Init

Author: totetmatt

.github/workflows/build_website.yml

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+name: Deploy to GitHub Pages
+
+on:
+  push:
+    branches:
+      - master
+    # Review gh actions docs if you want to further define triggers, paths, etc
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#on
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+jobs:
+  deploy:
+    name: Deploy to GitHub Pages
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+          cache: npm
+      - name: Configure Git
+        run: |
+          git config user.name "Publisher"
+          git config user.email "publisher@users.noreply.github.com"
+      - name: Build website
+        run: npm install
+      - name: Build website
+        run: npm run build
+      - name: Switch to branch 'gh-pages'
+        run: |
+          git branch -f gh-pages HEAD
+          git checkout gh-pages
+      - run: |
+          git add -f build/
+          git commit -m "Publish"
+          git push -f origin `git subtree split -P build`:refs/heads/gh-pages

.gitignore

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+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*

README.md

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+# Website
+
+This website is built using [Docusaurus 2](https://docusaurus.io/), a modern static website generator.
+
+### Installation
+
+```
+$ yarn
+```
+
+### Local Development
+
+```
+$ yarn start
+```
+
+This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
+
+### Build
+
+```
+$ yarn build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+### Deployment
+
+Using SSH:
+
+```
+$ USE_SSH=true yarn deploy
+```
+
+Not using SSH:
+
+```
+$ GIT_USER=<Your GitHub username> yarn deploy
+```
+
+If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the `gh-pages` branch.

babel.config.js

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+module.exports = {
+  presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
+};

docs/01_Intro.md

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+---
+sidebar_position: 1
+---
+
+# Gephi Developper Documentation
+

docs/02_Manuals/Code-Style.md

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+---
+id: code-style
+title: Code Style
+tags:
+  - Code Style
+  - Development
+---
+The source code uses the [CheckStyle](https://checkstyle.sourceforge.io/) tool to keep the code style consistent.
+
+In addition, we check for code style when building the project using the [Maven CheckStyle Plugin](http://maven.apache.org/plugins/maven-checkstyle-plugin/). A pull request without proper code style would fail to build.
+
+### IntelliJ Setup
+
+On IntelliJ follow these steps to configure CheckStyle:
+
+1. Install the [CheckStyle plugin](https://plugins.jetbrains.com/plugin/1065-checkstyle-idea)
+2. Open `Preferences/Settings` and go to `Editor > Code Style`.
+3. Select `Project` as `Scheme` and click the settings icon next to it.
+4. Select `Import Scheme > CheckStyle Configuration` and locate the `checkstyle.xml` file at the root of Gephi's repository.
+
+You're done. You can now use the built-in **Code > Reformat Code** tool. The resulting code style will match what is on the Gephi repository.

