26 September 201727 September 2017 by Mathieu Jacomy

Gephi 0.9.2 : a new CSV importer

A new version of Gephi has been released! Thanks to Eduardo’s relentless issue fixing, Gephi’s overall stability has been improved. Eduardo is the author of the Data Laboratory, and at this occasion he revamped its CSV importer for a more flexible and straightforward user experience.

The new CSV/spreadsheet importer

Did you know that Gephi can export and import just the table of nodes or the table of edges? This feature is useful in many situations, for instance to produce charts in Excel or to clean data in Open Refine. Below we will showcase the new features and more generally explain how to import a spreadsheet as a list of nodes.

To import a spreadsheet you have to reach the Data Laboratory and click on Import Spreadsheet. In the example below a network is already loaded: we will decide later whether the imported nodes will be merged into the existing ones or not.

Tuto01

Gephi is now able to recognize the type of file you upload, and the support of Excel files has been added. Choosing the right separator is crucial since improperly separated columns would compromise the data. In the example below Gephi recognized that the separator is the Comma (as in a properly formatted CSV file).

Tuto02

The encoding of the file is a common issue, notably with languages using accents and special characters. Gephi can guess the encoding and you can manually edit it if necessary. In the example below Gephi correctly guessed the UTF-8 encoding.

Tuto04

Selecting a different encoding would produce errors. Fortunately the Preview table allows you to see them and fix the encoding. In the screenshot below, see how the wrong encoding produces exotic characters in the data.

Tuto03

When you validate these settings, Gephi now opens the exact same panel as when you open a new network. I personally love this addition since it brings more consistency to the user experience. It allows Gephi to provide a number of useful informations like the number of nodes detected or the issues found during the import process.

Tuto05bis

Do not miss an important feature here: in this panel you decide either to create a new workspace with the imported data or to merge the new nodes with the old ones. This very useful feature was already present at the opening of a new network, but many users still ignore it exists. Mind to select the Append option if you intend to merge the nodes. In that case when an imported node has the same Id than an already present one, the new node data will override the old one.

Tuto06

More info

Take a look at the full list of improvements there:
https://github.com/gephi/gephi/releases/tag/v0.9.2

How do I get this release?

If you have a recent Gephi, the update will be automatically proposed to you
If you have an older version (0.8 or before) you have to download and install manually
This update can be downloaded from http://gephi.org

15 February 2016 by Mathieu Bastian

Gephi updates with 0.9.1 version

splash091 A new Gephi version has been released and can be downloaded from gephi.org. This version is an update from the 0.9.0 version released last December and mostly addresses issues discovered since.

One notable improvement is a new localization: German! Gephi is now localized in nine languages (English, French, Spanish, Japanese, Brazilian Portuguese, Russian, Chinese, Czech and German) and we hope to continue the momentum on this effort in the future.

new_german_l10n

Other notable improvements include a better support for parallel edges, appending to existing workspaces and how filters are saved in .gephi files. More than 60 bugs were fixed with a majority of them reported by the community. Thanks to all users who took the time to help! The complete list of bugfixes and improvements can be found in the changelog on GitHub.

In the next few weeks we would like to focus on documentation as there’s still many features brought in the 0.9.0 version without up-to-date documentation. This is especially important for more complex features such as dynamic graphs, which got a major upgrade.

As usual, please share your experience/feedback on our Facebook group or on Twitter.

21 December 201521 December 2015 by Mathieu Bastian

Gephi 0.9 released: Play with network data again

splash

We’re proud to announce the release of the next major version of Gephi! This 0.9.0 version has been more than three years in the making but today brings an exciting new life to this project, and the graph/network analytics community at large. You can download it here for Windows, Mac OS X and Linux.

Gephi is the leading graph visualization software – known as the “Photoshop for networks” and is open-source and free. It has been downloaded more than a million times and is used by many scholars and data scientists around the world. This new release brings new features in the area of dynamic networks (i.e. network over time) and major compatibility and performance improvements.

Since the last release in 2013, users were facing compatibility issues with Java, which have been resolved with this release. Development had slow down three years ago but had never stopped. In fact, in March 2013 the time had come to think about what Gephi 1.0 would look like and realize it needed a new core. This was by far the most complex project the team had to overcome but developers had a long-term vision and know that future developments will now rely on a robust and extensible core, with world-class performances.

The world is increasingly complex and interconnected. Gephi’s purpose is to unfold this complex relational data in a way anyone can understand them. It allows you to visualize graph data as a map and create the visualizations to support your narratives. State-of-the-art algorithms make readable layouts, highlighting communities or influential nodes. Visual tools tweak colors and shapes to reveal hidden patterns in the data, helping solving complex problems. More and more network-maps are pictured in online, offline press and other communication media. They spread from science to business, art and activism. People are increasingly exposed to them and learn how to read them. Gephi aims to accelerate this commoditization process by providing free and easy-to-use tools.

What’s new in Gephi 0.9?

The list is too long! The complete changelog for this version can be found on GitHub’s release page.

Next steps

There are a few immediate next steps coming up right after this release. Following-up on the recent plugin development announcement we’ll get in touch with plugin developers and start migrating plugins to this version. There’s more than 80 plugins to update!

Then, we’ll identify and resolve new issues that appeared with this version. A future Gephi 0.9.1 release will come next year to address those.

A Gephi Toolkit release will also be made very soon so developers can update their application built on top of Gephi’s modules. In the meantime, we’re interested in users’ feedback and want to hear from you on Twitter or Facebook. Issues can directly be reported on GitHub as well, where the developers are.

Finally, thanks to all contributors and the community for supporting this project!

