransform_float_3_3")
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)
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if affine is None:
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raise NotImplementedError("Unsupported transform type")
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"""Read the struct from string."""
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tf = cls()
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sa = tf.structarr
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lines = [l.strip() for l in string.splitlines() if l.strip()]
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lines = [line.strip() for line in string.splitlines() if line.strip()]
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if not lines or not lines[0].startswith("#"):
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raise TransformFileError
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if lines[1][0] == "#":
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lines = lines[1:] # Drop banner with version
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parameters = np.eye(4, dtype="f4")
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sa["index"] = int(lines[0][lines[0].index("T") :].split()[1])
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sa["index"] = int(lines[0][lines[0].index("T"):].split()[1])
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sa["offset"] = np.genfromtxt(
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[lines[3].split(":")[-1].encode()], dtype=cls.dtype["offset"]
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)
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def from_string(cls, string):
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"""Read the struct from string."""
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_self = cls()
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lines = [l.strip() for l in string.splitlines() if l.strip()]
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lines = [line.strip() for line in string.splitlines() if line.strip()]
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if (
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not lines

‎nitransforms/io/lta.py

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lta = klass()
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sa = lta.structarr
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lines = [
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l.strip()
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for l in string.splitlines()
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if l.strip() and not l.strip().startswith("#")
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line.strip()
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for line in string.splitlines()
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if line.strip() and not line.strip().startswith("#")
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]
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if not lines or not lines[0].startswith("type"):
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raise TransformFileError("Invalid LTA format")

‎setup.cfg

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doctests = False
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ignore =
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E266
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E231
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[tool:pytest]

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