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test.yml
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on:
push:
branches:
- main
- maint/*
tags:
- "*"
pull_request:
branches:
- main
- maint/*
workflow_dispatch:
inputs:
debug_enabled:
type: boolean
description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
required: false
default: false
defaults:
run:
shell: bash
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
permissions:
contents: read
jobs:
get-dataset:
runs-on: ubuntu-latest
name: Datalad install and get
steps:
- name: Checkout
uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Get Submodule Hash
id: get-smhash
run: |
echo "smhash=$(git submodule status contarg/test/data)" >> $GITHUB_OUTPUT
- name: Cache Dataset
id: restore-dataset
uses: actions/cache/restore@v3
with:
path: |
./contarg/test/data
.git/modules/contarg/test/data
key: ${{ runner.os }}-${{steps.get-smhash.outputs.smhash}}
- name: Install datalad
if: steps.restore-dataset.outputs.cache-hit != 'true'
uses: datalad/datalad-action/install@main
- name: Download Dataset
if: steps.restore-dataset.outputs.cache-hit != 'true'
run: |
datalad get -r contarg/test/data/derivatives/contarg/seedmap/ \
contarg/test/data/derivatives/contarg/hierarchical/testing2subs/sub-*/func/*mask.nii.gz \
contarg/test/data/ds002330/*.json \
contarg/test/data/ds002330/*.tsv \
contarg/test/data/derivatives/fmriprep/*.json \
contarg/test/data/derivatives/fmriprep/sub-*/anat/sub-*_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 \
contarg/test/data/derivatives/fmriprep/sub-*/anat/*preproc_T1w.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*preproc_bold.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*brain_mask.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*boldref.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*confounds_timeseries.* \
contarg/test/data/derivatives/contarg/hierarchical/testing*_ref/ \
contarg/test/data/derivatives/contarg/hierarchical/testing1sub/sub-*/func/*mask.nii.gz \
contarg/test/data/derivatives/contarg/cluster/
- name: Cache Dataset
if: steps.restore-dataset.outputs.cache-hit != 'true'
uses: actions/cache/save@v3
with:
path: |
./contarg/test/data
.git/modules/contarg/test/data
key: ${{ runner.os }}-${{steps.get-smhash.outputs.smhash}}
- name: Setup tmate session
uses: mxschmitt/action-tmate@v3
if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled && (success() || failure())}}
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- uses: actions/setup-python@v4
with:
python-version: 3
- run: pip install --upgrade build twine
- name: Build sdist and wheel
run: python -m build
- run: twine check dist/*
- name: Upload sdist and wheel artifacts
uses: actions/upload-artifact@v3
with:
name: dist
path: dist/
- name: Build git archive
run: mkdir archive && git archive -v -o archive/archive.tgz HEAD
- name: Upload git archive artifact
uses: actions/upload-artifact@v3
with:
name: archive
path: archive/
test-package:
runs-on: ubuntu-latest
needs: [get-dataset, build]
strategy:
matrix:
package: ['wheel', 'sdist', 'archive']
steps:
- name: Download sdist and wheel artifacts
if: matrix.package != 'archive'
uses: actions/download-artifact@v3
with:
name: dist
path: dist/
- name: Download git archive artifact
if: matrix.package == 'archive'
uses: actions/download-artifact@v3
with:
name: archive
path: archive/
- uses: actions/setup-python@v4
with:
python-version: 3
- name: Display Python version
run: python -c "import sys; print(sys.version)"
- name: Update pip
run: pip install --upgrade pip
- name: Install wheel
if: matrix.package == 'wheel'
run: pip install dist/*.whl
- name: Install sdist
if: matrix.package == 'sdist'
run: pip install dist/*.tar.gz
- name: Install archive
if: matrix.package == 'archive'
run: pip install archive/archive.tgz
- name: Install test extras
run: pip install contarg[test]
- name: Restore Dataset
id: restore-dataset
uses: actions/cache/restore@v3
with:
path: |
./contarg/test/data
.git/modules/contarg/test/data
key: ${{ runner.os }}-${{steps.get-smhash.outputs.smhash}}
- name: Move data
run: |
contarg_path=$(which contarg)
contarg_test_path=${contarg_path:0:-12}/lib/python*/site-packages/contarg/test
mv contarg/test/data $contarg_test_path/
rm -rf $contarg_test_path/data/.git
mv .git/modules/contarg/test/data .git/modules/contarg/test/.git
mv .git/modules/contarg/test/.git $contarg_test_path/data/
- name: Run tests
run: pytest --doctest-modules -v --pyargs contarg
- name: Setup tmate session
uses: mxschmitt/action-tmate@v3
if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled && (success() || failure())}}
publish:
runs-on: ubuntu-latest
needs: [test-package]
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
steps:
- uses: actions/download-artifact@v3
with:
name: dist
path: dist/
- uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}