Merge pull request #1478 from softmatterlab/develop

Release 2.0.0.a1

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitignore

@@ -1 +1,4 @@
-*.asv
+*.asv
+.DS_Store
+braph2/
+Tmp/

.zenodo.json

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+{
+    "creators": [
+        {
+            "orcid": "0000-0001-5057-1846",
+            "affiliation": "Gothenburg University",
+            "name": "Volpe, Giovanni"
+        },
+        {
+            "orcid": "0000-0002-5388-7712",
+            "affiliation": "Gothenburg University",
+            "name": "Gómez-Ruiz, Emiliano"
+        }, 
+        {
+            "orcid": "0000-0001-9598-2278",
+            "affiliation": "Gothenburg University",
+            "name": "Chang, Yu-Wei"
+        }, 
+        {
+            "orcid": "0000-0002-4604-2711",
+            "affiliation": "Karolinksa Institute",
+            "name": "Pereira, Joana"
+        }, 
+        {
+            "orcid": "0000-0001-7460-741X",
+            "affiliation": "Karolinksa Institute",
+            "name": "Canal-Garcia, Anna"
+        }, 
+        {
+            "orcid": "0000-0002-9844-4413",
+            "affiliation": "Karolinksa Institute",
+            "name": "Mijalkov, Mite"
+        }, 
+        {
+            "orcid": "0000-0003-2077-5252",
+            "affiliation": "Karolinksa Institute",
+            "name": "Véreb, Dániel"
+        },
+        {
+            "orcid": "0000-0002-3115-2977",
+            "affiliation": "Karolinksa Institute",
+            "name": "Westman, Eric"
+        }
+    ],
+
+    "title": "BRAPH 2: Brain Analysis Using Graph Theory 2",
+
+    "related_identifiers": [
+        {
+            "scheme": "doi",
+            "identifier": "10.1371/journal.pone.0178798",
+            "relation": "isDocumentedBy",
+            "resource_type": "publication-article"
+        }
+    ],
+
+    "description": "An object-oriented software that provides pipelines for conventional brain connectivity analysis as well as more advanced methods, including multilayer networks and deep learning methods." ,
+
+    "keywords": ["Brain", "Software", "Graph", "Multigraph", "Multiplex Graph", "MATLAB", "Neuroimaging", "Deep Learning"],
+
+    "upload_type": "software",
+
+    "communities": [
+        {"identifier": "www.braph.org"},
+        {"identifier": "https://github.com/softmatterlab/BRAPH-2-Matlab"}
+    ]
+}

CITATION.cff

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+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: 'BRAPH 2: Brain Analysis using Graph Theory 2'
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Giovanni
+    family-names: Volpe
+    email: giovanni.vole@physics.gu.se
+    affiliation: Gothenburg University
+    orcid: 'https://orcid.org/0000-0001-5057-1846'
+  - given-names: Joana
+    name-particle: B.
+    family-names: Pereira
+    email: joana.pereira@ki.se
+    affiliation: Karolinska Institute
+    orcid: 'https://orcid.org/0000-0002-4604-2711'
+  - given-names: Pablo Emiliano
+    family-names: Gómez Ruiz
+    email: emiliano.gomez@physics.gu.se
+    affiliation: Gothenburg University
+    orcid: 'https://orcid.org/0000-0002-5388-7712'
+  - given-names: Anna
+    family-names: Canal-Garcia
+    email: anna.canal@ki.se
+    affiliation: Karolinska Institute
+    orcid: 'https://orcid.org/0000-0001-7460-741X'
+  - given-names: Yu-Wei
+    family-names: Chang
+    email: yu-wei.chang@physics.gu.se
+    affiliation: Gothenburg University
+    orcid: 'https://orcid.org/0000-0001-9598-2278'
+  - given-names: Mite
+    family-names: Mijalkov
+    email: mite.mijalkov@ki.se
+    affiliation: Karolinksa Institute
+    orcid: 'https://orcid.org/0000-0002-9844-4413'
+  - given-names: Dániel
+    family-names: Véreb
+    email: daniel.vereb@ki.se
+    affiliation: Karolinska Institute
+    orcid: 'https://orcid.org/0000-0003-2077-5252'

