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Releases: gephi/gephi

Gephi 0.9.7

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Follow-up release from 0.9.3, 0.9.4, 0.9.5 and 0.9.6 with bugfixes.

Bugfixes

  • Adding a new node causes Exception - column store #2557
  • org.gephi.preview.spi.PreviewMouseListener receives wrong coordinates. #2561
  • NPE on PreviewUIControllerImpl due to PreviewSettingsTopComponent deserialization issues #2562
  • Newly added columns do not automatically appear in the Appearance Partition menu #2568
  • Partition filter panel doesn't properly display list types #2569
  • Recent Files doesn't not update with the latest saved file #2570
  • VNA file import fails with empty string values "" #2574
  • DisplayVersion not populated when installing on Windows #2575

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Gephi 0.9.6

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Follow-up release from 0.9.3, 0.9.4 and 0.9.5 with bugfixes.

Bugfixes

  • MacOS: Gatekeeper prevents versions 0.9.4 and 0.9.5 to open without malware warning #2532
  • NPE on Preview after workspace deleted #2550
  • RuntimeException: This observer has already been destroyed #2548
  • NPE when creating a new workspace after all workspaces have been deleted #2547
  • NPE when Partition filter is subfilter #2534
  • CDATA not recognised in GraphML parser #2533
  • Filter Parameter column changes are reloading saved file #2519
  • NullPointerException on StatisticalInferenceClustering #2504
  • copy to new workspace produce a "The configurations don't match" error #2020
  • Location of GEXF 1.3 schema #2019
  • Import csv dialog ignore "Graph Type" setting #1924
  • GraphML parser flags "graph" level attributes as an error. #1497

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Gephi 0.9.5

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Follow-up release from 0.9.3 and 0.9.4 with bugfixes.

Bugfixes

  • Deleting nodes results in program freezing and not responding #2485
  • Unable to set range for the Partition Count filter on Component ID #2493
  • NullPointerException in Preview StringBuilder #2495
  • ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 11 #2498
  • NullPointerException in ImporterSpreadsheetCSV.autoDetectFieldDelimiter #2499
  • ReportPanel: ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0 #2500
  • IllegalArgumentException: The object class does not match with the column type (java.lang.Integer) #2509
  • Display exception thrown in import in a report #2516

Miscellaneous

  • Windows installation in non-administrative mode #2507
  • Add Romanian as supported localization 🇷🇴 #2494

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Gephi 0.9.4

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Follow-up release from 0.9.3 with bugfixes.

Bugfixes

  • No file listed in the Open... dialog box, Mac OS Big Sur #2467
  • NullPointerException from TimelineControllerImpl.setInterval #2471
  • NullPointerException in ImportContainerImpl.isEdgeDirected #2472
  • NullPointerException in IndexImpl.values #2473
  • Appearance IllegalArgumentException: The view doesn't exist #2487
  • Visualization IllegalArgumentException: The view doesn't exist #2488
  • IllegalArgumentException: The column does not belong to the right column store #2489
  • Combining gexf files hangs in 093 #2476

Miscellaneous

  • Icon for MacOS Big Sur/Monterey #2480

Gephi 0.9.3

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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
  • Workspace tabs panel is missing when opening project file #1827
  • Regression setting node color by partition #1838
  • Not all selected nodes/edges are moved/copied to new workspace #2088

API Changes

  • Graph API
    • Add getEdges(int type) to Graph to allow retrieval of only edges of a specific type.
    • Add getEdgeTypeLabels(boolean) to GraphModel.
    • Add min/max to TimeSet and Element.getTimeBounds().
    • Add Column.exists() as new utility.
    • Add GraphLock to the API in Graph to expose locking states.
    • Make Table a Collection of Column.
    • Add new method Column.isDynamicAttribute().
    • Add toSet() in addition of toCollection() to element iterables.
    • Add new Table.countColumns(Origin) method.
    • Add getElementIndex() methods to GraphModel when providing a Table.
    • Add isNodeTable() and isEdgeTable() methods to Table.
  • Appearance API (under development)
    • Partition and Ranking now always receive the Graph as parameter for all methods that do need access to the underlying index to facilitate local scale support.
    • Add getColumn() to Ranking so it aligns with Partition.
    • Add getNormalizedValue() to Ranking to more easily retrieve the normalised value.
    • Partition now has a static DEFAULT_COLOR when the color is not found for a given value.
    • Removed Partition.setColors() as it was prone to confusion.
    • Add transformAll(Iterable<? extends Element>) to Function.
    • Split isLocalScale() into isRankingLocalScale() and isPartitionLocalScale() in AppearanceModel.
    • Make Function getters in AppearanceModel independent from Graph as this should be handled automatically based on the local/global state.
  • Preview API
    • A postProcess() method has been added to the Renderer SPI to allow customization once all items have been rendered.