2 November 2015 by Mathieu Bastian

Announcing Gephi 0.9 release date

Gephi 0.9

Gephi has an amazing community of passionate users and developers. In the past few years, they have been very dedicated creating tutorials, developing new plugins or helping out on GitHub. They also have been patiently waiting for a new Gephi release! Today we’re happy to share with you that the wait will come to an end December 20th with the release of Gephi 0.9 for Windows, MacOS X and Linux.

We’re very excited about this upcoming release and developers are hard at work to deliver its roadmap before the end of 2015. This release will resolve a serie of compatibility issues as well as improve features and performance.

Our vision for Gephi remains focused on a few fundamentals, which were already outlined in our Manifesto back in 2009. Gephi should be a software for everyone, powerful yet easy to learn. In many ways, we still have the impression that we’ve only scratched the surface and want to continue to focus on making each module of Gephi better. As part of this release, we’ve undertaken one of the most difficult project we’ve worked on and completely rewrote the core of Gephi. Although not very visible for the end-user, this brings new capabilities, better performance and a level of code quality we can be proud of. This ensure a very solid foundation for the future of this software and paves the way for a future 1.0 version.

Below is an overview of the new features and improvements the 0.9 version will bring.

Java and MacOS compatibility

This release will restore Gephi’s compatibility with the latest Java versions on all platforms. This will resolve issues our users encounter with Java 7 and 8. Compatibility issues with Mac OS will also be resolved and full support for Retina display screens added.

New redeveloped core

This release will improve performance and reliability by a large margin. The graph structure at Gephi’s core has been redeveloped from scratch and will bring multiple new features, better performance and lower memory consumption. On benchmarks, simple operations such as reading nodes or setting attributes see performance improvements ranging from 2X to 100X. This new core will make many operations in Gephi faster and push the envelope even further in large graphs exploration. Reducing memory usage has also been an area of focus and we have measured a 2X reduction compared to Gephi 0.8.2 on a medium-size graph.

New Appearance module

We’re introducing a new user module named Appearance designed to combine and replace Ranking and Partition modules. Appearance will group in one place all controls acting on the node or edge appearance. The partition capabilities will also greatly improve as part of this new module and a new palette selector is being added. In addition of the default palettes, we’re also adding a cool palette generator designed to find the optimal colors (i.e. partitions can be differentiated from each other). Moreover, it will be possible to “Auto-apply” partitions as well, which is a feature that was only available for Ranking so far.

Timestamp support

This 0.9 release adds a new way to represent networks over time: timestamps. So far, users could only represent time using intervals and that was cumbersome when the underlying network data was collected at fixed time intervals (e.g. one network per day). Starting with this release, Gephi will support both intervals and timestamps to represent evolving network topology and/or evolving attribute values.

GEXF 1.3 support

The GEXF format is also evolving to its 1.3 version. This version improves the support for graphs over time and introduces the ability to represent time using timestamps rather than intervals. In addition, it’s now possible to set a timestamp or an interval for the entire graph, allowing building collections of GEXF files where each represents a “slice”. This is a common request from the community and we hope this will greatly facilitate the exploration of longitudinal networks.

Multiple files import

With the 0.9 version users will be able to import multiple files in Gephi at the same time. Once the files have been read, two choices are offered, either to import each file into a separate workspace or merge them into the same workspace. The latter is a powerful option when used with dynamic graphs. Indeed, a collection of GEXF files representing the same network over time will be imported in Gephi in a single step.

Multi-graph support

Multi-graph example This release will bring support for multi-graphs, where multiple edges can exist between two nodes each with a different relationship. Users will be able to import, filter and run algorithms on these graphs but the support for visualizing these graphs will come in a further release.

New workspace selection UI

We’ve heard users’ feedback and the workspace selection user interface will be improved. The new interface will be a “tab-style” interface where each workspace is a tab and switching from one workspace to another only requires a single click. Tabs will be located at the top just under the perspective selection. The previous interface is located at the bottom right corner and will be entirely removed. Workspace Tabs

Gephi Toolkit release

A new release of the Gephi Toolkit, based on the 0.9 version will be made soon after December 20th.

Bug fixes

We’ve done a serious bug squash and already addressed many difficult issues, more to come until the release date.

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Follow us on Twitter or join the Facebook group to get the latest news. If you want to know more about this upcoming release, or want to help out please send us a note.

3 January 20133 February 2015 by Sébastien Heymann

0.8.2 beta released

The latest version of Gephi has been released, download it for Windows, Mac OS and Linux platforms. This release captitalizes the bugfixes and stability improvements we have done over the last few months. It also greatly improves the Mac OS X compatibility with the Gatekeeper and Retina Display support. Gephi should now starts right away when double-clicking on the App with a Gatekeeper-enabled computer. However if you have an older version of Gephi on your computer, you should uninstall it and remove the user directory, see the installation instructions.

This release is the first one based on our new Continuous Integration environment. This new system makes it easy for developers to create a new release and for beta-testers to test an early version. Users eventually get a software which has been tested much more heavily and by a larger population compared to previous releases.

Plugins need to be checked for compatibility. They will reappear on the Plugin Center in the coming days, as they are verified. Thanks for your patience.

Consult the release notes and the new Javadoc for more information.

