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tests.yml
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---
name: tests matlab
# Uses the cron schedule for github actions
#
# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
#
# ┌───────────── minute (0 - 59)
# │ ┌───────────── hour (0 - 23)
# │ │ ┌───────────── day of the month (1 - 31)
# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
# │ │ │ │ │
# │ │ │ │ │
# │ │ │ │ │
# * * * * *
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
on:
push:
branches: [main]
pull_request:
branches: [main]
schedule:
- cron: 0 0 1,15 * *
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
fast_tests:
if: github.repository_owner == 'cpp-lln-lab'
strategy:
matrix:
os: [ubuntu-latest, macos-13]
matlab: [R2023b]
fail-fast: false
runs-on: ${{ matrix.os }}
steps:
- name: Install Deno
uses: denoland/setup-deno@v1
with:
deno-version: v1.x
- name: Install python
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install dependencies
if: matrix.os == 'ubuntu-latest'
run: |
sudo apt-get -y -qq update
sudo apt-get -y install unzip wget git-annex
python -m pip install --upgrade pip setuptools
pip install datalad
- name: Clone bidspm
uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- name: Install validators
run: make install
- name: Install SPM
run: |
git clone https://github.com/spm/spm12.git --depth 1
- name: Get moae fmriprep data from OSF
run: |
mkdir -p demos/MoAE/inputs/
cd demos/MoAE/inputs/
wget https://osf.io/vufjs/download
unzip download
mv moae_fmriprep fmriprep
- name: Get data for testing QA
if: matrix.os == 'ubuntu-latest'
run: |
cd demos/openneuro/
make data_ds000114_mriqc
make data_ds000114_fmriprep
- name: Prepare test data unix
run: |
cd tests
make data
- name: Install Moxunit and MOcov
run: |
git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
git clone https://github.com/MOcov/MOcov.git --depth 1
- name: Install MATLAB
uses: matlab-actions/setup-matlab@v2.2.0
with:
release: ${{ matrix.matlab }}
- name: Run fast unit tests MATLAB
uses: matlab-actions/run-command@v2.1.1
with:
command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
- name: Code coverage matlab
uses: codecov/codecov-action@v4
with:
file: coverage.xml
flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_fast
name: codecov-matlab
fail_ci_if_error: false
token: ${{ secrets.CODECOV_TOKEN }}
slow_tests:
needs: [fast_tests]
if: github.repository_owner == 'cpp-lln-lab'
strategy:
matrix:
os: [ubuntu-latest, macos-13]
matlab: [R2023b]
fail-fast: false
runs-on: ${{ matrix.os }}
steps:
- name: Install Deno
uses: denoland/setup-deno@v1
with:
deno-version: v1.x
- name: Install python
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install dependencies
if: matrix.os == 'ubuntu-latest'
run: |
sudo apt-get -y -qq update
sudo apt-get -y install unzip wget git-annex
python -m pip install --upgrade pip setuptools
pip install datalad
- name: Clone bidspm
uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- name: Install validators
run: make install
- name: Install SPM
run: |
git clone https://github.com/spm/spm12.git --depth 1
- name: Get moae fmriprep data from OSF
run: |
mkdir -p demos/MoAE/inputs/
cd demos/MoAE/inputs/
wget https://osf.io/vufjs/download
unzip download
mv moae_fmriprep fmriprep
- name: Get data for testing QA
if: matrix.os == 'ubuntu-latest'
run: |
cd demos/openneuro/
make data_ds000114_mriqc
make data_ds000114_fmriprep
- name: Prepare test data unix
run: |
cd tests
make data
- name: Install Moxunit and MOcov
run: |
git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
git clone https://github.com/MOcov/MOcov.git --depth 1
- name: Install MATLAB
uses: matlab-actions/setup-matlab@v2.2.0
with:
release: ${{ matrix.matlab }}
- name: Run slow unit tests MATLAB
uses: matlab-actions/run-command@v2.1.1
with:
command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab;
- name: Code coverage matlab
uses: codecov/codecov-action@v4
with:
file: coverage.xml
flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_slow
name: codecov-matlab
fail_ci_if_error: false
token: ${{ secrets.CODECOV_TOKEN }}
system_tests:
needs: [fast_tests]
if: github.repository_owner == 'cpp-lln-lab'
strategy:
matrix:
script: [moae, facerep, fmriprep]
os: [ubuntu-latest, macos-13]
matlab: [R2023b]
include:
# only run bms on ubuntu because of datalad setup
- os: ubuntu-latest
matlab: R2023b
script: bms
fail-fast: false
runs-on: ${{ matrix.os }}
steps:
- name: test ${{ matrix.script }}
run: test ${{ matrix.script }}
- name: Install Deno
uses: denoland/setup-deno@v1
with:
deno-version: v1.x
- name: Install python
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install dependencies
if: matrix.os == 'ubuntu-latest'
run: |
sudo apt-get -y -qq update
sudo apt-get -y install unzip wget git-annex
python -m pip install --upgrade pip setuptools
pip install datalad
- name: Clone bidspm
uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- name: Install validators
run: make install
- name: Install SPM
run: |
git clone https://github.com/spm/spm12.git --depth 1
- name: Get moae fmriprep data from OSF
run: |
mkdir -p demos/MoAE/inputs/
cd demos/MoAE/inputs/
wget https://osf.io/vufjs/download
unzip download
mv moae_fmriprep fmriprep
- name: Prepare test data unix
run: |
cd tests
make data
- name: Get data for BMS
if: matrix.script == 'bms'
run: make -C demos/bayes data_ds000114
- name: Install MATLAB
uses: matlab-actions/setup-matlab@v2.2.0
with:
release: ${{ matrix.matlab }}
- name: Run system tests MATLAB ${{ matrix.script }}
uses: matlab-actions/run-command@v2.1.1
with:
command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};