Gephi 0.9.2

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New features highlight

  • New CSV/Spreadsheet importer migrated to Import API. More user friendly, autodetects imported columns types and data format. Integrated with the rest of file importer formats through import report. Now supports importing excel files.

Other new or improved features

  • Add support for MS SQL Server (#1648)
  • Add option for minimum edge width in preview mode (#1568)
  • Add support for edge kind in spreadsheet import/export (#1248)
  • Suggestions: improvements to spreadsheet import (#532)
  • Feature request: remember last save location (dir) (#1726)
  • Add column id tooltip to data laboratory column headers (#1711)

Bugfixes

  • Impossible to rename an Operator filter (#329)
  • BOM missing in exported GEXF and .Gephi (#474)
  • nodes position to NaN on applied layout (#603)
  • Spreadsheet import should be available in File > Open (#611)
  • Modularity Calculation Throws Exception On Empty Graph (#713)
  • svg class ids are invalid (#770)
  • Clearly present the range bound numbers as editable on Filter UI (#838)
  • Scaling factors for expension/contraction (#860)
  • Direct import of Excel adjacency matrix format data (#1143)
  • Gephi XML parser fails when encountering U+0001 (#1164)
  • Conditions should not unconditionally evaluate to "TRUE" or to "FALSE" (#1232)
  • Add support for edge kind in spreadsheet import/export (#1248)
  • multiple edges won't be merged (#1251)
  • Migrate spreadsheet importer to Import API (#1282)
  • Feature/db ignore unknown columns refactoring (#1284)
  • HITS centrality (#1290)
  • No Suitable driver found for jdbc:mysql:// (#1317)
  • Importing Adjacency Matrices (#1372)
  • Gephi 0.9 bug saving projects that are in Geo Layout? (#1373)
  • Exception on ranking with column with null values (#1387)
  • Stuck on DOT import (#1391)
  • Cannot rank according to attribute data (#1392)
  • Added per-node opacity property (#1407)
  • import spreadsheet (csv) The id class does not match with the expected type (#1418)
  • Getting null pointer error when trying to calculate modularity (#1419)
  • Error saving any dynamic network in gexf format (#1426)
  • filters and new workspace bugged (#1428)
  • csv data missing some information (#1431)
  • Duplicate statement in DirectoryChooserUI.java (#1434)
  • Duplicate statement in ExporterDL.java (#1435)
  • Java error message when running Geo Layout (#1441)
  • node size changed during gexf import (#1445)
  • Streaming Graphs Do Not Appear in Overview (#1447)
  • Suddenly not importing all of my edges (#1454)
  • Incorrect average degree for directed graphs (#1455)
  • Filter settings incorrect and causing crashes after reloading a .gephi file (#1458)
  • Node size options not available if node colour set to partition mode (#1459)
  • Spaces in header columns of edge CSV file fails to load (#1461)
  • No Suitable Driver Found for jdbc:postgresql (#1466)
  • Impossible to color arcs with a color gradient with 0.9.1 (#1469)
  • Self-loops not removed after filter>self-loop>export to new workspace (#1471)
  • Improve range slider user experience for manually setting values (#1476)
  • Import wizard 0.9.1 now showing any options. (#1477)
  • Node size by attribute issue (#1484)
  • Fix - add try/finally logic to wrap graph reentrant locks for layouts (#1487)
  • csv import error: found rows with empty source or target columns (#1489)
  • Some label characters fade away when zooming out! (#1494)
  • Fill column with value doesn't affect visualization immediately (#1499)
  • "Partition count" filter does not work (#1501)
  • Setting Labels using GraphML (#1502)
  • Get collection of selected nodes (#1506)
  • Undirected Average Path Length Not available (#1507)
  • added getSelectedNodes in SelectionManager (#1508)