docs/02_Manuals/Datasets.md

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+---
+id: datasets
+title: Datasets
+---
+
+The Gephi sample datasets below are available in various formats (GEXF, GDF, GML, NET, GraphML, DL, DOT). Feel free to add new datasets, but be sure to cite the original authors.
+
+**Supported graph formats are described [here](https://gephi.org/users/supported-graph-formats/).**
+
+Gephi can open zipped files directly.
+
+## Web and Internet
+
+- [GEXF file](https://gephi.org/datasets/eurosis.gexf.zip). **EuroSiS web mapping study**: Mapping interactions between Science in Society actors on the Web of 12 European countries. Original report and data can be found [here](http://www.webatlas.fr/exhibition/eurosis/).
+- [GML file](https://gephi.org/datasets/internet_routers-22july06.gml.zip). **Internet**: a symmetrized snapshot of the structure of the Internet at the level of autonomous systems, reconstructed from BGP tables posted by the [University of Oregon Route Views Project](http://routeviews.org/). This snapshot was created by Mark Newman on July 22, 2006 and was not previously published.
+
+## Social networks
+
+- [GML file](https://gephi.org/datasets/lesmiserables.gml.zip). **Les Miserables**: coappearance weighted network of characters in the novel Les Miserables. D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley, Reading, MA (1993).
+- [GEXF file](https://gephi.org/datasets/ht2009_15min.gexf.gz). **Hypertext 2009 dynamic contact network**: contact network during the Hypertext 2009 conference. Source: [Sociopatterns.org](http://www.sociopatterns.org/datasets/hypertext-2009-dynamic-contact-network/).
+- [GEXF file](https://zenodo.org/record/4612153#.YFIuQi1Xaw4). **CLASS OF 1880/81**: friendship network of a German boys' school class from 1880/1881. It's based on the probably first ever primarily collected social network dataset, assembled by the primary school teacher Johannes Delitsch. The data was reanalyzed and compiled for the article: [Heidler, R., Gamper, M., Herz, A., Eßer, F. (2014): Relationship patterns in the 19th century: The friendship network in a German boys' school class from 1880 to 1881 revisited. Social Networks 13: 1--13.](http://www.sciencedirect.com/science/article/pii/S0378873313000865).
+- [GML file](https://gephi.org/datasets/karate.gml.zip). **Zachary's karate club**: social network of friendships between 34 members of a karate club at a US university in the 1970s. W. W. Zachary, An information flow model for conflict and fission in small groups, Journal of Anthropological Research 33, 452-473 (1977).
+- [GML file](https://gephi.org/datasets/netscience.gml.zip). **Coauthorships in network science**: coauthorship network of scientists working on network theory and experiment, as compiled by M. Newman in May 2006. A figure depicting the largest component of this network can be found here. M. E. J. Newman, Phys. Rev. E 74, 036104 (2006).
+- [GEXF file](https://gephi.org/datasets/cpan-authors.gexf.zip). **CPAN authors**: CPAN Explorer is a visualization project aiming at analyzing the relationships between the developers and the packages of the Perl language, known as the CPAN community. This snapshot was created by Linkfluence in July 2009. This file contains the network of developers, linked when they use the same Perl module. Original data can be found [here](http://cpan-explorer.org/).
+- [GEXF file](https://gephi.org/datasets/cpan-distributions.gexf.zip). **CPAN distributions**: CPAN Explorer is a visualization project aiming at analyzing the relationships between the developers and the packages of the Perl language, known as the CPAN community. This snapshot was created by Linkfluence in July 2009. This file contains the network of Perl modules dependencies. Orginal data can be found [here](http://cpan-explorer.org/).
+- [NET file](https://gephi.org/datasets/jazz.net.zip). **Jazz musicians network**: List of edges of the network of Jazz musicians. P.Gleiser and L. Danon , Adv. Complex Syst.6, 565 (2003).
+- [TGZ file](http://franck.lumberjaph.net/graphs.tgz). **Github open source developers**: See <https://github.com/franckcuny/blog/blob/master/posts/2010-03-25-github-explorer.md/>
+- [DL file](https://gephi.org/datasets/OClinks_w.dl.zip). **Online Social Network** 1899 nodes - Opsahl, T., Panzarasa, P., 2009. Clustering in weighted networks. Social Networks 31 (2), 155-163
+- [GEPHI file](https://gephi.org/datasets/hero-social-network.gephi). **The Marvel Social Network** Networks of super heroes, constructed by Cesc Rosselló, Ricardo Alberich, and Joe Miro from the University of the Balearic Islands. Collected by [Infochimps](http://www.infochimps.com/datasets/marvel-universe-social-graph) and transformed & enhanced by Kai Chang.
