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Merge pull request #300 from cpp-lln-lab/release-0.2.0
[REL] Release 0.2.0
2 parents 1b890f3 + 075d002 commit c3511c7

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‎.github/workflows/check_markdown.yml‎

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name: Check Markdown
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on:
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push:
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branches:
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- master
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pull_request:
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branches: '*'
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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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: 1
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- uses: actions/setup-node@v2
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with:
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node-version: '10'
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- name: Install dependencies and check markdown
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run: |
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npm install `cat npm-requirements.txt`
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npx remark *.md --frail
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npx remark ./docs/ --frail
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npx remark ./demos/ --frail
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npx remark ./tests/ --frail

‎.github/workflows/check_md_links.yml‎

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push:
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branches:
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- master
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- dev
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pull_request:
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branches: '*'
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‎.github/workflows/miss_hit.yml‎

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push:
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branches:
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- master
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- dev
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pull_request:
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branches: '*'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools
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pip3 install miss_hit
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pip3 install -r requirements.txt
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- name: Miss_hit code quality
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- name: MISS_HIT Code style
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run: |
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mh_metric . --ci
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mh_style --process-slx
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- name: Miss_hit code style
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- name: MISS_HIT Metrics
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run: |
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mh_style .
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mh_metric --ci
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- name: MISS_HIT Bug finder
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run: |
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mh_lint

‎.github/workflows/run_system_tests.yml‎

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name: system tests
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# Uses the cron schedule for github actions
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#
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# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
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#
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# ┌───────────── minute (0 - 59)
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# │ ┌───────────── hour (0 - 23)
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# │ │ ┌───────────── day of the month (1 - 31)
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# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
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# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
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# │ │ │ │ │
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# │ │ │ │ │
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# │ │ │ │ │
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# * * * * *
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- 'master'
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- 'main'
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schedule:
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- cron: "* * 1 * *"
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env:
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OCTFLAGS: --no-gui --no-window-system --silent
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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 dependencies
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install octave liboctave-dev
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sudo apt-get -y install nodejs npm
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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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make -C spm12/src PLATFORM=octave distclean
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make -C spm12/src PLATFORM=octave
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make -C spm12/src PLATFORM=octave install
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
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- name: Update octave path
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run: |
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octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
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octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
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- name: Prepare data
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run: |
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output_folder='demos/MoAE/output/'
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mkdir $output_folder
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curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
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unzip $output_folder'MoAEpilot.zip' -d $output_folder
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- name: Run system tests
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run: |
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cd demos/MoAE
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octave $OCTFLAGS --eval "MoAEpilot_run"
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‎.github/workflows/run_tests.yml‎

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name: tests and coverage
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# Uses the cron schedule for github actions
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#
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# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
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#
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# ┌───────────── minute (0 - 59)
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# │ ┌───────────── hour (0 - 23)
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# │ │ ┌───────────── day of the month (1 - 31)
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# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
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# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
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# │ │ │ │ │
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# │ │ │ │ │
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# │ │ │ │ │
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# * * * * *
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on:
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push:
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branches:
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- dev
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pull_request:
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branches: '*'
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schedule:
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- cron: "* * 1 * *"
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env:
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OCTFLAGS: --no-gui --no-window-system --silent
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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 dependencies
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install octave liboctave-dev
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sudo apt-get -y install nodejs npm
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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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make -C spm12/src PLATFORM=octave distclean
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make -C spm12/src PLATFORM=octave
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make -C spm12/src PLATFORM=octave install
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
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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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make -C MOxUnit install
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git clone https://github.com/MOcov/MOcov.git --depth 1
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make -C MOcov install
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- name: Update octave path
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run: |
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octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
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octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
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- name: Prepare data
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run: |
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output_folder='demos/MoAE/output/'
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mkdir $output_folder
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curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
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unzip $output_folder'MoAEpilot.zip' -d $output_folder
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cd tests
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sh createDummyDataSet.sh
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cd ..
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- name: Run tests
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run: |
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octave $OCTFLAGS --eval "runTests"
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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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‎.gitignore‎

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*.zip
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*.ps
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options_task-*.json
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options_task-*date*.json
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onsets*_events.mat
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# files in the demo folder related to running the demo analysis
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demos/MoAE/*.zip
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demos/*/*.zip
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demos/*/derivatives/*
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demos/MoAE/output/*
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demos/MoAE/derivatives/*
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demos/spm*/raw
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demos/spm*/source
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# test folder
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# test folder and dummy data
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tests/sub-01/*
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tests/group/*
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tests/models/*.json
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.nii*
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.tsv
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.txt
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.json
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tests/dummyData/derivatives/cpp_spm/sub-*/stats/*/*/*.nii*
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# ignore content of the build folder of the doc
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docs/build/*
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# ignore virtual env
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cpp_bids_spm/*
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cpp_spm/*
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# visual studio code stuff
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.vscode

‎.gitmodules‎

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[submodule "lib/bids-matlab"]
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path = lib/bids-matlab
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url = https://github.com/cpp-lln-lab/bids-matlab.git
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url = https://github.com/bids-standard/bids-matlab.git
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[submodule "lib/spmup"]
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path = lib/spmup
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url = https://github.com/CPernet/spmup.git

‎.readthedocs.yml‎

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python:
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version: 3.7
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install:
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- requirements: docs/requirements.txt
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- requirements: requirements.txt

‎.travis.yml‎

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