  • Filter is changed after saving file and opening again (#1511)
  • Components don't show up as variable in partition filter (#1512)
  • NullPointerException on Modularity Statistics with gexf with kind / parallel nodes. (#1526)
  • Adapt crash reporter to send data to a new service (#1530)
  • ArrayIndexOutOfBoundsException in AutoLayout.InterpolateDynamicProperty (#1532)
  • Add Edge dialog only remembers source index (#1536)
  • Wrong quantity of connected component (#1545)
  • Export from Data Laboratory overwrites existing file without warning (#1550)
  • Implement VizualizationController.selectNodes/selectEdges (#1562)
  • NPE with trying to filter by partition with a null value (#1563)
  • Partition filter doesn't work with edges (#1564)
  • GePhi freezes after successfully importing dynamic gexf file (#1566)
  • Import of GraphML: Specific attribute IDs are dismissed (#1575)
  • GraphML export: Gephi doesn't generate the id attribute on edges (#1585)
  • Proposed fix for issue #1585 (#1586)
  • GML import: '.0' always added to numeric ids (#1588)
  • inconsistency in calculating degree and weighted degree (#1593)
  • Columns aren't properly sorted in appearance (#1604)
  • NullPointerException when no attribute is selected in Ranking or Partition (#1605)
  • How to make RankingLabelSizeTransformer work? (#1606)
  • Dynamic node attribute (from csv file) causes unexpected exception (#1607)
  • Ranking min/max for uncommon types - UnsupportedOperationException: 'commlist' is not a sortable column (int[]). (#1612)
  • Exporting data tables with the automatically added [Nodes] and [Edges] tags does not work (#1613)
  • Self loop edges display (#1619)
  • Fixed typo in german translation of statistics plugin (#1632)
  • gephi 0.9.1 freezes for dynamical graphs (#1633)
  • Ranking operation not working (node color and size) (#1636)
  • taken screenshot will be overwritten (#1640)
  • Presets not working (#1643)
  • Node size by attribute not listing property (#1650)
  • Add dynamic edge attribute (weight),using csv file (#1653)
  • GraphML Importer Attribute Loading Problem (#1656)
  • Export data table with large numbers in metrics rows (#1658)
  • DNA - import .CSV (from DNA software) in GEPHI (#1661)
  • Merge CSV and Spreadsheet import (#1662)
  • StackOverflowError while using GraphStream (#1668)
  • icon pencil for "creating node" and "creating edge" should not be the same? (#1672)
  • count the average path length of directed graph (#1683)
  • v0.9.1 unable to read v0.9 gephi file (#1691)
  • Add support for excel (xls and xlsx) import (#1699)
  • Make sure all layouts + timeline work fine with dynamic weights (#1709)
  • Incorrect graph import from GraphML file (#1719)
  • Node colors fade to white regardless of background color choice (#1728)
  • Setting graph space size/borders (#1729)
  • Very Lost Newbie: Even Dynamic Graph Example (through Gephi) Doesn't Work with Timeline? (#1730)
  • ImporterDOT supports # comments (#1739)
  • Import of GEXF format rearranges order of node attributes (#1742)
  • NullPointerException on DL Ucinet Exporter when exporting as List mode (#1746)
  • Windows installer should use 64 bit exe when available (#1748)
  • Settings get stored in a specific language (#1749)
  • Cytoscape to Gephi (#1753)
  • Add full screen mode to view menu (#1762)
  • MacOS build cleanup (#1766)
  • Appearance: add partition label color transformer (#1768)
  • Fix timeline graphics (#1771)
  • Gephi freezes with specific network (#1774)

API Changes

  • A new optional FileAware interface in FileImporter in ImporterAPI. This allows file importers to receive the file to import in a setFile method instead of the setReader method being called. If your FileImporter implements this interface, setFile will be called, and setReader will not be called.