+- [GDF file](https://gephi.org/datasets/comic-hero-network.gdf.zip). **Comic and Hero Network** Same data as above, but this includes the comics the heroes appear in.
+- [DOT file](http://rankinfo.pkqs.net/twittercrawl.dot.gz). **Twitter mentions and retweets** of some part of the Twitter network. The file is updated from time to time.
+- [GEXF file](http://www.sociopatterns.org/datasets/primary-school-cumulative-networks/). **Contact networks** in a primary school, SocioPatterns team, 2011.
+- [GEXF file](https://github.com/mbingenheimer/ChineseBuddhism_SNA). **Historical Social Network of Chinese Buddhism 漢傳佛教歷史社會網絡** 17,000+ persons, 25,000+ connections.
+
+## Biological networks
+
+- [GEXF](http://gephi.org/datasets/diseasome.gexf.zip). **Diseasome**: A network of disorders and disease genes linked by known disorder–gene associations, indicating the common genetic origin of many diseases. Genes associated with similar disorders show both higher likelihood of physical interactions between their products and higher expression profiling similarity for their transcripts, supporting the existence of distinct disease-specific functional modules. The original dataset can be found here: The Human Disease Network, Goh K-I, Cusick ME, Valle D, Childs B, Vidal M, Barabási A-L (2007), Proc Natl Acad Sci USA 104:8685-8690
+- [GEXF](http://gephi.org/datasets/celegans.gexf.zip). **C. Elegans neural network**: A directed, weighted network representing the neural network of C. Elegans. Data compiled by D. Watts and S. Strogatz and made available on the web here. Please cite D. J. Watts and S. H. Strogatz, Nature 393, 440-442 (1998). Original experimental data taken from J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, Phil. Trans. R. Soc. London 314, 1-340 (1986).
+- [GEXF](https://gephi.org/datasets/yeast.gexf.zip). **Yeast**: Protein-Protein interaction network in yeast. Original data can be found [here](http://vlado.fmf.uni-lj.si/pub/networks/data/bio/Yeast/Yeast.htm).
+
+## Infrastructure networks
+
+- [GML](https://gephi.org/datasets/power.gml.zip). **Power grid**: An undirected, unweighted network representing the topology of the Western States Power Grid of the United States. Data compiled by D. Watts and S. Strogatz and made available on the web here. Please cite D. J. Watts and S. H. Strogatz, Nature 393, 440-442 (1998).
+- [GRAPHML](https://gephi.org/datasets/airlines.graphml.zip). **Airlines**: unknown source.
+- [NET](https://gephi.org/datasets/us-air97.net.zip). **US Air97**: North American Transportation Atlas Data (NORTAD). Original data can be found [here](http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/gphs.htm).
+
+## Other networks
+
+- [GEXF](https://gephi.org/datasets/codeminer.gexf.zip). **Java code**: Source code structure of a Java program, by S.Heymann & J.Palmier, 2008.
+- [GEXF](https://gephi.org/datasets/photoviz-dynamic.gexf.zip). **Dynamic Java code**: Dynamic source code structure of a Java program by evolution of commits on the SVN, by S.Heymann & J.Bilcke, 2008.
+- [GML](https://gephi.org/datasets/word_adjacencies.gml.zip). **Word adjacencies**: adjacency network of common adjectives and nouns in the novel David Copperfield by Charles Dickens. Please cite M. E. J. Newman, Phys. Rev. E 74, 036104 (2006).
+- [NET](https://gephi.org/datasets/wordnet3.net.zip). **Wordnet English dictionary**: unknown source.
+- [DOT](https://gephi.org/datasets/hex.dot.zip). **Abstract mesh**: 331 nodes.
+
+## Sources
+
+Some of the above datasets are from:
+- [Mark Newman](http://www-personal.umich.edu/~mejn/netdata/)
+- [Alexandre Arenas](http://deim.urv.cat/~aarenas/data/welcome.htm)
+- [Albert-László Barabási](http://www.nd.edu/~networks/resources.htm)
+- [Vladimir Batagelj and Andrej Mrvar](http://vlado.fmf.uni-lj.si/pub/networks/pajek/data/gphs.htm)
+- [Tore Opsahl](http://toreopsahl.com/datasets/)
+
+## Other network data repositories
+
+- [Duncan Watts](http://cdg.columbia.edu/cdg/datasets)
+- [Kevin Chai](http://kevinchai.net/datasets/)
+- [Indiana University](http://iv.slis.indiana.edu/db/index.html)
+- [Trust networks dataset at trustlet.org](http://www.trustlet.org/wiki/Trust_network_datasets#Released_datasets)
+- [Data sets at CFinder.org](http://cfinder.org/data)
+- [SNAP data](http://snap.stanford.edu/data)
+- [UC Irvine Network Data Repository](http://networkdata.ics.uci.edu/)
+- [The Internet Topology Zoo](http://topology-zoo.org/)
+- [Yahoo! Graph Datasets](http://webscope.sandbox.yahoo.com/catalog.php?datatype=g)

