CI - aaq

.github/workflows/aa_test_aaq.yml

@@ -0,0 +1,99 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Testing aaq
+
+# 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_aaq:
+    name: Testing aaq (batch) 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)
+        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
+        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_aaq','haltonerror',true)
+
+      - name: Archive results
+        uses: actions/upload-artifact@v2
+        with:
+          name: aatest_ds000114_aaq
+          path: |
+            ~/projects/

developer/testscripts/aatest_ds000114_aaq.m

@@ -0,0 +1,47 @@
+function aatest_ds000114_aaq(parameterfile, deleteprevious, wheretoprocess)
+
+% developer PR test script
+%
+% description: test aaq (batch)
+% dataset: ds000114
+
+% -------------------------------------------------------------------------
+% init
+% -------------------------------------------------------------------------
+
+aap = aa_test_inittest(mfilename('fullpath'), parameterfile, deleteprevious, wheretoprocess);
+
+% -------------------------------------------------------------------------
+% analysis options - batch
+% -------------------------------------------------------------------------
+
+aap.options.wheretoprocess = 'matlab_pct'; % localsingle
+aap.directory_conventions.poolprofile = 'local';
+aap.options.aaparallel.numberofworkers = 2;
+aap.options.aaparallel.memory = 2;
+aap.options.aaparallel.walltime = 1;
+aap.options.aaworkermaximumretry = 0; % do not retry; it would remove files
+aap.options.aaworkerGUI = 0;
+
+% -------------------------------------------------------------------------
+% BIDS
+% -------------------------------------------------------------------------
+
+% anatomy data is in session 3
+aap = aas_processBIDS(aap,[],{'finger_foot_lips','line_bisection'},{'sub-01','sub-02'});
+
+% -------------------------------------------------------------------------
+% run
+% -------------------------------------------------------------------------
+
+aa_doprocessing(aap);
+
+% if directory_conventions.reportname is undefined, skip reporting
+
+if isfield(aap.directory_conventions,'reportname') && ~isempty(aap.directory_conventions.reportname)
+    aa_report(fullfile(aas_getstudypath(aap),aap.directory_conventions.analysisid));
+end
+
+
+aa_close(aap);
+

developer/testscripts/aatest_ds000114_aaq.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="utf-8"?>
+<aap>
+    <tasklist>
+
+        <initialisation>			
+            <module><name>aamod_study_init</name></module>
+        </initialisation>
+
+        <main>
+
+            <module><name>aamod_structuralfromnifti</name></module>
+            <module><name>aamod_diffusionfromnifti</name></module>
+            <module><name>aamod_epifromnifti</name></module>
+
+            <module><name>aamod_reorienttomiddle_structural</name></module>
+            <module><name>aamod_reorienttomiddle_diffusion</name></module>
+            <module><name>aamod_reorienttomiddle_epi</name></module>
+            <module><name>aamod_tsdiffana</name></module>
+
+        </main>
+
+    </tasklist>
+</aap>