Gephi 0.9.1

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New features highlight

  • New German localization

Other new or improved features

  • Implement new mutual edge filter (#1312)
  • Re-add import wizard support (#1322)
  • Merge dynamic attributes and timeset when merging parallel edges (#1345)
  • Hide Edit Window description area (#1354)
  • Add label properties in Edit (#1355)

Bugfixes

  • Filter Saved queries not saved in project files (#123)
  • Filter not applied when opening Gephi file (#734)
  • SVG, PDF export generate 'null pointer' exception (#1239)
  • App Hangs - OS X El Capitan (#1241)
  • Attributes not appearing in Size setting (#1242)
  • Edge weights are not read (#1243)
  • Data laboratory shows double precision error decimals for columns with type Float/Double (#1245)
  • CSV import only show one node (#1247)
  • Improvements in spreadsheet import and fix default weight when not indicated (#1249)
  • Multiple edges won't be merged (#1251)
  • Workspace persistence XML duplicate markup in .gephi (#1262)
  • Partitions filters not available at start (#1263)
  • Gexf liststring attribute type not working (#1266)
  • Screenshot in overview: Dialog shows "Saved in {0}" (#1271)
  • NullPointerException on SQLite import (#1272)
  • GEXF export doesn't properly export list types (#1279)
  • Array attributes aren't properly printed in Overview and Preview (#1280)
  • Data laboratory - NullPointerException when switching workspaces (#1281)
  • Data laboratory - Convert column to dynamic does not accept timestamps, only dates (#1283)
  • Edge weights not available as a label choice (#1287)
  • Silent fail on merge columns > create time interval (#1288)
  • Red Roses palette generator freezes Gephi (#1296)
  • Modularity class percentages multiplied by an additional factor of 100 (#1297)
  • Inter and Intra edges filter raises null pointer exception (java.lang.NullPointerException)(#1298)
  • Rotation layouts both counter clockwise (#1304)
  • Select on Overview not working 0.9 (#1306)
  • Cannot delete a column (#1310)
  • PNG export looses alpha value (#1314)
  • "Set Label color to be of same color of the Object" in Overview does not work (#1315)
  • Exception on opening project with multiple workspaces (#1318)
  • Attributes not appearing in Appearance dropdown list (#1319)
  • Gephi 0.9 doesn't display node attributes from a .gephi file saved by Gephi 0.8.2b (#1320)
  • StringIndexOutOfBoundsException after Import Spreadsheet (#1321)
  • Appearance Window hangs after setting size (#1324)
  • Equal filter does not work with array columns (#1331)
  • Use Interval time representation by default on new workspaces (#1332)
  • "Convert column to dynamic" does not obey chosen time representation (#1334)
  • Time interval graphics don't work correctly often (#1335)
  • Error when parsing spells in gexf files (#1337)
  • Exception when editing array types (#1338)
  • Closeness in GraphDistance incorrect (#1341)
  • Current time format is not respected when representing TimestampSet in data laboratory (#1343)
  • NPE when opening dynamic graph from Data Laboratory on Mac OS X (#1344)
  • Exception when appending parallel edges (#1347)
  • Appending edges with auto-created nodes resets existing node's label (#1348)
  • Merge multiple workspaces doesn't work with timestamp representation (#1349)
  • Edge colour - overview - always remain grey, no node colour, no change of colour (#1353)
  • Edit window doesn't respect current time format (#1358)
  • Exception when right click on double array in Data Laboratory (#1359)
  • Table alternative rows sometimes have the wrong highlight color (unreadable) (#1360)
  • Selecting nodes with object coloring mode doesn't highlight neighbours (#1361)
  • Edge label position should be in the middle of the edge when undirected (#1362)
  • Edge labels don't respect the "Hide non-selected" option (#1363)
  • Label color and size modes are not localized (#1364)
  • IllegalArgumentException when importing sliced gexf with attvalues (#1366)
  • Dynamic metrics don't work with interval time representation (#1367)
  • VNA file error in Gephi 0.9.0 (#1369)
  • Workspace panel sometimes doesn't select the proper tab when adding workspaces (#1378)

API Changes

  • A new setColors method has been added to Partition in AppearanceAPI.
  • The SpigotImporter and SpigotImporterBuilder interfaces in ImportAPI have been renamed to WizardImporter and WizardImporterBuilder. Methods have been accordingly renamed in ImportController as well.
  • The FilterBuilder.getFilter() and CategoryBuilder.getBuilders() methods in FiltersAPI now take a Workspace as a parameter.

