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# This is a basic workflow to help you get started with Actions
name: Use case tests
# Controls when the workflow will run
on:
# Triggers the workflow on push or pull request events but only for the master branch
push:
branches: [ master ]
pull_request:
branches: [ master ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# Default settings
defaults:
run:
shell: bash
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
aatest_ds000114_dartel:
name: Testing SPM DARTEL
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 0
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-01 /test/data/aa_demo/ds000114/sub-01 --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_dartel','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_ds000114_dartel
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_ds000114_diffusion:
name: Testing Diffusion (with FSL)
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 1
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-01/ses-test /test/data/aa_demo/ds000114/sub-01/ses-test --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_diffusion','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_ds000114_diffusion
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_ds000114_fmrisymlinks:
name: Testing fMRI with symlinks
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 0
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-01 /test/data/aa_demo/ds000114/sub-01 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-02 /test/data/aa_demo/ds000114/sub-02 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-03 /test/data/aa_demo/ds000114/sub-03 --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_fmrisymlinks','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_ds000114_fmrisymlinks
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_ds000114_fmrilocalpipeline:
name: Testing fMRI using local pipeline connection
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 0
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-01 /test/data/aa_demo/ds000114/sub-01 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-02 /test/data/aa_demo/ds000114/sub-02 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-03 /test/data/aa_demo/ds000114/sub-03 --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_fmrilocalpipeline','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_ds000114_fmrilocalpipeline
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_ds000114_scrubbing:
name: Testing fMRI frame censoring
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 0
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114 /test/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-01 /test/data/aa_demo/ds000114/sub-01 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-02 /test/data/aa_demo/ds000114/sub-02 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-03 /test/data/aa_demo/ds000114/sub-03 --quiet --recursive --no-sign-request
aws s3 cp s3://openneuro.org/ds000114/sub-04 /test/data/aa_demo/ds000114/sub-04 --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_scrubbing','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_ds000114_scrubbing
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_ds002737_deface:
name: Testing (Freesurfer) Deface and FaceMasking
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 1
LOAD_FREESURFER: 1
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://openneuro.org/ds002737/sub-01/ses-03 /test/data/aa_demo/ds002737/sub-01/ses-03 --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_ds002737_deface','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_ds002737_deface
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_lemon_meegsensor:
name: Testing the M/EEG (with statistics)
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 1
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://fcp-indi/data/Projects/INDI/MPI-LEMON/EEG_MPILMBB_LEMON/EEG_Raw_BIDS_ID/sub-032301 /test/data/aa_demo/LEMON_EEG/sub-032301 --quiet --recursive --no-sign-request
aws s3 cp s3://fcp-indi/data/Projects/INDI/MPI-LEMON/MRI_MPILMBB_LEMON/MRI_Raw/sub-032301/ses-01/anat /test/data/aa_demo/LEMON_MRI/sub-032301/ses-01/anat --quiet --recursive --no-sign-request
aws s3 cp s3://fcp-indi/data/Projects/INDI/MPI-LEMON/EEG_MPILMBB_LEMON/EEG_Raw_BIDS_ID/sub-032302 /test/data/aa_demo/LEMON_EEG/sub-032302 --quiet --recursive --no-sign-request
aws s3 cp s3://fcp-indi/data/Projects/INDI/MPI-LEMON/MRI_MPILMBB_LEMON/MRI_Raw/sub-032302/ses-01/anat /test/data/aa_demo/LEMON_MRI/sub-032302/ses-01/anat --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_lemon_meegsensor','haltonerror',true,'wheretoprocess','batch'); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_${{github.job}}
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log
aatest_lemon_meegsource:
name: Testing the M/EEG (with source reconstruction)
# The type of runner that the job will run on
runs-on: ubuntu-24.04
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
with:
tool-cache: true
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true
- name: Create test space
run: |
sudo mkdir /test
sudo chown runner: /test
sudo chmod u+w /test
echo "Free space:"
df -h
- name: Set git to use LF
run: |
git config --global core.autocrlf false
git config --global core.eol lf
- name: Check out repository under $GITHUB_WORKSPACE
uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
- name: Set up Python 3.12.11
uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
with:
# Semantic version range syntax or exact version of a Python version
python-version: '3.12.11'
# Optional - x64 or x86 architecture, defaults to x64
architecture: 'x64'
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@a0180c939fb1a28de13f44f7b778b912384ced1f # v3.0.1
with:
# MATLAB release to set up R2024a
release: R2024a
products: >
Computer_Vision_Toolbox
Image_Processing_Toolbox
Optimization_Toolbox
Parallel_Computing_Toolbox
Signal_Processing_Toolbox
Statistics_and_Machine_Learning_Toolbox
- name: Install tools and configure aa
run: |
python trigger_install.py
working-directory: ${{github.workspace}}/.github/workflows
env:
LOAD_FSL: 1
LOAD_FREESURFER: 0
PARAMETER_XML: aap_parameters_defaults_GitHub.xml
- name: Retrive test data under /test/data/aa_demo
run: |
mkdir -p /test/data/aa_demo
aws s3 cp s3://fcp-indi/data/Projects/INDI/MPI-LEMON/EEG_MPILMBB_LEMON/EEG_Raw_BIDS_ID/sub-032301 /test/data/aa_demo/LEMON_EEG/sub-032301 --quiet --recursive --no-sign-request
aws s3 cp s3://fcp-indi/data/Projects/INDI/MPI-LEMON/MRI_MPILMBB_LEMON/MRI_Raw/sub-032301/ses-01/anat /test/data/aa_demo/LEMON_MRI/sub-032301/ses-01/anat --quiet --recursive --no-sign-request
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
AWS_EC2_METADATA_DISABLED: true
- name: Run script
uses: matlab-actions/run-command@2970c890bd6dfbc8ba4d640879c4c496dec4e426 # v3.1.0
with:
command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('glob','aatest_lemon_meegsource','haltonerror',true); aa_test_getreport('/test/projects','/test/projects/report')
- name: Archive data
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: aatest_${{github.job}}
path: |
/test/projects/report/
- name: Archive log
uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
with:
name: testlog_${{github.job}}
path: |
${{github.workspace}}/developer/aa_test.log