Merge pull request #184 from automaticanalysis/resync

Resync
tiborauer · Nov 13, 2021 · fcf01fc · fcf01fc
2 parents 6fef5f9 + 2254c89
commit fcf01fc
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diff --git a/.github/workflows/aa_test.yml b/.github/workflows/aa_test.yml
@@ -20,6 +20,83 @@ defaults:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
+  aatest_ds000114_AROMA:
+    name: Testing AROMA on fMRI
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - name: Maximize build space
+        uses: easimon/maximize-build-space@master
+        with:
+          root-reserve-mb: 51200
+          swap-size-mb: 1024
+          remove-dotnet: 'true'
+          remove-android: 'true'
+          remove-haskell: 'true'
+
+      - 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@v2
+
+      - name: Set up Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '2.7'
+          # Optional - x64 or x86 architecture, defaults to x64
+          architecture: 'x64'
+
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v1
+        with:
+          # MATLAB release to set up R2020a
+          release: R2020a
+
+      - name: Install tools under $HOME/tools (SPM, FaceMasking, FSL)
+        run: |
+          source $GITHUB_WORKSPACE/.github/workflows/tools_install.sh
+        env:
+          LOAD_FSL: 1
+          LOAD_FREESURFER: 0
+
+      - name: Retrive test data under $HOME/data/aa_demo
+        run: |
+          mkdir -p $HOME/data/aa_demo
+          aws s3 cp s3://openneuro.org/ds000114 $HOME/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114 $HOME/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114/sub-01 $HOME/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: Configure aa
+        run: |
+          echo "Free space:"
+          df -h
+          mkdir $HOME/.aa
+          cp $GITHUB_WORKSPACE/.github/workflows/aap_parameters_defaults_GitHub.xml $HOME/.aa/aap_parameters_user.xml
+          mkdir $HOME/projects
+
+      - name: Run script
+        uses: matlab-actions/run-command@v1
+        with:
+          command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile(getenv('HOME'),'tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_AROMA','haltonerror',true)
+
+      - name: Archive results
+        uses: actions/upload-artifact@v2
+        with:
+          name: aatest_ds000114_AROMA
+          path: |
+            ~/projects/
+            
   aatest_ds000114_dartel:
     name: Testing SPM DARTEL
 
@@ -45,6 +122,14 @@ jobs:
       - name: Check out repository under $GITHUB_WORKSPACE
         uses: actions/checkout@v2
 
+      - name: Set up Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '2.7'
+          # Optional - x64 or x86 architecture, defaults to x64
+          architecture: 'x64'
+
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v1
         with:
@@ -114,6 +199,14 @@ jobs:
       - name: Check out repository under $GITHUB_WORKSPACE
         uses: actions/checkout@v2
 
+      - name: Set up Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '2.7'
+          # Optional - x64 or x86 architecture, defaults to x64
+          architecture: 'x64'
+
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v1
         with:
@@ -183,6 +276,14 @@ jobs:
       - name: Check out repository under $GITHUB_WORKSPACE
         uses: actions/checkout@v2
 
+      - name: Set up Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '2.7'
+          # Optional - x64 or x86 architecture, defaults to x64
+          architecture: 'x64'
+
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v1
         with:
@@ -229,6 +330,86 @@ jobs:
           path: |
             ~/projects/
 
+  aatest_ds000114_scrubbing:
+    name: Testing fMRI frame censoring
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - name: Maximize build space
+        uses: easimon/maximize-build-space@master
+        with:
+          root-reserve-mb: 51200
+          swap-size-mb: 1024
+          remove-dotnet: 'true'
+          remove-android: 'true'
+          remove-haskell: 'true'
+
+      - 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@v2
+
+      - name: Set up Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '2.7'
+          # Optional - x64 or x86 architecture, defaults to x64
+          architecture: 'x64'
+
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v1
+        with:
+          # MATLAB release to set up R2020a
+          release: R2020a
+
+      - name: Install tools under $HOME/tools (SPM, FaceMasking, FSL standards)
+        run: |
+          source $GITHUB_WORKSPACE/.github/workflows/tools_install.sh
+        env:
+          LOAD_FSL: 0
+          LOAD_FREESURFER: 0
+
+      - name: Retrive test data under $HOME/data/aa_demo
+        run: |
+          mkdir -p $HOME/data/aa_demo
+          aws s3 cp s3://openneuro.org/ds000114 $HOME/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114 $HOME/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114/sub-01 $HOME/data/aa_demo/ds000114/sub-01 --quiet --recursive --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114/sub-02 $HOME/data/aa_demo/ds000114/sub-02 --quiet --recursive --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114/sub-03 $HOME/data/aa_demo/ds000114/sub-03 --quiet --recursive --no-sign-request
+          aws s3 cp s3://openneuro.org/ds000114/sub-04 $HOME/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: Configure aa
+        run: |
+          echo "Free space:"
+          df -h
+          mkdir $HOME/.aa
+          cp $GITHUB_WORKSPACE/.github/workflows/aap_parameters_defaults_GitHub.xml $HOME/.aa/aap_parameters_user.xml
+          mkdir $HOME/projects
+
+      - name: Run script
+        uses: matlab-actions/run-command@v1
+        with:
+          command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile(getenv('HOME'),'tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_scrubbing','haltonerror',true)
+
+      - name: Archive results
+        uses: actions/upload-artifact@v2
+        with:
+          name: aatest_ds000114_scrubbing
+          path: |
+            ~/projects/
+
   aatest_ds002737_deface:
     name: Testing (Freesurfer) Deface and FaceMasking
 