Gephi 0.9.0

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New features highlight

  • Compatibility with Java 7 and 8 on all platforms
  • Performance and memory-usage improvements thanks to a redesigned core
  • New Appearance module that merges the Ranking and Partition modules
  • New palette chooser and generator for partitions. The generator algorithm is designed to find the most suitable color palette
  • Multi-graph support, it's now possible to import multiple edges with different relationship types between nodes
  • Dynamic graphs can now be represented by a collection of timestamps, in addition of intervals
  • Multiple graphs can be imported at the same time, typically a collection of graphs at different timestamps

Other new or improved features

  • Auto-apply on dynamic partition (#606)
  • Workspace selection as tabs (#1105)
  • Add Applications shortcut in DMG file (#1117)
  • Implement directional zoom (#1126)
  • Add progress when taking screenshots (#1133)
  • Add support for color names and hex/oct codes in importers (#1146)
  • Add edge color parsing in GML importer (#1147)
  • Add multiple files import support (#1150)
  • GEXF 1.3 support for import/export (#1152)
  • Add Import Spreadsheet option to File menu (#1155)
  • Update ForceAtlas2 adaptive speed to better formula (#1158)
  • Add Noverlap layout (#1161)
  • Add OpenOrd layout (#1162)
  • Add clear UI hook for mouse selection configuration panel (#1165)
  • Bundle JRE in Mac OS App (#1170)
  • Print application log to output window (#1171)
  • Add copy to clipboard context menu on Import's report panel (#1182)
  • Add new edge filter based on edge type (#1189)
  • Add filter that keeps only nodes that have self-loop (#1203)
  • Add import support for TGF graph format (#1240)

Removed features

  • Remove hierarchical graphs support
  • Remove support for 3D graph navigation
  • Remove proprietary DB drivers (SQLServer, Teradata)
  • Remove pie charts in context and partition modules
  • Removed HITS statistics
  • Removed Clustering module

Project file compatibility

The .gephi files created with Gephi 0.9.0 won't work on earlier versions as the format code has been redesigned. However, files from 0.8.2 and anterior can be opened by Gephi 0.9.0. Therefore, we advise not to overwrite your project files if you still plan to use earlier versions of Gephi.

Bugfixes

  • graphml edgedefault not handled to spec (#147)
  • Misleading average edge weights in dynamic networks (#156)
  • Color the edge with the opposite node color when selected in Overview (#292)
  • ImportController.getFileImporter() should match importer name and extension (#319)
  • DOT parser is broken (#320)
  • Control Command on Mac (#327)
  • Can't import two files on the same time (#338)
  • Excessive Redrawing of windows Mac OS X (#401)
  • Database edge list UI not remembering settings, and a validation error (#451)
  • Partition colors generated at each workspace switch (#453)
  • Colors in partition filter inconsistent with real partition colors Filters (#455)
  • Freeze color mappings across graphs (#461)
  • Partition not applicable after filtering (#471)
  • Change filter button aspect to "Stop" when filtering is active Filters (#476)
  • No way to reset workspace layout (#480)
  • Picking a second partition colour does not bring up the colour picker, but changes the colour (#533)
  • Edge filter reduces displayed thickness of UNfiltered edges (#538)
  • Preview outputs margin automatic fitting (#572)
  • Node label outlines offset in Preview (#654)
  • Appending to exiting graph resets layout (#657)
  • Export filter as a true/false column does nothing (#680)
  • Reset size option/dialog should default to the current default node size (10.0?) and not 1.0 (#699)
  • Catch blank nodes during CSV import (#723)
  • NumberFormatException when loading dot file containing "[H,S,V]" colors (#739)
  • Gephi isn't compatible with Java 7 and 8 on all platforms (Windows, Mac OS X, Linux) (#748)
  • No way to filter out nodes that do not have a particular value? (#750)
  • WTF: Gephi deletes my GML file (#757)
  • Make partition colors persistent with the attribute column (#760)
  • Incorrect average degree on directed graphs (#767)
  • Add edge issue: node id not displayed in the GUI Data Laboratory (#782)
  • UNION filter does not work (#809)
  • Gephi hangs when applying degree filter (#813)
  • Networkx gexf parser conflict with gephi (#818)
  • Error and file deletion when importing non-gzipped .gexf files (#835)
  • Error while exporting a graph as a GML file (#905)
  • GDF import defaults to "directed" edge type, should be "undirected" (#906)
  • Center on graph is not working on flat graph (#916)
  • Cannot open graph files in /tmp (#918)
  • Gephi generates invalid GML files (#919)
  • File can't have repeated column names (#921)
  • Gephi should be DPI-aware or offer a DPI setting (#961)
  • Duplicate dynamic attribute value in GEFX causes Gephi to fail silently (#964)
  • gephi shouldn't delete files when it can't open them (#1041)
  • fail to parse valid DOT file if no node attribute present (#1053)
  • Edge colors are unnecessarily dark (#1060)
  • GraphML Importer doesn't recognize node attributes (#1084)
  • Add icon to rename workspace action (#1104)
  • Upgrade DBDrivers JDBC dependencies versions (#1115)
  • Error when saving a project file if the file has been deleted (#1119)
  • Gephi.app won't start from case-sensitive filesystem (#1144)
  • ImportGML forces all columns to be string even though Double is parsed (#1151)
  • Window title is truncated in some cases (#1156)
  • Memory leak when closing projects (#1157)
  • Control zoom so it can't move further than viewfield (#1159)
  • Rectangle selection with ctrl key doesn't work on OS X (#1166)
  • Filter duplicate doesn't properly clone properties (#1190)
  • Support quoted attributes in DOT import (#1195)
  • Color undirected edge with mixture of adjacent node colors in Overview (#1211)
  • Preview display with retina display support (#1222)
  • Make data laboratory refresh when the graph is filtered (#1238)

