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Merge pull request #13 from cpp-lln-lab/use_schema
[DOC & INFRA] misc
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‎.github/workflows/run_tests.yml‎

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‎.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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- master
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- dev
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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-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 spm_2_bids
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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 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: get bids-matlab and JSONio
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run: |
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make install_dev
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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 tests_matlab;
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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: 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)

‎.github/workflows/tests_matlab.m‎

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%
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% (C) Copyright 2022 spm_2_bids developers
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root_dir = getenv('GITHUB_WORKSPACE');
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disp(root_dir);
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ls(root_dir);
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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(root_dir);
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init_spm_2_bids();
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cd(root_dir);
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run run_tests();

‎CITATION.cff‎

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cff-version: 1.2.0
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title: "spm_2_bids"
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version: v0.1.0dev
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abstract: Toolbox to convert SPM output files to valid BIDS derivatives.
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repository-code: "https://github.com/cpp-lln-lab/spm_2_bids.git"
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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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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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- MRI
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- MATLAB
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- Octave
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- SPM

‎Makefile‎

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install_dev:
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git clone https://github.com/bids-standard/bids-matlab.git lib/bids-matlab
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cd lib/bids-matlab && git checkout dev
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git clone https://github.com/gllmflndn/JSONio.git --depth 1 lib/JSONio
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.PHONY: clean
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install_dev_octave: install_dev
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cd lib/JSONio && mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
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install_dev: lib/bids-matlab lib/JSONio
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install_dev_octave:
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lib/bids-matlab:
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git clone https://github.com/bids-standard/bids-matlab.git lib/bids-matlab
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cd lib/bids-matlab && git checkout dev
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git clone https://github.com/gllmflndn/JSONio.git --depth 1 lib/JSONio
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cd lib/JSONio && mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
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lib/JSONio:
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git clone https://github.com/gllmflndn/JSONio.git --depth 1 lib/JSONio
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clean:
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rm -rf lib/bids-matlab
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rm -rf lib/JSONio
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rm -rf 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

‎README.md‎

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<!--
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[![code quality](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_quality.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_quality.yml)
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[![code style](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_style.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_style.yml)
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[![tests](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/run_tests.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/run_tests.yml)
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[![codecov](https://codecov.io/gh/cpp-lln-lab/spm_2_bids/branch/master/graph/badge.svg?token=yaL40GJK9y)](https://codecov.io/gh/cpp-lln-lab/spm_2_bids)
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When you have set up your repo
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# spm_2_bids
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**Unit tests and coverage**
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Small code base to help convert the MRI spm output to a valid bids derivatives.
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[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/Remi-gau/template_matlab_analysis/actions)
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![](https://github.com/Remi-gau/template_matlab_analysis/workflows/CI/badge.svg)
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This code only generates the plausible BIDS derivatives filename for given file
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that has been preprocessed with SPM.
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[![codecov](https://codecov.io/gh/Remi-gau/template_matlab_analysis/branch/master/graph/badge.svg)](https://codecov.io/gh/Remi-gau/template_matlab_analysis)
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Most of the renaming is based on the SPM prefixes combinations.
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**Miss_hit linter**
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It is configurable to adapt to new set of prefixes.
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[![Build Status](https://travis-ci.com/Remi-gau/template_matlab_analysis.svg?branch=master)](https://travis-ci.com/Remi-gau/template_matlab_analysis)
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## Dependencies
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-->
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- [BIDS-matlab](https://github.com/bids-standard/bids-matlab)
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# spm_2_bids
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Can be installed with :
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Small code base to help convert the MRI spm output to a valid bids derivatives.
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For MATLAB
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This code only generates the plausible BIDS derivatives filename for given file that has
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been preprocessed with SPM.
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```bash
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make install_dev
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```
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Most of the renaming is based on the SPM prefixes combinations.
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For Octave
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It is configurable to adapt to new set of prefixes.
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```bash
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make install_dev_octave
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```
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## Usage
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```matlab
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file = 'wmsub-01_desc-skullstripped_T1w.nii';
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new_filename = spm_2_bids(file);
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new_filename =
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'sub-01_space-IXI549Space_desc-preproc_T1w.nii');
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```
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- [Dependencies](./lib/README.md)
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- [Documentation](https://spm-2-bids.readthedocs.io/en/latest/)
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For more see the [documentation](https://spm-2-bids.readthedocs.io/en/latest/).

‎docs/requirements.txt‎

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# doc
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Sphinx
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sphinxcontrib-matlabdomain
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sphinxcontrib-napoleon
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sphinx-copybutton
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sphinx_rtd_theme
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rstcheck
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myst-parser

‎docs/source/conf.py‎

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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../..'))
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sys.path.insert(0, os.path.abspath("../.."))
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# -- Project information -----------------------------------------------------
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project = 'spm_2_bids'
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author = 'Rémi Gau'
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project = "spm_2_bids"
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author = "Rémi Gau"
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# The full version, including alpha/beta/rc tags
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release = 'v0.1.0'
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release = "v0.1.0"
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# -- General configuration ---------------------------------------------------
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinxcontrib.matlab',
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'sphinx.ext.autodoc']
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matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
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primary_domain = 'mat'
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"sphinxcontrib.matlab",
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"sphinx.ext.autodoc",
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"sphinx_copybutton",
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"myst_parser",
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]
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matlab_src_dir = os.path.dirname(os.path.abspath("../../src"))
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primary_domain = "mat"
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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templates_path = ["_templates"]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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pygments_style = "sphinx"
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# The master toctree document.
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master_doc = 'index'
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master_doc = "index"
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# source_suffix = ['.rst', '.md']
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source_suffix = '.rst'
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source_suffix = ".rst"
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autodoc_member_order = 'bysource'
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autodoc_member_order = "bysource"
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'sphinx_rtd_theme'
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html_theme = "sphinx_rtd_theme"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# }
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html_sidebars = {
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'**': [
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'about.html',
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'navigation.html',
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'relations.html', # needs 'show_related': True theme option to display
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'searchbox.html',
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'donate.html',
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"**": [
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"about.html",
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"navigation.html",
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"relations.html", # needs 'show_related': True theme option to display
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"searchbox.html",
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"donate.html",
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]
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}

‎docs/source/function_details.rst‎

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Function details
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****************
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``spm_2_bids`` only provides names to use but does not actually rename the files.
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.. automodule:: src
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.. autofunction:: spm_2_bids
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.. automodule:: src.defaults
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.. autofunction:: check_cfg
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.. autoclass:: Mapping
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:members:

‎docs/source/general_information.md‎

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../../README.md

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