New and Noteworthy

* Data Laboratory’s time interval merge strategy now supports custom date format
* Improved parser for dynamic types. Literal strings are now supported.
* Add Retina Display support to the Mac OS X version

Bug fixes

* Filters ‘Duplicate’ does not work (Issue 176)
* Exporting SVG File throws DomException due to invalid stroke-widths (Issue 697)
* File name entered is lost when changing folder (Issue 463)
* Datalab: can’t export all columns (Issue 628)
* NullPointerException when importing from database (Issue 691)
* Filter on column created with regex causes crash (Issue 663)
* “Long cannot be cast to a String” when either exporting a graph or saving a gephi file (Issue 679)
* Mapping of Escape Keyboard Shortcut for “Save changes before closing?” dialog box (Issue 686)
* DataLab: filling edge weight column doesn’t work when dynamic (Issue 619)
* Spreadsheet import of dynamic data: support of “infinity” (Issue 631)
* Missing license headers (Issue 664)
* Spreadsheet import and self-loops (Issue 683)
* Timelime interval set in infinite loop (Issue 712)
* OutDegreeRange broken (Issue 651)
* Shortest path on filtered graphs fails (Issue 650)
* Weighted degree computation fails (all values 0) when a filter is applied (Issue 636)
* Dot parser fixes (Issue 621)
* Filtering leads to Null Pointer exception when saving (Issue 617)
* Partition percentages incorrectly composed across filters (Issue 637)
* Start/end attributes are always imported using DATETIME format (Issue 649)
* HeatMap / Shortest Path on undirected Graph wrongly paints / calculates (Issue 630)
* Typo fix connetion to connection (Issue 642)
* Timeline sparkline bug (Issue 615)
* Fixes calculation of clustering coefficient on graph (Issue 625)
* Unix timestamp support (Issue 612)
* GML loading cannot accept scientific notation for float-type edge property (Issue 300)
* GML export does not respect specs (Issue 604)
* GEXF export outputs incorrect files (Issue 570)
* Problems with export of PNG files (Issue 601)
* Edge pencil: unable to set edge directedness (Issue 549)
* Presets of “Preview settings” are incorrectly / not saved (Issue 575)
* Option “Time intervals as dates” in Timeline (Issue 613)
* 8.1 and 8.0 both freeze at start-up when on network (Issue 592)
* Data laboratory max columns unintuitive (Issue 590)
* Modularity with Edge Weight Causes Array Out-of-Bounds (Issue 577)

Do Gephi technologies matter for your research or business? You can support us by donating to the Gephi Consortium, or becoming a member to have an impact on our roadmap.

The next version will be a new serie (0.9) and will bring a strengthen core and new features. Stay tuned for that.

Feel free to reach to us if you are willing to organize events (meetups, workshops, hackathon, etc.), we will support them.

16 October 20123 February 2015 by Sébastien Heymann

Beta Tester program starts

Hi all, today we are announcing a new program and it’s all about testing the latest versions of Gephi. Anyone can join the program and test the development version, send feedback and discuss features. We want to build a team of beta-testers who the developers can work with to detect issues before the software reaches the standard users.

So far, testing has been done by a small group of developers and users but we would like to extend it to a larger audience. There are many different versions of Windows, Mac OS X and Linux Gephi supports. Testers will help to detect compatibility issues specific on a single platform and overall participate in testing new features.

To make this effort successful, we’re making it super easy to test the latest development version without requiring to know about programming or how Gephi is built. We’re introducing a nightly build package which gets updated automatically every night with the latest version of the code. Once downloaded and installed, this version of Gephi will ask you to update itself every time a new version is available so you don’t have to download and install Gephi over and over again. If you’re already familiar with Gephi’s auto update capability, this is using the same system.

How to get started?

Join the gephi-tests@lists.gephi.org mailing list

Developers and testers will discuss on this list.

Fill this questionnaire online.

Cuple of questions on your hardware and software configurations.

Questions? Feel free to stop by on this forum thread.

29 March 201214 February 2015 by Sébastien Heymann

0.8.1 beta released

The latest version of Gephi has been released, download it for Windows, Mac OS and Linux platforms. This release delivers a complete new timeline component with many awaited features. The timeline is at the heart of our dynamic network analysis (longitudinal networks) effort at Gephi and this feature is the result of last year’s Google Summer of Code. It gives the ability to explore a network over time in a very powerful way.

timeline_sparkline
New Timeline with embedded sparkline. Example with a Twitter user network.

The timeline new features include animation (play button), custom bounds and embedded sparkline. In the previous Gephi version we added the ability to run metrics over time. For instance, one can calculate the average degree over time or simply the number of nodes (like in the example above). With the new timeline it’s possible to display a dynamic attribute directly in the component. For example if you’re looking at a Twitter network you can plot the total number of tweets as a sparkline.

This release also ships with three new languages: Czech, Chinese and Russian. Special Thanks to our awesome localization team.

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We just started the Google Summer of Code with exciting projects! We’re looking for talented students this summer (apply here). The team will also work on the next major release of Gephi (0.9). If you have ideas or suggestions, please don’t hesitate to express then on our forum or through GitHub issues. Our roadmap is open and most ideas comes from users’ experience.

Because it’s a major release, changes are not deployed through the AutoUpdate, you need to download and install the new version. Plug-ins also need to be checked for compatibility. They will reappear on the Plugin Center in the coming days, as they are verified. Thanks for your patience.

Consult the release notes and the new Javadoc for more information.

New features

New Timeline

Exciting new timeline with animation, custom bounds settings and embedded spakline. The timeline interval and bounds can now be set manually by the user. By hitting the play button the interval moves automatically. All parameters can be configured. The timeline date support has been completely rewritten, now showing dates and periods in a readable way.

Local/Global Ranking

Compare networks over time or with different filters is now easier as Ranking lets you decide whether the scale should be local or global. In local scale, sizes and colors depend on the visible sub-graph. In global scale (set by default) they depend on the whole graph, thus allowing comparisons over time.

Weighted community-detection

Louvain Modularity (Community detection) adds edge weight support and resolution setting.

New and Noteworthy

* Better Preview performance when hidden edges (good for large graphs)
* Self-loop filter. Remove self loops in the graph.

