0.9.3 Release Candidate #2440

mbastian · 2022-03-16T11:41:18Z

mbastian
Mar 16, 2022
Maintainer

We're close from releasing the 0.9.3 version of Gephi. You can see the list of changes below. Before making the release final, we want to identify any new issues, bugs or regressions that might have been introduced. We therefore ask users already familiar with Gephi to give it a try.

How to try it out?

Use the following links depending on your platform:

gephi-0.9.3-SNAPSHOT-windows.exe (Windows)

gephi-0.9.3-SNAPSHOT-macos.dmg (Mac OS X)

gephi-0.9.3-SNAPSHOT-linux.tar.gz (Linux)

Note that plugins aren't supported in pre-releases. They will be supported as usual in the final release.

Changelog

New features

Added Statistical Inference community detection algorithm, a more advanced alternative to Modularity #2431
Windows and Linux versions now also embed JRE so that it isn't needed anymore to install Java separately #2336
FlatLaf look and feel is now used by default on all platforms #2415
Appearance attributes like colors used in partition are now saved in the project #1861
Last Export settings are now saved as Preferences so they persist between session #1790

Bugfixes

Improve UI to better suit HighDPI displays #2332
Graph Toolbar items overlap on smaller screen sizes #765
Some layouts act on settled nodes #2385
Ignoring GraphML desc standard tags #2030
java.util.MissingResourceException gephi version 0.9.2 #2063
NullpointerException on filtering datalab columns that have empty attribute values #2015
Leaving "Create missing nodes" unchecked does not have the desired effect #1878
'Interval' not copied to new workspace #1988
CSV Edges file not importing because Gephi does not detect Source and Target columns #2178
ArrayIndexOutOfBoundsException on when deleting nodes #1623
No mode indicator in Appearance panel in Gephic Mac 0.9.2 #2098
Neighbors Network filter freezes with max depth #2099
Unable to import a large file #1841
Update crash reporter and make it GDPR compliant #2340
ClassCastException: org.gephi.graph.api.types.TimestampSet cannot be cast to org.gephi.graph.api.types.TimeMap #2297
Support INF, -INF in GEXF for double-type ±∞ values #2158
Node betweenness is negative for big graphs when normalized #2139
generatePalette is wrong #2112
Loading gexf file with 0-weighted edges crashes import #1945
Crash when exporting VNA graph file #1909
Import CSV error edges #1848
Import of graphml still confuses d3 and label fields #1840
Add support of Byte Order Mark to CSV parser #1815
CSV files are no longer imported correctly when double quotes inside strings are delimited with backslashes #1812
NullPointerException on EdgeTypeFilter #1811
GephiFormatException can cause ArrayIndexOutOfBoundsException: 0 #1810
Exception with no-merge strategy in some cases. Incompatible edge should not be created #1802
NullPointerException: The fileObject parameter cannot be null #1789
GephiFormatException: Gephi failed saving the project. #1788
Edge labels not retained on graphml export #1516
Unhide toggle global/local ranking button #2146
Unwanted and inconsistent behavior for "node size" #2224
Infinite repulsion in ForceAtlas with negative weights #1714
Citation for PageRank algorithm #1944
Dynamic attributes for dynamic network not properly merged with multiple files #1885
Add 'postProcess()' method to Preview's Renderer SPI #1490
Changes in labels not rendered in preview mode #1877
Sum edges merge strategy gives surprising results #2038
Use timezone in GEXF import, export and Create time interval in Data Laboratory #1864
Overview viewport too small #1518
Wrong edge coloring of selected nodes for directed graphs #2259
Modularity index groups are allways 0-index based. #1977

How to give feedback?

Either on this discussion or by creating a new issue.

This discussion was created from the release 0.9.3.

rzo1 · 2022-03-16T13:31:38Z

rzo1
Mar 16, 2022

Tested with the bundled JRE (11) on Ubuntu 20.04 LTS. Loading a > 120k N (500k E) graph worked just fine. Played around with some mini graphs and couldn't find any big issues.

Any chance to support Java 17 without warnings / errors?

