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FIX: Add per-volume transforms as single transform in chain #471

FIX: Add per-volume transforms as single transform in chain

FIX: Add per-volume transforms as single transform in chain #471

Workflow file for this run

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