New localization (Go to Tools > Languages)

* Russian
* Chinese (China)
* Czech

Bug fixes

* Exception when deserializing a preview preset (Issue 554)
* ClassCastException when saving a gephi file after PDF export (Issue 552)
* Cannot Preserve Z-Coordinate in GEXF exporter (Issue 547)
* Gephi won’t start on Mac OS X Lion because of a missing JAWT library (Issue 542)
* Add a local/global scale button to Ranking (Issue 541)
* Spreadsheet import: edge weight not imported (Issue 540)
* NOT operator wrong with topology filters (Issue 539)
* Multiple partition filters not named: cannot tell them apart (Issue 537)
* AttributeContollerImpl should be renamed to AttributeControllerImpl (Issue 530)
* Timeline – Set Custom Bounds does not support DATETIME (Issue 529)
* Data Laboratory – Dynamic Attributes Edit function resets values (Issue 528)
* DL exporter fix (Issue 525)
* Validator of MySQL’s “host” field (Issue 521)
* Edge/Node attributes don’t support datetime format (Issue 518)
* Directed Graph cluster coefficient provides incorrect values in certain situations (Issue 517)
* NullPointer in GUI when defining range Filters (Issue 516)
* datalab: empty column fails edge csv import (Issue 515)
* updateDimensions in PreviewController does not take into account node size (Issue 514)
* Overview’s graph area does not redraw edges automatically (Issue 513)
* c+p correction: HITS hub chart was repeated twice in output. (Issue 510)
* database import from Postgres does not handle node color attribute (Issue 506)
* Incorrect Teradata JDBC url (Issue 505)
* [Datalab] Duplicated nodes on import spreadsheet (Issue 498)
* [Datalab] Failing silently to load attribute values on import spreadsheet (Issue 497)
* Attribute Columns Property editors don’t support dynamic numbers (Issue 494)
* Arrows not hidden when edges hidden on Preview (Issue 493)
* Some text appears garbled when loaded from a project file (Issue 488)
* Exception when adding a new Perspective plugin development (Issue 486)
* NullPointer Exception with Edge Labels (Issue 478)
* Filter range does not filter if min == max (Issue 477)
* Heatmap Tool Sometimes Doesn’t Work (Issue 472)
* deleting a field in data lab yields an error (Issue 468)
* Email imports can’t be cancelled (Issue 466)
* Invalid XML character error when loading a gephi file (Issue 465)
* Range Slider writes N/A if the min and max values are the same (Issue 464)
* datalab: exception on hiding a column used to sort the table (Issue 454)
* Can’t build without Netbeans installed (Issue 452)
* Auto-refresh not updated after changing the spline (Issue 448)
* AttributeRangeFilter returns main graph when nothing matches filter (Issue 435)
* Timeline need more precision when dealing with dates (Issue 202)
* Degree Filter Not Filtering as Subfilter in Tookit (Issue 69)
* UnsatisfiedLinkError on startup on Mac OS X (Issue 44)

Plugins development

Last november we migrated our source code from Launchpad to GitHub and have seen an increase of activity in plugin development. We also simplified the environment and wrote more documentation how to get started. We created a dedicated repository on GitHub and compiled a list of more than 20 different code examples on the Gephi Plugins Bootcamp.

Do Gephi technologies matter for your research or business? You can support us by donating to the Gephi Consortium, or becoming a member to have an impact on our roadmap.

Feel free to reach to us if you are willing to organize events (meetups, workshops, hackathon, etc.), we will support them.

4 October 201114 February 2015 by Sébastien Heymann

Gephi 0.8 beta released

The latest beta version of Gephi has been released, download it for Windows, Mac OS and Linux platforms. This release focus on new features for both users and developers, and the new license unlocks opportunities for business. The Ranking and Preview modules have been completely rewritten in a modular way and can be now extended with plug-ins! Preview can now be extended in many ways, for instance group shapes or edge bundling. Moreover, continuous progress have been made on the dynamic network support and we release today the last big part: statistics over time, available from the Statistics module when the network is dynamic. Thanks to users who reported bugs, it’s the only way to fix them.

The team will now start developing the 0.9 version of Gephi (please consider joining us!) and integrate the latest Google Summer of Code projects, including a new timeline. We are also willing to help as much as possible plug-ins developers to get things done and improve documentation. We want to leverage the new Preview and will help newcomers to get started.

Consult the release notes and the new Javadoc for more information.

Features highlight

	Dynamic Ranking Ranking now works with dynamic networks and it’s easy! When manipulating a dynamic network with the Timeline simply enable the ‘Auto Apply’ and the color/size is updated in real-time. To import a dynamic node size simply import a regular dynamic column in your GEXF and select it in Ranking like before.
	PNG Export A new powerful PNG export has been added to the existing PDF and SVG export. One can create high-resolution network images with all the customization available in Preview. You can even create transparent background images!
	New Preview Major effort to completely rewrite the Preview module in a modular way. One can now create plug-ins for Preview! The new Preview includes new opacity options, a text outline, radius (customize edge start/end points) and a simplified list of properties.
	Dynamic Metrics New dynamic metrics in the Statistics module: Dynamic Degree, Dynamic Node Count, Dynamic Edge Count and Dynamic Clustering Coefficient. Dynamic metrics are executed on a dynamic network and allow to analyze how network properties evolve over time.