@@ -254,6 +435,14 @@ jobs:
       - name: Check out repository under $GITHUB_WORKSPACE
         uses: actions/checkout@v2
 
+      - name: Set up Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '2.7'
+          # Optional - x64 or x86 architecture, defaults to x64
+          architecture: 'x64'
+
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v1
         with:

diff --git a/.github/workflows/aap_parameters_defaults_GitHub.xml b/.github/workflows/aap_parameters_defaults_GitHub.xml
@@ -21,6 +21,14 @@
             <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
                 <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>spm</name>
                 <dir ui='dir'>/home/runner/tools/spm12</dir>
+            </toolbox>                       
+            <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
+                <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>wls</name>
+                <dir ui='dir'>/home/runner/tools/rwls</dir>
+            </toolbox>
+            <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
+                <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>aroma</name>
+                <dir ui='dir'>/home/runner/tools/ICA-AROMA</dir>
             </toolbox>
             <linuxshell desc='Linux shell used to run linux commands' ui='text'>bash</linuxshell>
             <fsldir desc='Path to fsl' ui='dir'>/home/runner/tools/fsl</fsldir>

diff --git a/.github/workflows/tools_install.sh b/.github/workflows/tools_install.sh
@@ -5,10 +5,12 @@ TEMPLATEDIR=$TOOLDIR/templates
 
 sudo apt-get update
 sudo apt-get install libtinfo5 libtinfo6 dc libxml2-utils
+curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o $TOOLDIR/get-pip.py
+python $TOOLDIR/get-pip.py --force-reinstall
 
 # All MATLAB tools MUST be installed referred by the parameterset
 source $GITHUB_WORKSPACE/.github/workflows/tools_urls.sh
-source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_matlabtools.sh $GITHUB_WORKSPACE/.github/workflows/aap_parameters_defaults_GitHub.xml $TOOLDIR
+source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_tools.sh $GITHUB_WORKSPACE/.github/workflows/aap_parameters_defaults_GitHub.xml $TOOLDIR
 
 echo "FSL: ${LOAD_FSL}; FREESURFER: ${LOAD_FREESURFER}"
 

diff --git a/.github/workflows/tools_urls.sh b/.github/workflows/tools_urls.sh
@@ -1,4 +1,6 @@
 # Set of variables (URL_<tool name with lower case>) describing the source of tools
 
 URL_spm=git+https://github.com/spm/spm12
-URL_facemasking=git+https://github.com/mmilch01/mask_face
+URL_facemasking=git+https://github.com/mmilch01/mask_face
+URL_aroma=git+https://github.com/maartenmennes/ICA-AROMA
+URL_wls=git+https://github.com/jdiedrichsen/rwls
diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@ for supporting research at the MRC Cognition and Brain Science Unit. It
 is made available to the academic community in the hope that it may
 prove useful.
 
+![CI](https://github.com/automaticanalysis/automaticanalysis/actions/workflows/aa_test.yml/badge.svg?event=push)
 [![Docker image available!](https://img.shields.io/badge/docker-bids%2Faa-brightgreen.svg?logo=docker&style=flat)](https://hub.docker.com/r/bids/aa/)
 [![manuscript](https://img.shields.io/badge/doi-10.3389%2Ffninf.2014.00090-blue.svg?style=flat)](http://doi.org/10.3389/fninf.2014.00090)
 [![resource](https://img.shields.io/badge/RRID-SCR__003560-blue?style=flat)](https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/SCR_003560/resolver)