LICENSE

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+BRAPH Software License Terms
+
+1	General
+
+1.1	The Braph software is developed by Prof. Giovanni Volpe (the “Licensor”, “we” or “us”) and related
+contributors as further set forth on the Braph website located at www.braph.org. By installing and 
+using Braph, you and your organisation is granted a license to use Braph subject to these terms. If 
+you do not accept these terms, please do not install and do not use Braph.
+
+1.2	This license pertains solely to use of Braph in combination with Matlab® and requires that that 
+you also have a proper and valid license to use Matlab® in addition to this license.
+
+1.3	Braph is provided together with its source code and intended to be viewed and used as open source.
+The intent is that you shall be able to freely use and develop Braph for your research, development 
+and educational purposes. However, as much as we encourage use and development of Braph, we want to 
+restrict redistribution and commercial sublicensing, which means that there are some restrictions to 
+your use set forth in Section 2.4.
+
+2	Intellectual property rights and license
+
+2.1	Any and all intellectual property rights, including without limitation copyright protected 
+materials, source code, database rights, registered and unregistered trade-marks, registered and 
+unregistered design rights, patents and patentable inventions, know how (regardless if patentable or 
+not) and all other rights in or relating to Braph is the exclusive property of the Licensor, or the 
+property of the Licensor’s contributing licensors as applicable.
+
+2.2	You are granted a non-exclusive, royalty-free right and license to use Braph for your internal 
+research and development, including commercial research and development, as well as for educational 
+and academic purposes. The license furthermore includes the right to access and amend the source code
+of Braph and implement such changes in Braph as you deem fit.
+
+2.3	Any amendments made by you to Braph are your intellectual property that you may use freely as long 
+as such use is not contrary to these terms. We encourage that you share amendments with us, in which 
+case we are given the right (but not the obligation) to include them in future versions of Braph and 
+make them available on these terms or terms materially similar, but you are (i) not required to share 
+such amendments and (ii) your amendments if shared are subject to the same limitations of liability 
+as set forth in clause 3.
+
+2.4	Unless you have our prior written consent (which consent may be subject to further terms), you 
+are expressly not permitted to re-distribute Braph, amended or in its original form, or any part 
+thereof, regardless if such re-distribution is made for free or for a fee. You can however point 
+third parties to download Braph directly from our website www.braph.org or other official sources. 
+Furthermore, you may not integrate Braph or parts thereof into other software regardless if such 
+software is licensed on open source or so called “proprietary” terms. Use contrary to this clause 2.4 
+shall in addition render your license to use Braph null and void.
+
+3	Limitation of liability
+
+3.1	BRAPH IS PROVIDED “AS IS” AND “WHERE IS” WITHOUT ANY WARRANTY OF ANY KIND, INCLUDING WITHOUT 
+LIMITATION ANY IMPLIED, EXPRESS OR STATUTORY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY 
+WARRANTIES OF FUNCTIONALITY, COMPLETENESS OR ACCURACY, FITNESS FOR A PARTICULAR PURPOSE, 
+MERCHANTABILITY, LACK OF VIRUSES OR FREEDOM FROM INFRINGEMENT. FURTHERMORE, YOU ACKNOWLEDGE THAT THE 
+SOFTWARE IS NOT, AND WILL NOT BE, ERROR FREE AND RUN WITHOUT ANY INTERRUPTION.
+
+3.2	We do not accept any liability of any kind, whether direct or indirect, in tort or under any form 
+of contractual liability or other doctrine for any damage or claim that may arise as a result of your 
+use of Braph, regardless if such use is with our version without any amendment to Braph that you may 
+have made.
+
+3.3	Furthermore, if any third party makes a claim against us as a result of your amended or unamended 
+use of Braph, you shall indemnify and hold us harmless from any such claim, including related cost and 
+expense such as legal fees.
+
+4	Attribution
+
+When publishing scientific results or research reports where Braph has been used in such research, we 
+encourage and appreciate that you include references to your use of Braph in such research, as well 
+as the scientific publications cited on www.braph.org.
+
+5	Choice of law, disputes
+
+These terms shall be governed and construed in accordance with the substantive laws of Sweden, without 
+regard to its conflicts of law principles. Any dispute, controversy or claim arising out of or in 
+connection with this Agreement, or the breach, termination or invalidity thereof, shall be settled by 
+the courts of Sweden with the district court of Stockholm as first instance.
+