März 16, 2022 2:27:41 PM org.netbeans.ProxyURLStreamHandlerFactory register
SCHWERWIEGEND: No way to find original stream handler for jar protocol
java.lang.reflect.InaccessibleObjectException: Unable to make field transient java.net.URLStreamHandler java.net.URL.handler accessible: module java.base does not "opens java.net" to unnamed module @53c4a559
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
	at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
	at org.netbeans.ProxyURLStreamHandlerFactory.register(ProxyURLStreamHandlerFactory.java:59)
	at org.netbeans.JarClassLoader.<clinit>(JarClassLoader.java:117)
	at org.netbeans.MainImpl.execute(MainImpl.java:153)
	at org.netbeans.MainImpl.main(MainImpl.java:60)
	at org.netbeans.Main.main(Main.java:58)

WARNING: A terminally deprecated method in java.lang.System has been called
WARNING: System::setSecurityManager has been called by org.netbeans.TopSecurityManager (file:/home/zowallar/Downloads/gephi-0.9.3-20220315.194445-318-linux/gephi-0.9.3-SNAPSHOT/platform/lib/boot.jar)
WARNING: Please consider reporting this to the maintainers of org.netbeans.TopSecurityManager
WARNING: System::setSecurityManager will be removed in a future release

2 replies

mbastian Mar 16, 2022
Maintainer Author

Nice to hear! Thanks for the report. We indeed have a couple of Warnings that we need to take care but some are from Netbeans Plartform and I would need to check whether they are working on it. No immediate action though, we will ship with those warnings.

During development, I noticed a couple of issues with Java 17 so we preferred to stick to 11 for now. We shall revisit that again for next release 0.9.4 and see if Java 17 can be used as default.

rzo1 Mar 16, 2022

Fine. I am very happy that there will be a new release! Thanks for your (and all of the other contributors) efforts and time .

wetneb · 2022-03-16T16:23:05Z

wetneb
Mar 16, 2022
Collaborator

Any reason why you are incrementing the patch release number and not the minor / major ones? Looking at the list of changes, there are some important new features / improvements, so from my end I would expect 0.10.0 more than 0.9.3 (but maybe that's too late now that this RC is out).

2 replies

mbastian Mar 16, 2022
Maintainer Author

Yes you're right. We are following our legacy at this point. I think once we have a 1.0 we can follow the more standard versioning. It might be too confusing to switch now as we've always marked major released as increment in the "minor": 0.8, 0.9 etc.

mbastian Mar 28, 2022
Maintainer Author

For the record, the discussion should continue here: #2444

NuLL3rr0r · 2022-03-17T11:36:47Z

NuLL3rr0r
Mar 17, 2022

Thank you very much for this release! I've been waiting for this release for years.

0 replies

jacomyma · 2022-03-19T09:47:15Z

jacomyma
Mar 19, 2022
Maintainer

I found an issue with CSV import. With the same file, it works well in 0.9.2:

but the file is not parsed correctly in 0.9.3:

It does not generate an error, but the CSV is not interpreted as it should.

2 replies

mbastian Mar 19, 2022
Maintainer Author

Thanks @jacomyma, please share the CSV with me here or over Slack and I'll look into it!

jacomyma Mar 21, 2022
Maintainer

So for the record:

The CSV has an issue (last column missing a header)
CSV files without this error are parsed correctly
Although the 0.9.3 behavior is different from 0.9.2, it does not mean that it is not desirable. Indeed, having a malformed CSV trigger an error at parsing is nothing wrong by itself.

So in short, arguably, there is nothing to see here.

Haaroon · 2022-03-28T14:52:21Z

Haaroon
Mar 28, 2022

A release after 5 years?? Very surprising, very refreshing!

1 reply

acralkmim Mar 29, 2022

How to use the streaming twitter pra other importer API v2.

ngmaclaren · 2022-03-29T21:25:30Z

ngmaclaren
Mar 29, 2022

Testing on Manjaro 21.2.5. My normal tasks seem quicker with this version and everything works as expected. Outstanding!

