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Merge pull request #18 from cpp-lln-lab/dev
[REL] rc0.2.0
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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();

‎.gitignore‎

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*DS_Store
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*.m~
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*octave-workspace
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.vscode
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*.json
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env/
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# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
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# Windows default autosave extension
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*.asv
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‎CITATION.cff‎

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cff-version: 1.2.0
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title: "spm_2_bids"
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version: 0.2.0
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abstract: Toolbox to convert SPM output files to valid BIDS derivatives.
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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/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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- converter
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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:
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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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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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lib/bids-matlab:
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git clone https://github.com/bids-standard/bids-matlab.git --branch dev lib/bids-matlab
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clean:
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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: clean_doc clean_tests
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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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clean_doc:
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cd docs && make clean
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clean_tests:
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rm -rf coverage_html
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rm -f coverage.xml
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rm -f *.log
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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, pth, json] = 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/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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clean:
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rm -rf build

‎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

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