docs/02_Manuals/Developer-Handbook.md

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+---
+id: developer-handbook
+title: Developer Handbook
+---
+
+This page explains how to contribute to Gephi's development.
+
+## How to download the development version of Gephi
+
+### Prerequisites
+
+- Note: Gephi uses multi-platforms tools, so all the following steps should be the same (well, mostly) whatever the OS you are running
+- First, you will need [git](http://git-scm.com/download) to download the files.
+- You also need [Netbeans 8.0+](http://netbeans.org/)
+
+### Getting the source code
+
+- Read the full instructions: [[Checkout Code]]
+
+Now you should have a Gephi fork and a master branch.
+
+Set up your account credentials to Git:
+```sh
+git config --global user.name "Firstname Lastname"
+git config --global user.email "your_email@youremail.com"
+```
+
+### Compiling and Running Gephi
+
+Read full instructions: [[Configuring NetBeans]]
+
+## How to create and publish your own feature
+
+### Configure your forked repository
+
+- You’ve successfully forked the Gephi repository and got the code in a gephi folder by doing
+
+``git clone git@github.com:username/gephi.git``
+
+When a repo is cloned, it has a default remote called origin that points to your fork on GitHub, not the original repo it was forked from. To keep track of the original repo, you need to add another remote named upstream:
+
+```sh
+cd gephi
+git remote add upstream git://github.com/gephi/gephi.git
+git fetch upstream master
+```
+
+This keeps your fork up to date. Each time you run ``git fetch upstream master`` it downloads the latest changes from the main repository (not your fork). Note that this does NOT change any of your files. You'll need a merge to actually apply the latest changes to your fork.
+
+### Push commits
+
+When you work on the code, commit often!
+The commit process is straightforward. First add all the files you want to include in your commit:
+
+``git add .``
+
+Then commit these files
+
+``git commit -m "This is my first commit hourray"``
+
+Run git status often to see what your repository is up to.
+Your commits are local. To send them to GitHub run:
+
+``git push origin master``
+
+### Merge from the main repository
+
+When we update the main gephi repository, your fork doesn't get updated automatically. To merge the latest commits to your fork, run a merge from upstream:
+
+```sh
+git fetch upstream master
+git merge upstream/master
+```
+
+To fetch and merge in one line, simply run
+
+``git pull upstream master``
+
+When you merge, you may run into conflicts. This is normal if you worked on the same files.
+Note that ``git fetch upstream`` or ``git pull upstream`` will download the data from all branches, which you probably don't need. That's why we add 'master' to specify which branch to fetch to.
+
+### Send pull requests
+
+That's the standard and easiest way to contribute to the project. It's fully integrated into GitHub and well explained [here](http://help.github.com/send-pull-requests/).
+
+## How to contribute to the main project
+
+When you are a member of the gephi team, you have the write rights on the main repository. Instead of submitting pull requests you simply commit to the repository, including the master branch.
+Change your upstream push url to authenticated version:
+
+``git remote set-url upstream git@github.com:gephi/gephi.git``
+
+Push to the master branch. Make sure you pulled to the latest revision before (git pull upstream master).
+
+``git push upstream master``