Merge pull request #277 from khanlab/download-osf #926
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
--- | |
# 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: Lint and test workflow | |
on: | |
push: | |
workflow_dispatch: | |
jobs: | |
quality: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Install non-python dependencies | |
run: | | |
sudo apt-get install -y graphviz-dev | |
- name: Setup Python environment | |
uses: khanlab/actions/.github/actions/[email protected] | |
with: | |
python-version: "3.9" | |
- name: isort | |
run: poetry run isort hippunfold/*.py -c | |
- name: Black | |
run: poetry run black hippunfold --check | |
- name: snakefmt | |
run: poetry run snakefmt hippunfold --check | |
test: | |
runs-on: ubuntu-latest | |
needs: ["quality"] | |
strategy: | |
matrix: | |
python-version: ["3.7", "3.8", "3.9"] | |
steps: | |
- name: Install non-python dependencies | |
run: | | |
sudo apt-get install -y graphviz-dev | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v3 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Setup Python environments | |
uses: khanlab/actions/.github/actions/[email protected] | |
with: | |
python-version: ${{ matrix.python-version }} | |
install-library: true | |
- name: Setup env for hippunfold | |
run: | | |
echo "HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models" >> $GITHUB_ENV | |
- name: Test single T2w bids | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w | |
- name: Test running on existing folder | |
run: | | |
mkdir test_newout | |
poetry run hippunfold test_data/bids_singleT2w test_newout participant -np --modality T2w | |
- name: Test single T2w bids, right hemi | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R | |
- name: Test single T2w bids, left hemi | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L | |
- name: Test multiple T2w bids | |
run: | | |
poetry run hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w | |
- name: Test T1w bids | |
run: | | |
poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w | |
- name: Test hipp b500 bids | |
run: | | |
poetry run hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 | |
- name: Test T1w multi-session/longitudinal bids | |
run: | | |
poetry run hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w | |
- name: Test single T2w multi-session/longitudinal bids | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w | |
- name: Test manual seg T2w bids | |
run: | | |
poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w | |
- name: Test cropseg bids, with path override | |
run: | | |
poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz | |
- name: Test cropseg bids, with path override, left hemi | |
run: | | |
poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L | |
- name: Test T2w with T1w template registration | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template | |
- name: Test T2w with T1w output space | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w | |
- name: Test modality T2w with myelin map | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --generate-myelin-map | |
- name: Test modality T1w with myelin map | |
run: | | |
poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T1w --generate-myelin-map | |
- name: Test modality T1w with magdeburg atlas | |
run: | | |
poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas magdeburg | |
- name: Test modality T1w with freesurfer atlas | |
run: | | |
poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer | |
- name: Test modality T1w with bigbrain and freesurfer atlas | |
run: | | |
poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas bigbrain freesurfer |