API Changes

  • The functionalities of DynamicAPI have either been replaced by native GraphAPI support or added to the TimelineAPI, effectively removing DynamicAPI from the codebase. The TimeFormat can be set via setTimeFormat() on GraphModel. Estimators are now configurable per column and can directly be set from the Column. Obtaining the minimum time bounds can now be obtained from the TimeIndex directly from GraphModel.
  • The createQuery() method in FilterController now takes a FilterBuilder instead of a Filter. It allows to track down builders down to the query level.
  • The ImportAPI now supports importing multiple graphs at the time and supports graph slices through an additional parameter on ContainerLoader. The setTimestamp() and setInterval() allows to define a point or period of existence for the entire graph. The ImportController also allow multiple containers to be processed through a new process() method. In parallel, ImporterUI now takes multiple importers and so does the Processor interface that now takes multiple containers.
  • The NodeFilter and EdgeFilter interfaces now inherit from a new ElementFilter so it's easier to create filters that work at the element level.
  • The filter() method in Operator now takes an array of Subgraph instead of Graph. This gives access to operations such as union or not.
  • Remove ClusteringAPI from codebase. It needs a complete rewrite.
  • Add ability to configure timezone with setTimeZone() on ContainerLoader in ImportAPI.
  • Remove standalone ContainerFactory class in ImportAPI and replace it with Container.Factory. Also add the ability to configure the TimeRepresentation in ContainerLoader. Finally, add color parsing utility in ImportUtils. It can be used to parse color names or codes.
  • The AttributeModel parameter in the execute() method of Statistics interface in StatisticsAPI has been removed as all features are now in GraphModel.
  • The ChangeListener in WorkspaceInformation has been replaced with a PropertyChangeListener.
  • Both RankingAPI and PartitionAPI have been replaced by a new AppearanceAPI, which supports both concepts. The SPI allows to create Transformer services, which can support either ranking or partition transformations. Ranking and Partition instances are defined in the API and gives access to underlying data. The core concept in appearance are functions, which wrap the transformation entirely and can be accessed in AppearanceModel.
  • The Processing dependency in PreviewAPI has been removed and replaced by regular Java2D. Therefore, the ProcessingTarget is now the G2DTarget. Also add a resize() method to facilitate integration.
  • Addition of a EdgeWeightMergeStrategy enum to control the way parallel edge weights are merged in ImportAPI.
  • Add ability to create WorkspacePersistenceProvider with a new SPI interface: WorkspaceBytesPersistenceProvider. The XML-based interface has being renamed into WorkspaceXMLPersistenceProvider.
  • Importers can now use the setValueString() method on ElementDraft. This will automatically parse the value based on the declared type reducing parsing code on the importer side. If the type is already in the right type, use the setValue() instead.
  • Refactoring of the import API. Introduction of a ColumnDraft interface which represents a to-be-created column and the method to manipulate them in ContainerLoader. The NodeDraft and EdgeDraft classes now inherits from a new ElementDraft, centralizing a lot of the code. The EdgeDraftGetter and NodeDraftGetter have been removed and their methods moved directly to the node/edge draft. New elements are now created using the ElementDraft.Factory, which can be obtained with the factory() method on ContainerLoader. Previously the ContainerUnloader returned an AttributeModel. This has been replaced with iterables over column drafts. The EdgeDefault enum becomes EdgeDiretionDefault and represents a graph-level configuration. The EdgeDefault is now edge-level configuration and can be set by setEdgeDirection() on EdgeDraft. Finally, convenient setColor() methods have been added to ElementDraft.
