nipy · effigies · Apr 1, 2021 · Mar 31, 2021
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -0,0 +1,89 @@
+name: Stable tests
+
+# This file tests the claimed support range of nipype including
+#
+# * Operating systems: Linux, OSX
+# * Dependencies: minimum requirements, optional requirements
+# * Installation methods: setup.py, sdist, wheel, archive
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+  pull_request:
+    branches:
+      - master
+      - maint/*
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  stable:
+    # Check each OS, all supported Python, minimum versions and latest releases
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-18.04']
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        check: ['test']
+        pip-flags: ['']
+        depends: ['REQUIREMENTS']
+        deb-depends: [false]
+        nipype-extras: ['doc,tests,profiler']
+        include:
+          - os: ubuntu-18.04
+            python-version: 3.8
+            check: test
+            pip-flags: ''
+            depends: REQUIREMENTS
+            deb-depends: true
+            nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+    env:
+      DEPENDS: ${{ matrix.depends }}
+      CHECK_TYPE: ${{ matrix.check }}
+      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
+      INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
+      NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
+      INSTALL_TYPE: pip
+      CI_SKIP_TEST: 1
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Create virtual environment
+        run: tools/ci/create_venv.sh
+      - name: Build archive
+        run: |
+          source tools/ci/build_archive.sh
+          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
+      - name: Install Debian dependencies
+        run: tools/ci/install_deb_dependencies.sh
+        if: ${{ matrix.os == 'ubuntu-18.04' }}
+      - name: Install dependencies
+        run: tools/ci/install_dependencies.sh
+      - name: Install Nipype
+        run: tools/ci/install.sh
+      - name: Run tests
+        run: tools/ci/check.sh
+        if: ${{ matrix.check != 'skiptests' }}
+      - uses: codecov/codecov-action@v1
+        with:
+          file: coverage.xml
+        if: ${{ always() }}
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v2
+        with:
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: test-results.xml
+        if: ${{ always() && matrix.check == 'test' }}
diff --git a/tools/ci/activate.sh b/tools/ci/activate.sh
@@ -0,0 +1,9 @@
+if [ -e virtenv/bin/activate ]; then
+    source virtenv/bin/activate
+elif [ -e virtenv/Scripts/activate ]; then
+    source virtenv/Scripts/activate
+else
+    echo Cannot activate virtual environment
+    ls -R virtenv
+    false
+fi
diff --git a/tools/ci/build_archive.sh b/tools/ci/build_archive.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+echo "Building archive"
+
+source tools/ci/activate.sh
+
+set -eu
+
+# Required dependencies
+echo "INSTALL_TYPE = $INSTALL_TYPE"
+
+set -x
+
+if [ "$INSTALL_TYPE" == "sdist" ]; then
+    python setup.py egg_info  # check egg_info while we're here
+    python setup.py sdist
+    export ARCHIVE=$( ls dist/*.tar.gz )
+elif [ "$INSTALL_TYPE" == "wheel" ]; then
+    python setup.py bdist_wheel
+    export ARCHIVE=$( ls dist/*.whl )
+elif [ "$INSTALL_TYPE" == "archive" ]; then
+    export ARCHIVE="package.tar.gz"
+    git archive -o $ARCHIVE HEAD
+elif [ "$INSTALL_TYPE" == "pip" ]; then
+    export ARCHIVE="."
+fi
+
+set +eux
diff --git a/tools/ci/check.sh b/tools/ci/check.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+echo Running tests
+
+source tools/ci/activate.sh
+source tools/ci/env.sh
+
+set -eu
+
+# Required variables
+echo CHECK_TYPE = $CHECK_TYPE
+
+set -x
+
+if [ "${CHECK_TYPE}" == "test" ]; then
+    pytest --capture=no --verbose --doctest-modules -c nipype/pytest.ini \
+        --cov-config .coveragerc --cov nipype --cov-report xml \
+        --junitxml=test-results.xml nipype
+else
+    false
+fi
+
+set +eux
+
+echo Done running tests
diff --git a/tools/ci/create_venv.sh b/tools/ci/create_venv.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+echo Creating isolated virtual environment
+
+source tools/ci/env.sh
+
+set -eu
+
+# Required variables
+echo SETUP_REQUIRES = $SETUP_REQUIRES
+
+set -x
+
+python -m pip install --upgrade pip virtualenv
+virtualenv --python=python virtenv
+source tools/ci/activate.sh
+python --version
+python -m pip install -U $SETUP_REQUIRES
+which python
+which pip
+
+set +eux
+
+echo Done creating isolated virtual environment
diff --git a/tools/ci/env.sh b/tools/ci/env.sh
@@ -0,0 +1,17 @@
+SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
+
+# Minimum requirements
+REQUIREMENTS="-r requirements.txt"
+# Minimum versions of minimum requirements
+MIN_REQUIREMENTS="-r min-requirements.txt"
+
+# Numpy and scipy upload nightly/weekly/intermittent wheels
+NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple"
+STAGING_WHEELS="https://pypi.anaconda.org/multibuild-wheels-staging/simple"
+PRE_PIP_FLAGS="--pre --extra-index-url $NIGHTLY_WHEELS --extra-index-url $STAGING_WHEELS"
+
+for CONF in (/etc/fsl/fsl.sh /etc/afni/afni.sh); do
+    if [ -r $CONF ]; then source $CONF; fi
+done
+
+FSLOUTPUTTYPE=NIFTI_GZ
diff --git a/tools/ci/install.sh b/tools/ci/install.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+echo Installing nipype
+
+source tools/ci/activate.sh
+source tools/ci/env.sh
+
+set -eu
+
+# Required variables
+echo INSTALL_TYPE = $INSTALL_TYPE
+echo CHECK_TYPE = $CHECK_TYPE
+echo NIPYPE_EXTRAS = $NIPYPE_EXTRAS
+echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
+
+set -x
+
+if [ -n "$EXTRA_PIP_FLAGS" ]; then
+    EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
+fi
+
+if [ "$INSTALL_TYPE" == "setup" ]; then
+    python setup.py install
+else
+    pip install $EXTRA_PIP_FLAGS $ARCHIVE
+fi
+
+# Basic import check
+python -c 'import nipype; print(nipype.__version__)'
+
+if [ "$CHECK_TYPE" == "skiptests" ]; then
+    exit 0
+fi
+
+pip install $EXTRA_PIP_FLAGS "nipype[$NIPYPE_EXTRAS]"
+
+set +eux
+
+echo Done installing nipype
diff --git a/tools/ci/install_deb_dependencies.sh b/tools/ci/install_deb_dependencies.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+echo "Installing NeuroDebian dependencies"
+
+set -eu
+
+echo "INSTALL_DEB_DEPENDENCIES = $INSTALL_DEB_DEPENDENCIES"
+
+if $INSTALL_DEB_DEPENDENCIES; then
+    bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+    sudo apt update
+    sudo apt install -y -qq fsl afni elastix fsl-atlases xvfb fusefat graphviz
+fi
diff --git a/tools/ci/install_dependencies.sh b/tools/ci/install_dependencies.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+echo Installing dependencies
+
+source tools/ci/activate.sh
+source tools/ci/env.sh
+
+set -eu
+
+# Required variables
+echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
+echo DEPENDS = $DEPENDS
+
+set -x
+
+if [ -n "$EXTRA_PIP_FLAGS" ]; then
+    EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
+fi
+
+if [ -n "$DEPENDS" ]; then
+    pip install ${EXTRA_PIP_FLAGS} --prefer-binary ${!DEPENDS}
+fi
+
+set +eux
+
+echo Done installing dependencies