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Remi-GauRemi-Gau
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Merge pull request #180 from cpp-lln-lab/dev
[FIX] apply patch end of line extra tab
2 parents 269aa60 + 7764ad6 commit 46b475f

39 files changed

+278
-267
lines changed

‎.github/workflows/bids_validator.yml

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branches:
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- master
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pull_request:
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branches: 'master'
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branches: ['master']
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env:
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OCTFLAGS: --no-gui --no-window-system --silent
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- name: Make jsonread for octave
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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
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sudo apt-get -y install octave
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sudo apt-get -y install liboctave-dev
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cd lib/JSONio
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mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
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cd ..
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- name: Update octave path
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run: |
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octave $OCTFLAGS --eval "addpath(pwd); savepath();"
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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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octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
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- name: Install BIDS validator
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run: |
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sudo npm install -g [email protected]
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- name: Create dummy dataset and validate it
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- name: Create dummy dataset and validate it
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run: |
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cd tests/manualTests
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octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
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‎.github/workflows/check_markdown.yml

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‎.github/workflows/check_md_links.yml

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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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branches: ['*']
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jobs:
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markdown-link-check:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@master
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- uses: gaurav-nelson/github-action-markdown-link-check@v1
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- uses: gaurav-nelson/github-action-markdown-link-check@v1

‎.github/workflows/miss_hit.yml

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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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branches: ['*']
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jobs:
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build:
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‎.github/workflows/run_tests.yml

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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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branches: ['*']
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jobs:
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build:
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- name: Make jsonread for octave
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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
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sudo apt-get -y install octave
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sudo apt-get -y install liboctave-dev
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cd lib/JSONio
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mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
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uses: joergbrech/moxunit-action@master
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with:
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tests: tests # files or directories containing the MOxUnit test cases
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src: src # directories to be added to the Octave search path before running the tests.
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src: src # directories to be added to the Octave search path before running the tests.
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ext: tests/utils # External resources to add to the search put (excluded from coverage)
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# data: # Directory for test data
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with_coverage: true

‎.pre-commit-config.yaml

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repos:
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- repo: local
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hooks:
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- id: mh_version
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name: mh_version
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entry: mh_style
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args: [-v]
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verbose: true
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language: python
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additional_dependencies: [miss_hit_core]
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# - id: mh_style
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# name: mh_style
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# entry: mh_style
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# args: [--process-slx, --fix]
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# files: ^(.*\.(m|slx))$
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# language: python
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# additional_dependencies: [miss_hit_core]
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# - id: mh_metric
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# name: mh_metric
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# entry: mh_metric
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# args: [--ci]
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# files: ^(.*\.(m|slx))$
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# language: python
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# additional_dependencies: [miss_hit_core]
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# - id: mh_lint
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# name: mh_lint
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# entry: mh_lint
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# files: ^(.*\.(m|slx))$
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# language: python
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# additional_dependencies: [miss_hit]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files

‎.readthedocs.yml

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

‎.remarkrc

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‎.travis.yml

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‎.zenodo.json

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],
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"license": "MIT license",
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"upload_type": "software"
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}
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}

‎README.md

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2020
[![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS)
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**BIDS validator and linter**
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[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS)
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**Contributors**
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[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)

‎binder/postBuild

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cd ${HOME}
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cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
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‎checkCppBidsDependencies.m

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% (C) Copyright 2020 CPP_BIDS developers
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function checkCppBidsDependencies(cfg)
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%
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% Adds dependencies to the Matlab / Octave path and make sure we got all of them.
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%
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% USAGE::
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%
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% checkCppBidsDependencies(cfg)
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%
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% :param cfg: Configuration. See ``checkCFG()``.
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% :type cfg: structure
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if nargin < 1
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cfg.verbose = 2;
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end
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global CPP_BIDS_INITIALIZED
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if isempty(CPP_BIDS_INITIALIZED)
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GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');
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if strcmp(GITHUB_WORKSPACE, '/github/workspace')
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pth = GITHUB_WORKSPACE;
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addpath(genpath(fullfile(pth, 'lib')));
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elseif isempty(GITHUB_WORKSPACE) % local
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pth = fullfile(fileparts(mfilename('fullpath')));
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addpath(pth);
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addpath(fullfile(pth, 'lib', 'utils'));
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checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
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checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
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addpath(genpath(fullfile(pth, 'src')));
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end
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printCreditsCppBids(cfg);
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CPP_BIDS_INITIALIZED = true();
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else
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fprintf(1, '\n\nCPP_BIDS already initialized\n\n');
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end
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end
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function checkSubmodule(pth)
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% If external dir is empty throw an exception
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% and ask user to update submodules.
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if numel(dir(pth)) <= 2 % Means that the external is empty
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error(['Git submodules are not cloned!', ...
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'Try this in your terminal:', ...
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' git submodule update --recursive ']);
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else
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addpath(pth);
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end
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end

‎docs/Makefile

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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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doc:
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@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)"

‎docs/source/conf.py

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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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'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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'searchbox.html',
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'donate.html',
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]
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}
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}

‎docs/source/contributing.rst

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end
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.. autofunction:: templateFunction
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.. autofunction:: templateFunction
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Example code in the help section
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end
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.. autofunction:: templateFunctionExample
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