New And Noteworthy

* Data Lab node merging
* ForceAtlas2 layout algorithm, with multi-thread option
* Node and Edge transparency in Preview
* Edge labels on curved edges in Preview
* Text outline now in Preview
* Database importer now supports time columns (start & end)
* DL Export (Thanks to Taras Klaskovsky)
* GML Export (Thanks to Taras Klaskovsky)
* NET Export (Thanks to Daniel Bernardes)
* K-core filter
* Inter and Intra partition filter
* Now supports SQLite databases
* Display the number of layout iterations in status bar when ended
* Recent Palette in Ranking
* Weighted degree now also for directed graphs

New localization (Go to Tools > Languages)

* Portuguese (Brazilian) (Thanks to Célio Faria Jr)
* Japanese (Thanks to Siro Kida and Koji Chono)

Performance

* Memory starvation manager, warns the user before running out of memory
* Less memory usage with attributes

Bug fixes

* Timeline need more precision when dealing with dates (bug 521937)
* Exception on range slider (bug 541808)
* Inconsistent label data from Overview to Preview (bug 660204)
* Statistics: sub-optimal modularity (bug 727701)
* Timeline cann’t drag if the two sliders moved to the left (bug 745476)
* Missing Polish characters when exporting to pdf (bug 746740)
* Edge selection color is not correct on OSX (bug 752300)
* Workspace name truncated, hard to read (bug 758578)
* Average degree cannot be switched to directed / undirected (bug 760454)
* Window->Favorites appears in 0.8 alpha (bug 764494)
* Disable ‘directed’ on metric settings if the graph is undirected (bug 771318)
* Timeline does not work (exception) (bug 774455)
* Layout properties can’t be saved in a language and loaded in another language (bug 783637)
* Preview: edge label not shown (bug 783868)
* Possible memory leak on Dynamic Range Filter (bug 784606)
* Edge attributes not saved in .gephi project file (bug 785268)
* Data Lab: Exception when selecting only one column for merging (bug 785269)
* Data Lab Import Spreadsheet should not ignore parallel edges (bug 785635)
* Data Laboratory: wrong edge type created (mutual instead of directed) (bug 787401)
* Data Lab: impossible to edit time intervals in a date format (bug 793163)
* Spelling of Proportionnal (bug 794358)
* Graphics errors when JOGL installed as a JRE/JDK extension (bug 799545)
* NPE if source/target is empty in GEXF import (bug 799574)
* Toolkit can’t open .gephi files (bug 802101)
* Resizing edge sizes changes edge weight values (bug 803763)
* Preview does not use node label settings from overview tab (bug 805763)
* Data Lab ‘Import Spreadsheet’ dialogue should accept other file types than .csv (bug 806798)
* Edge weights not imported from CSV matrix (bug 808078)
* Preview tab: no option to switch off node borders? (bug 808606)
* Gephi runs out of memory without warning the user (bug 811373)
* Counter-intuitive filename in Data export dialog (bug 814178)
* NullPointerException when creating newProjects too quickly (bug 817170)
* Nodes and edges Id attribute dictionary is not properly created when loading a .gephi file (bug 818181)
* Database driver doesn’t persist in Edge List Database import UI (bug 822316)
* NodeEqualNumberFilter does not work (bug 823038)
* Gephi does not build on JDK 7 (bug 823543)
* SVG node, edge export should include relevant node IDs as classes (bug 827706)
* Import Spreadsheet: need to trim column names (bug 829956)
* Layout list not sorted by name (bug 830149)
* In/Out degree metric is computed on the main graph instead of the visible graph (bug 830752)
* Layout is not giving the algorithm’s number of iterations (bug 831782)
* Banner height issues, need a fixed height (bug 834400)
* NPE when running ClusteringCoefficient on a filtered graph (bug 852799)
* Missing node properties from dot file (bug 855410)
* ‘The value column doesn’t exist’ error when opening a gephi file (bug 857595)
* Import fails for NET (Pajek) file with position/color data (bug 860825)
* GEXF export referes to v1.1 schema, should be v1.2 schema (bug 864484)

New Plug-ins documentation

Checkout the documentation for the newly created Preview module: HowTo write a Preview Renderer. Learn also how to extend the Data Laboratory features in a new tutorial.

New license

Gephi is now released in the dual license CDDL + GNU GPLv3. We abandon the GNU AGPL to offer new opportunities to reuse and integrate parts of Gephi in a full Open Source way. The dual license system means the possibility to choose to apply either the CDDL or the GNU GPLv3 when Gephi source code is integrated to a derivative work. When modified, original files of Gephi should always be published publicly so that the community benefit from the improvements. However, the CDDL license does not require to publish the whole work, so you can build commercial applications for free using Gephi source code!
The CDDL is a license created by Sun and approved by the Open Source Initiative. It is business-friendly. Read the Legal FAQs to learn more, and ask questions on the forum.

Contribute

It’s fun to contribute to an open-source project! Contribute whatever the time you can give: few minutes to report a bug, some hours to fix one or to translate the user interface or more to create a plug-in. If you’re a student and looking for cool and challenging semester projects check out the Gephi Student Program or contact us.

Do Gephi technologies matter for your research or business? You can support us by donating to the Gephi Consortium, or becoming a member to have an impact on our roadmap.

Feel free to reach to us if you are willing to organize events (meetups, workshops, hackathon, etc.), we will support them.

8 April 201125 February 2015 by Sébastien Heymann

Gephi 0.8alpha released

The latest version of Gephi has been released today, download it for Windows, Mac OS and Linux platforms. Focus has again been made on stability with more than 80 bug fixes, and performance improvements. Thanks to users who reported bugs, that always makes the difference.

The team will now focus on the Google Summer of Code. Have a look at the exciting projects developed this summer. We are also willing to help as much as possible plug-ins developers to get things done and improve documentation.

Consult the release notes and the new Javadoc for more information.

Features highlight

Localization

Localization is coming with this release, with French and Spanish! In Gephi, simply go to Tools -> Languages to switch.

