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Remi-GauRemi-Gau
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Merge pull request #479 from Remi-Gau/rc1.1.4
rc1.1.4
2 parents c761ebb + 6e94d5f commit 5eb3263

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‎.github/workflows/matlab_workflow_script.m‎

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%
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% (C) Copyright 2021 CPP_SPM developers
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root_dir = getenv('GITHUB_WORKSPACE');
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addpath(fullfile(root_dir, 'spm12'));
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addpath(fullfile(root_dir, 'MOcov', 'MOcov'));
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cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
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run moxunit_set_path();
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cd(fullfile(root_dir));
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initCppSpm();
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addpath(fullfile(root_dir, 'tests', 'utils'));
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run run_tests();

‎.github/workflows/run_tests_matlab.yml‎

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name: tests and coverage with matlab
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on:
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push:
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branches:
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- main
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- dev
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pull_request:
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branches: ["*"]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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build:
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runs-on: ubuntu-20.04
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steps:
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- name: Install MATLAB
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uses: matlab-actions/[email protected]
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with:
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# MATLAB release to set up R2020a
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release: R2020a
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- name: Clone cpp_spm
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uses: actions/checkout@v2
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with:
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submodules: true
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fetch-depth: 2
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- name: Install SPM
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run: |
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git clone https://github.com/spm/spm12.git --depth 1
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- name: Install Moxunit and MOcov
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run: |
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git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
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git clone https://github.com/MOcov/MOcov.git --depth 1
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- name: Prepare data
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run: |
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inputs_folder='demos/MoAE/inputs/'
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mkdir $inputs_folder
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curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
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unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
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mv $inputs_folder/MoAEpilot $inputs_folder/raw
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cd tests
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make data
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- name: Run commands
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uses: matlab-actions/[email protected]
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with:
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command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run matlab_workflow_script;
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- name: Run tests
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run: |
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cat test_report.log | grep 0
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bash <(curl -s https://codecov.io/bash)
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- name: Upload coverage
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uses: actions/upload-artifact@v1
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with:
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name: coverage_file
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path: coverage.xml
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- name: Code coverage
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uses: codecov/codecov-action@v1
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with:
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file: coverage.xml # optional
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flags: unittests # optional
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name: codecov-umbrella # optional
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fail_ci_if_error: true # optional (default = false)

‎.zenodo.json‎

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This file was deleted.

‎CITATION.cff‎

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cff-version: 1.2.0
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title: "CPP SPM"
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version: 1.1.4
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abstract: CPP_SPM is a set pipelines and tools for Octave/MATLAB to process and analyze BIDS data sets using SPM.
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message: "If you use this software, please cite it as below."
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repository-code: "https://github.com/cpp-lln-lab/CPP_SPM"
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identifiers:
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- description: This is the collection of archived snapshots of all releases of CPP SPM
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type: doi
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value: "10.5281/zenodo.3554331"
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contact:
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- affiliation: "Université catholique de Louvain"
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email: [email protected]
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family-names: Gau
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given-names: Rémi
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authors:
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- family-names: "Gau"
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given-names: "Rémi"
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orcid: "https://orcid.org/0000-0002-1535-9767"
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affiliation: "Université catholique de Louvain"
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- family-names: "Barilari"
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given-names: "Marco"
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orcid: "https://orcid.org/0000-0002-3313-3120"
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affiliation: "Université catholique de Louvain"
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- family-names: "Battal"
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given-names: "Ceren"
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orcid: "https://orcid.org/0000-0002-9844-7630"
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affiliation: "Université catholique de Louvain"
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- family-names: "Rezk"
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given-names: "Mohamed"
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orcid: "https://orcid.org/0000-0002-1866-8645"
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affiliation: "Université catholique de Louvain"
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- family-names: "Collignon"
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given-names: "Olivier"
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orcid: "https://orcid.org/0000-0003-1882-3550"
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affiliation: "Université catholique de Louvain"
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- family-names: "Gurtubay"
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given-names: "Ane"
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orcid: "https://orcid.org/0000-0003-3824-2219"
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affiliation: "Université catholique de Louvain"
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- family-names: "Falagiarda"
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given-names: "Federica"
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orcid: "https://orcid.org/0000-0001-7844-1605"
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affiliation: "Université catholique de Louvain"
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- family-names: "MacLean"
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given-names: "Michèle"
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orcid: "https://orcid.org/0000-0002-0174-9326"
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affiliation: "Université de Montréal"
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- family-names: "Cerpelloni"
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given-names: "Filippo"
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orcid: "https://orcid.org/0000-0001-8070-5753"
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affiliation: "Université catholique de Louvain"
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license: GPL-3.0
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keywords:
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- BIDS
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- brain imaging data structure
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- neuroimaging
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- automated pipeline
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- MRI
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- MATLAB
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- Octave
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- SPM

‎Makefile‎

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.PHONY: clean
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clean:
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rm version.txt
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version.txt: CITATION.cff
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grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
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validate_cff: CITATION.cff
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cffconvert --validate
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‎docs/source/function_description.rst‎

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.. autofunction:: getVersion
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.. autofunction:: isOctave
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.. autofunction:: loadAndCheckOptions
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.. autofunction:: manageWorkersPool
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.. autofunction:: printBatchName
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.. autofunction:: printCredits
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.. autofunction:: printProcessingRun

‎lib/miss_hit.cfg‎

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enable: false

‎miss_hit.cfg‎

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project_root
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octave: true
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# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
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line_length: 100
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regex_function_name: "[a-z]+([a-zA-Z0-9]){1}[a-zA-Z0-9]+"
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regex_script_name: "[a-z0-9]+(_[a-z0-9]+)*"
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suppress_rule: "naming_parameters"
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exclude_dir: "lib"
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copyright_entity: "JH"

‎requirements.txt‎

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sphinxcontrib-matlabdomain
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sphinxcontrib-napoleon
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sphinx_rtd_theme
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miss_hit==0.9.22
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miss_hit==0.9.29
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pre-commit

‎src/QA/anatomicalQA.m‎

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fprintf(1, ' ANATOMICAL: QUALITY CONTROL\n\n');
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parfor iSub = 1:numel(opt.subjects)
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for iSub = 1:numel(opt.subjects)
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subLabel = opt.subjects{iSub}; %#ok<*PFBNS>
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