README.md

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-# Braph-2.0-Matlab
+<p align="center">
+  <img width="350" src=https://github.com/softmatterlab/BRAPH-2-Matlab/blob/develop/braph2genesis/src/util/braph2icon.png>
+</p>
+
+<h3 align="center">Brain Analysis using Graph Theory.</h3>
+<p align="center">
+  <a href="https://twitter.com/braph2software" alt="tweeter"><img src="https://img.shields.io/twitter/url?label=BRAPH%202&style=social&url=https%3A%2F%2Ftwitter.com%2Fbraph2software"></a>
+  <a href="http://braph.org/" alt="website"><img src="https://img.shields.io/website?up_message=braph.org&url=http%3A%2F%2Fbraph.org%2F"></a>
+  <a href="https://doi.org/10.1371/journal.pone.0178798" alt="DOI"><img src="https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0178798-blue">
+  </a>
+</p>
+<p align="center">
+  <a href="#installation">Installation</a> •
+  <a href="#braph-2-usage-examples">Examples</a> •
+  <a href="#cite-us">Cite us</a> •
+  <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/blob/develop/LICENSE">License</a> 
+</p>
+
+
+An object-oriented software that provides pipelines for conventional brain connectivity analysis as well as more advanced methods, including multilayer networks and deep learning methods.
+
+# Installation
+
+BRAPH 2 requires at least **MATLAB R2021a**. BRAPH 2 requires both **Statistics and Machine Learning Toolbox** and **Parallel Computing Toolbox**. For deep learning analysis, **Deep Learning Toolbox** and **Deep Learning Toolbox Converter for ONNX Model Format** are also needed.
+
+To install BRAPH 2, first download BRAPH 2.
+From our GitHub repository, you can find the latest stable version in the branch <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/tree/master">master</a> and the latest development version in the branch <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/tree/develop">develop</a>.
+You can also download BRAPH 2 from our <a href="http://braph.org/software/braph-2/">website</a>.
+
+After unzipping the downloaded file into the desired directory and launching MATLAB, change the current folder to **braph2genesis** and run *braph2genesis* (you may have to add it to the path). This installation takes around 5 minutes.
+The installation will be only needed once.
+You can also follow the <a href="http://braph.org/software/braph-2/">Installation</a> section from our website.
+
+# BRAPH 2 usage examples
+
+BRAPH 2 is a powerful tool that transforms scripts to pipelines. We provide example data in order to test the different analyses and comparisons from the provided pipelines. Please check the <a href="http://braph.org/tutorials/">Tutorials</a> section from our website for the step-by-step instructions and more details.
+
+# Cite us!
+If you use BRAPH 2 in your project, please cite us here:
+
+```
+Emiliano Gomez-Ruiz, Anna Canal-Garcia, Yu-Wei Chang, Daniel Vereb, 
+Eric Westman, Mite Mijalkov, Joana Pereira, Giovanni Volpe
+BRAPH 2: A software for brain connectivity analysis 
+with multilayer graphs and deep learning.
+```
+
+See also:
+
+<https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178798>:
+```
+Mite Mijalkov, Ehsan Kakaei, Joana B Pereira, Eric Westman, Giovanni Volpe
+BRAPH: A graph theory software for the analysis of brain connectivity.
+PLOS ONE 12, e0178798 (2017).
+```