You speak German, Russian or Italian? All three? Localization need your help, show up on the Forum to get started.

Email spigot

Now import emails from files or servers and look at communication networks. Spigots in Gephi are more advanced way to import networks, look for ‘Import Spigots’ in the File menu. Using wizards to configure settings, new spigots like Twitter or New York Times API are available as plug-ins.

New And Noteworthy

* GEXF 1.2 support (partial)
* Add Neighbour Filter
* Improve support of meta-edges in Statistics and Filters
* Improve usability of Filters
* Edge weight option in PageRank, which can now be used by the algorithm
* Duplicate workspaces (Edit Menu)
* Graph files now supports GZ compression
* Better Filters support in .gephi files
* VNA Import

Performance

* Label Adjust algorithm 3 times faster
* Saving/Loading projects is faster and use less memory

Bug fixes

* Windows installer should not require admin privileges (bug 663337)
* Cancelled Vector Export Disabled “File” Menu (bug 728871)
* Misformated SQL-Server JDBC url (bug 745414)
* Partition Filter Loses Categories As Subfilter (bug 726107)
* Workspace name does not increment (bug 711185)
* Ranking Color can’t be changed on OSX (bug 737727)
* Filter panel not cleared after query removed (bug 737992)
* Ego Filter “with self” option doesn’t work with depth > 1 (bug 671007)
* Maximum Degree Range Doesn’t Update on Subfilter (bug 725688)
* Cannot save and reload dynamic network as project (bug 709270)
* GDF exports attributes when option is disabled (bug 735927)
* Rename “Edit” menu to “Workspaces”? (bug 735475)
* Data laboratory context menu takes too much time to appear when a lot of nodes are selected (bug 735721)
* export svg/pdf with no edges causes NPE (bug 693789)
* Can’t import the same file twice in Welcome window (bug 598157)
* Graph Window in Overview Tab Fails to Load (bug 659773)
* Timeline appears first wrong when timeformat=”date” (bug 709234)
* Filter query not saved when Filter button is active (bug 671004)
* GEXF option doesn’t work(bug 709235)
* Ego Network Filter Searches for Substring, Does Not Match Value (bug 726114)
* Label text settings not saved in .project (bug 660205)
* saved preset for layouts creates several instances (bug 612848)
* Partition colors in Filters are different from those in Partition (bug 616037)
* import of pajek net has floating pt problem (bug 619893)
* NullPointerException on saving project (bug 622154)
* Name of currently opened file not updated after a “save as” (bug 629374)
* Labels are not hidden on Preview (bug 654006)
* Chaining Dynamic Filter (bug 654018)
* NullPointerException on importing CSV data in Data Laboratory (bug 654030)
* Statistics report not refreshed after a new execution (bug 654036)
* Maximum lock count exceeded error when running Label Adjust (bug 655544)
* GEXF export: missing attvalues element (bug 655975)
* Can’t use ranking label transformers with toolkit (bug 656172)
* GEXF export: attribute definitions exported even if Attributes option is unchecked (bug 656276)
* Preview throws an Exception with negative edges (bug 656955)
* Closeness centrality chart empty with normalized values (bug 658361)
* Statistics fail to work on a hierarchy level different from the leaves (bug 658394)
* Exported Data Table doesn’t use sorted columns (bug 658816)
* Importing a TIME_INTERVAL column in Data Laboratory CSV import doesn’t enable dynamic features (bug 659017)
* Error when using filter export features and filtering off (bug 659229)
* Exception when using flatten filter (bug 659270)
* GDF export generates invalid files (bug 660200)
* Wrong color type exported in GraphML (bug 660356)
* GEXF exporter doesn’t export the label if they are the same as the id (bug 660382)
* Tool Selection tooltip under the graph window (bug 660459)
* Column settings in Data Lab are not saved in .project (bug 660469)
* Data Lab filter not executed when changing the column (bug 660471)
* Data Lab: column used by node filter is automatically reset (bug 660517)
* Personalized color of a specific partition is rolled back (bug 660529)
* DOT importer ignores edge weight and .gv file extension (bug 661257)
* Exceptions when importing mixed graph (bug 662488)
* Error on selecting nodes from filter if graph window not shwn at startup (bug 663561)
* Blank preview screen (bug 664300)
* Edge text not visible on preview with other attributes (bug 664444)
* Data does not appear on nodes table (bug 667440)
* saving a project uses too much memory for large graphs (bug 672071)
* Data Lab: search/replace only on a given column (bug 676087)
* Workspace number incremented by opening a new project (bug 681038)
* Filter “out degree range” does not work (bug 681184)
* NullPointerException on exporting dynamic GEXF file with Toolkit (bug 686432)
* Wrong relative betweenness (bug 687267)
* graphml generated syntax is incorrect (bug 688678)
* Import Report freezes when the number of issues or logs is too high (bug 688865)
* Filters fail to work on a hierarchy level different from the leaves (bug 691278)
* Wrong edge count in Context Panel with hierarchies (bug 692225)
* RepaintCell exception on Mac OS X (bug 692379)
* Exceptions when group/ungroup from Partition after delete (bug 692382)
* GML importer don’t process ‘weight’ column as weight (bug 703877)
* Degree doesn’t take edge weight into account (bug 703933)
* Edge attribute values not imported from graphml file (bug 707390)
* PageRank not for weighted networks (bug 715621)
* Data Lab: boolean column edition facility (bug 717869)
* Exception on Delete Column if sorted by this column (bug 719987)
* Data Lab: edge rows not displayed when the hierarchy level /= 0 in Overview (bug 720033)
* Java Null Pointer when using Merge Columns (bug 722287)
* Open Recent files doesn’t work with project files (bug 734105)
* Timeline disappears after saving project.gephi file (bug 695558)
* Exception on Visualization Settings if opened before Overview (bug 734117)
* Database import is not cancelable (bug 734126)
* ‘A task is still executing’ error after cancelling a custom importer, not LongTask (bug 734132)
* Edge weight slider not refreshed between workspaces (bug 731599)
* Exception on New workspace after deleting last workspace (bug 735273)
* Colors not imported in Pajek Net format (bug 530028)

To 0.8 beta and beyond

Following the Gephi Manifesto, we continue our way to the release 1.0 with goals sets in the Roadmap. You can speed up our progresses in many ways whatever the time you can give: few minutes to report a bug, some hours to fix one or to translate the user interface, some weeks to create a plug-in…you will be always greatly welcomed!