3 replies

ngmaclaren Mar 29, 2022

I have some warnings as well in case they're informative. These are startup warnings from running zsh ./gephi from inside [SNAPSHOT]/bin/:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.netbeans.ProxyURLStreamHandlerFactory (file:/home/neil/gephi-0.9.3-20220327.193704-345-linux/gephi-0.9.3-SNAPSHOT/platform/lib/boot.jar) to field java.net.URL.handler
WARNING: Please consider reporting this to the maintainers of org.netbeans.ProxyURLStreamHandlerFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

paulgirard Mar 30, 2022

I've got the same warnings but it works perfectly for the little test made on ubuntu 20.04 lunix mint flavor.
Congrats !
Next week I am participating a workshop where I might ind Mac Os and Windows users. I might ask them to test this release.

mbastian Mar 30, 2022
Maintainer Author

Thank you. These warnings cause no harm, feel free to ignore them. We need to look deeper into it but not super high priority.

sarepal · 2022-04-01T14:33:01Z

sarepal
Apr 1, 2022

Tested the pre-release with a small network and found that a bug I was experiencing in 0.9.2 (erroneous edge in the graph layout) has been resolved. Eager for the full release as I need GeoLayout for this work. When might the full release come out?

1 reply

mbastian Apr 1, 2022
Maintainer Author

Cool! If all goes well, early next week. Plugins shortly after that.

acralkmim · 2022-04-02T12:42:02Z

acralkmim
Apr 2, 2022

How to streaming twitter API 2 whith the New version?

1 reply

mbastian Apr 5, 2022
Maintainer Author

Hi @acralkmim, I'll let @totetmatt address questions related to the Twitter plug-in

guillaumebuffet · 2022-04-11T11:57:55Z

guillaumebuffet
Apr 11, 2022

Hi there. A can't wait... but have to as, once Gephi 0.9.3 installed, it's impossible to access existing files / import files from my computer (Mac OS 12.2.1).
Seems that Gephi hasn't he permission to access my files. Works perfectly with previous version.

Uninstalled and re-installed. Still the same.

I've tried with 0.9.2. When I re-install, I've a permission windows to access my files. Not with 0.9.3.

An idea ?

Thanks for your help.

Guillaume

3 replies

eduramiba Apr 11, 2022
Maintainer

@guillaumebuffet See #2467

guillaumebuffet Apr 11, 2022

Thanks !

guillaumebuffet Apr 11, 2022

Sauvé ! Fantastic ! Much - much - faster than the previous version.
Guillaume

Splines · 2022-06-15T21:52:45Z

Splines
Jun 15, 2022

Thank you so much for this update and all your efforts you put into this amazing program, the new look & feel is great and I also appreciate that Java comes bundled now.

0 replies

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0.9.3 Release Candidate #2440

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Select a reply

0.9.3 Release Candidate #2440

mbastian Mar 16, 2022 Maintainer

How to try it out?

Changelog

New features

Bugfixes

How to give feedback?

Replies: 10 comments · 15 replies

mbastian Mar 16, 2022 Maintainer Author

wetneb Mar 16, 2022 Collaborator

mbastian Mar 16, 2022 Maintainer Author

mbastian Mar 28, 2022 Maintainer Author

jacomyma Mar 19, 2022 Maintainer

mbastian Mar 19, 2022 Maintainer Author

jacomyma Mar 21, 2022 Maintainer

mbastian Mar 30, 2022 Maintainer Author

mbastian Apr 1, 2022 Maintainer Author

mbastian Apr 5, 2022 Maintainer Author

eduramiba Apr 11, 2022 Maintainer

mbastian
Mar 16, 2022
Maintainer

Replies: 10 comments 15 replies

mbastian Mar 16, 2022
Maintainer Author

wetneb
Mar 16, 2022
Collaborator

mbastian Mar 16, 2022
Maintainer Author

mbastian Mar 28, 2022
Maintainer Author

jacomyma
Mar 19, 2022
Maintainer

mbastian Mar 19, 2022
Maintainer Author

jacomyma Mar 21, 2022
Maintainer

mbastian Mar 30, 2022
Maintainer Author

mbastian Apr 1, 2022
Maintainer Author

mbastian Apr 5, 2022
Maintainer Author

eduramiba Apr 11, 2022
Maintainer