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further simplify cli for use-template-seg #872

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further simplify cli for use-template-seg

further simplify cli for use-template-seg #872

Workflow file for this run

.github/workflows/python-testing.yml at 7e4bfda
# 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: Python package
on:
push:
workflow_dispatch:
# branches: [ main ]
# pull_request:
# branches: [ main ]
jobs:
quality:
runs-on: ubuntu-latest
steps:
- name: Clone repo
uses: actions/checkout@master
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: '3.8'
- uses: actions/cache@v3
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-3.8
restore-keys: ${{ runner.os }}-pip-3.8
- name: Install non-python dependencies
run: |
sudo apt-get install -y graphviz-dev
#----------------------------------------------
# ----- install & configure poetry -----
#----------------------------------------------
- name: Install Poetry
uses: snok/install-poetry@v1
with:
virtualenvs-create: true
virtualenvs-in-project: true
- name: Disable Poetry modern installation
run: |
poetry config installer.modern-installation false
#----------------------------------------------
#----------------------------------------------
# load cached venv if cache exists
#----------------------------------------------
- name: Load cached venv
id: cached-poetry-dependencies
uses: actions/cache@v3
with:
path: .venv
key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-3.8
#----------------------------------------------
# install dependencies if cache does not exist
#----------------------------------------------
- name: Install dependencies
if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction --no-root
#----------------------------------------------
# install your root project, if required
#----------------------------------------------
- name: Install library
run: poetry install --no-interaction
#----------------------------------------------
# run python style checks
#----------------------------------------------
- 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: ['3.8']
steps:
- uses: actions/checkout@master
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- uses: actions/cache@v3
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ matrix.python-version }}
restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
- name: Install non-python dependencies
run: |
sudo apt-get install -y graphviz-dev
#----------------------------------------------
# ----- install & configure poetry -----
#----------------------------------------------
- name: Install Poetry
uses: snok/install-poetry@v1
with:
virtualenvs-create: true
virtualenvs-in-project: true
- name: Disable Poetry modern installation
run: |
poetry config installer.modern-installation false
#----------------------------------------------
# load cached venv if cache exists
#----------------------------------------------
- name: Load cached venv
id: cached-poetry-dependencies
uses: actions/cache@v3
with:
path: .venv
key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-${{ matrix.python-version }}
#----------------------------------------------
# install dependencies if cache does not exist
#----------------------------------------------
- name: Install dependencies
if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction --no-root
#----------------------------------------------
# install your root project, if required
#----------------------------------------------
- name: Install library
run: poetry install --no-interaction
- name: Set-up 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