Do Gephi technologies matter for your research or business? You can support us by donating to the Gephi Consortium, or becoming a member to have an impact on our roadmap.

Proud to be part of the Gephi Community? On our fresh new store you can buy mugs, T-shirts and more to show it!

Go to the Gephi store

The stores sells in Europe (EUR). To get a tee-shirt in the US, check our official Gephi tee-shirt.

1 October 201025 February 2015 by Sébastien Heymann

Gephi 0.7beta released

Major milestone for Gephi today. The 0.7 beta version is ready for download for Windows, Mac OS and Linux platforms. It brings many awaited features and more than 80 bug fixes!. Stability and productivity improvements are the main objectives of this release. A complete support for longitudinal network is part of this release, it is now more easy and flexible to import and explore dynamic networks. Consult this new tutorial to see how input longitudinal networks in Gephi. We support three different methods, to cover all use cases.

Because it’s a major release, changes are not deployed through the AutoUpdate, you need to download and install the new version if you had the alpha. Plug-ins also need to be checked for compatibility. They will reappear on the Plugin Center in the coming days, as they are verified.

Consult the release notes and the new Javadoc for more informations.

An announcement for modules developed this summer by the Google Summer of Code students, in particular Neo4j and Social Network import. They may be fully integrated in Gephi for its 0.8 version, in the meantime they will be released as plug-ins through our Plugin Center. Stay tuned, it will be fast.

A new version of the Gephi Toolkit will be released in a few days, based on the beta codebase.

Features highlight

New Data Laboratory

The Data Laboratory receives tons of new features, developed this summer by Eduardo Ramos. It now proposes to manipulate and edit data in a broader and more productive way. A detailed list of features is available on the Introducing Data Laboratory post. The laboratory is also now auto-refreshing when filters are manipulated. Another essential point is that the laboratory is easily extensible with plug-ins.

Longitudinal networks

They are now fully supported in Gephi. Explore how the network topology change over time by using the Timeline component, which now appears automatically. The major improvement is the dynamic attributes support. The edge weight or any attribute value can evolve over time as well, and the visualization shows the value in the right range. Enable the timeline with a single button. See tutorial.

	Edit Simple edit by selecting one or several nodes or edges in the Data Laboratory. Keep Control key on the table to select several rows and change values of several elements in one action. Edit also manually visualization variables like color, size or position. The Edit window is available by right-clicking on rows. Many other features are now available through the context menu, and more can be added with plug-ins.
	Search/Replace General Data Laboratory actions like Add node/edge, Search/Replace or Import CSV. The Search/Replace feature shows an advanced UI to search and replace values in the table cells. It can do a normal search or a regular expression based search, among other useful options. It is implemented in a separate controller that is part of the Data Laboratory API.
	Columns merge Manipulate columns and do basic calculations. On numerical columns one can get sum, average, median, … from several other columns. New columns can be created from a regular expression based on a existing column. Among other merge strategies, a Time Interval column can be get from a simple numerical column. Get a longitudinal network from a simple ‘year’ column in your data.
	Label visibility Decide whether a label should be visible or not from the filter result. Nodes and edges not in the filtered graph will have their labels hidden. Can be reset by the ‘Reset Visible’ action (left of graph window).
	Copy and Move to a workspace New option when right-clicking on the graph. You can copy or move the selection to a new or existing workspace.
	Import ‘Missing Nodes’ option New option in the import panel to import nodes which were not properly defined in the file. Use this option to create nodes only from their reference in edges.
	Import Time Frame Their are different way to import longitudinal network in Gephi. One of them is to import multiple ‘static’ files, where each is a particular snaphsot in time (one file per day or per month). There is a new option for that in the import report. See this tutorial section to use it.
	Time Frame settings Decides whether the time format is a date or a real number. The processor will look for existing elements in the workspace and append the time frame to nodes and edges. The network becomes longitudinal, each node, edge and attribute is defined with time intervals.
	Preview Presets The Preview settings has now default presets: Default Curved, Highlight Mutual Edges, Small Labels and more.
	Rescale weight in Preview New option in preview to have edge weight look the same as Overview. Meta-edges have also now a separate scale slider in Visualization settings. This scale value is used in Preview to respect dimensions.
	Original color option When edges color are imported from a file or set by Partition, they have a custom color. This color mode can now be rendered by Preview by setting ‘Original’ in the color dialog.
	Localization Localization is now possible in Gephi, French and Spanish versions will be available soon. Please consider helping us, show up on the Translations forum section.

New And Noteworthy

* NOT Operator (Filters)
* MASK Operator (Filters) – keep edges according to source/target/both/any – can easily obtain neighbors of a set of nodes
* Display edge weight as labels on visualization
* New StAX GEXF importer and exporter, with hierarchy and dynamic support
* New List/Arrays attribute types. Can only be imported from GEXF for now.
* Flatten Filter – Flatten a hierarchical graph to the visible view, transform meta-edges into normal edges
* New Giant Component Filter
* Set size for the ‘Reset Size’ action, by right-clicking on the reset size button
* Get degree column from Undirected graphs
* Statistics reports now saved in Gephi projects
* When parallel edges are found during import, it now increases the weight of the edge by default
* Option in Ego Filter to include the parent node or not
* Meta-edges have now a separate scale slider in Visualization settings, change how thick they are compared to normal edges
* Ranking and Partition list of attributes are now sorted
* Ranking now updates itself with filtered graphs. Clicking on Apply will refresh bounds and the transformation (color, size)
* It’s now possible to drag a filter sub query to become a main query
* With dynamic attributes, Ranking, Partition, Visualization and Filters will use the current Timeline range to find values
* Edge weight can be dynamic, type DYNAMIC_FLOAT. Force Atlas layout will use the current Timeline range
* Filters are refreshed when the graph is modified, the current filter is reexecuted

Bug fixes

* Nodes not unselected after turning off Selection on Filter Panel bug 649920
* PDF Export only with default font bug 651273
* Ego Filter doesn’t include the node itself bug 649908
* Exception on opening project file bug 648617
* Partition filter automatically filters null value bug 648600
* Edges weight not merged with parallel edges bug 648600
* Negative edges not rendered in Preview bug 628223
* Edge weight scale is different between Graph and Preview bug 569329
* Edges native color are not displayed in Preview bug 586237
* Text not displayed in Preview bug 627567
* Errors at PDF export when labels have font size zero bug 626865
* Filtering not refreshed when sub-queries set or removed bug 594511
* Wrong stroke weight when SVG imported in Illustrator bug 626378
* Generating a graph on a previously loaded undirected graph bug 624671
* Wrong folder selected in the Export Panel when changing file type bug 620337
* Node Degree not in Label Text settings bug 598170
* Ranking and Partition parameters list not ordered bug 594520
* Read positions from dot files bug 594793
* Wrong node size when Ranking has same min and max size bug 631689
* SVG files not listed in Export dialog bug 626394
* Export to pdf background is always white bug 583386
* Selected filter query not properly refreshed in UI bug 626483
* Wrong node positions when setting X or Y to zero bug 615844
* z-coordinate not exported in GraphML bug 614606
* Partitions don’t refresh when opening project not from Overview bug 612902
* duplicate label in filter window bug 604003
* Visualization size limitation bug 602470
* Can’t close project when generating a graph bug 631341
* csv file export problem bug 598767
* Can’t import the same file twice in Welcome window bug 598157
* “CommandLineParsing null” message when error on opening file from command line or desktop bug 594630
* Default selection of Nodes in Data Laboratory necessary bug 594515
* Preview ratio not available at first time bug 594176
* Impossible to cancel the Average Path Length Statistic calculation bug 590226
* Auto-scale flips the graph bug 577843
* “Node must be in the graph” error when importing a hierarchical graph with height greater than 1 bug 577180
* FileNotFoundException during saving of PDF file bug 572876
* dynamic graph unrecognized if everlasting nodes bug 555637
* Edit window not hidden on tabs bug 552494
* ‘Format’ not recognized on DL import bug 619069
* Visualization selection color inversion between ‘out’ and ‘both’ color bug 618726
* Workspace Selection failed to refresh after closing workspace bug 616814
* NullPointerException when selecting “–Choose a Layout” in the Layout ComboBox bug 606964
* In/Out degree metric doesn’t work with undirected graphs bug 606305
* Right click on workspace after deleting a node throws “node can’t be null” bug 605947
* Import transform to Undirected don’t merge weight bug 603478
* Can’t display edge weight as text bug 603134
* Can’t select Postgresql driver in database import settings bug 595223
* Error when opening Plugin Center bug 616829
* Node invisible (too small) when created with the node pencil bug 574807
* Ranking not refreshed when graph filtered bug 632459
* Ranking parameters re-initialized at each new ranking bug 594231
* Can’t drag a filter sub-query to become a root query bug 626495
* NullPointerException when switching between workspaces while a layout is running bug 597458
* NullPointerException when executing the “Eigenvector Centrality” Statistic bug 589731
* Memory Leak in Graph Distance bug 587450
* ForceAtlas and Fruchterman Reingold not layouting with meta-edges bug 584286
* Cannot save / saves as when opening a Gephi by doubleclick a graph in Windows bug 583397
* GraphML importer doesn’t import node labels data bug 581629
* Exception on clicking on ‘Hierarchy’ while running multilevel layout bug 631663
* Opening Archived ZIP files is broken bug 578876
* Partition Settings in Filter not saved on switching workspaces bug 616052
* Filtered graph not exported with “Select” pressed bug 573685
* Partition “All Blacks” feature randomizes colors bug 601066
* ‘start’ and ‘end’ attributes are missing when exporting dynamic GEXF bug 521848
* EdgeList Database Configuration is not saved bug 571263
* Slowness on picking a partition entry bug 519549
* Unable to cancel a project opening bug 616415
* Progress is not shown when opening/saving project bug 594644
* Incorrect mutual edge weight on Preview bug 610469
* Memory Leak in GEXF/GraphML Parser bug 596872
* Node Size Mode and Filter Paramaters don’t save in project bug 596430
* Errors with Yifan Hu MultiLevel Layout on a filtered graph bug 594643
* Preview is not displaying meta-edges bug 584289
* Meta-edges are not displayed bug 584283
* gtk+ slider problem bug 529913
* NullPointerException on importing dynamic graph bug 581872
* NullPointerException when filtering undirected graphs bug 571153
* Filtering with convex hulls displayed bug 541819
* Wrong edge removed from Edge Weight filter bug 603469