  • Complete rewrite of the GraphAPI and add GraphStore as dependency. The new API is entirely defined in the GraphStore project and Gephi makes it available through the GraphAPI. The AttributesAPI functionalities have been consolidated into the new graph API and therefore has been removed. There is too many API changes to be listed all but notable ones are the following.
    • All attribute features (e.g. add column) are now directly accessible from the GraphModel, and there's no more AttributeModel.
    • The AttributeColumn is renamed into Column, the AttributeTable is renamed into Table, AttributeOrigin is renamed into Origin and the AttributeType has been replaced by the direct usage of Class objects. Moreover, the AttributeUtils is now entirely static (i.e. no more needed to obtain an instance) and has multiple important additions such as full parse support.
    • The support for hierarchical graphs has been removed, but multi-graph support added. Each edge now can have a relationship type, and is zero by default. These types can be associated with an arbitrary label object, which can be configured in GraphModel.addEdgeType().
    • All node/edge data are now directly accessible from the interface. For instance, attribute values can be retrieved with the getAttribute() methods. All properties such as color or position are also accessible directly on the Node/Edge interfaces.
    • Dynamic graphs can now be represented with timestamps as well. Intervals are still supported but the API user must configure the preferred representation through the Configuration (must be done at initialization). The way elements' existence overtime has been greatly simplified with the addition of timestamp/interval management methods on Element, which both Node and Edge extends. See for instance addTimestamp(), addInterval(), getTimestamps() or getIntervals(). Similarly, each attribute getter or setter in Element is available with timestamps and intervals parameters so attribute values over time can be configured. Behind the scenes, the dynamic types used are defined in org.gephi.graph.api.types.
    • There's a new Subgraph interface that extends Graph and is available from GraphModel.getGraph(GraphView). This subgraph interface has additional features such as union() or intersection().
    • The graph listening system with GraphListener has been entirely replaced with a pull-based system of observers. The system no longer sends events at each update but listeners can create observers, which periodically check if something has changed. There's multiple types of observers: GraphObserver for topology changes, TableObserver for new/removed columns and ColumnObserver for attribute value changes. These observers can obtain diff objects such as GraphDiff or TableDiff to exactly obtain what has changed.

Gephi 0.8.2

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How to fix connection issues when downloading updates and plugins

After installing Gephi 0.8.2, open it and go to Tools - Plugins - Configuration. Then change the source URLs to:

New features

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

Bugfixes

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

API Changes

  • Add support for mouse listeners in Preview plugins. Create a PreviewMouseListener and implement MouseResponsiveRenderer interface in the renderers that use the listener.

Gephi 0.8.1

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New features

  • New Timeline with animation, custom bounds settings, date ticks and embedded sparkline.
  • Ranking now supports local and global scale.
  • Modularity (Community detection) adds edge weight support and resolution setting.
  • Self-loop filter

New localization

  • Russian
  • Chinese (China)
  • Czech

Performance

  • Better Preview performance when edges hidden

Bugfixes

  • Exception when deserializing a preview preset (issue 554)
  • ClassCastException when saving a gephi file after PDF export (bug 553)
  • Dynamics: DateTime values are converted to numbers when workspace is duplicated. (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)

API Changes

  • Add a needsItemBuilder method to Renderer in Preview API. This helps to avoid building unnecessary items while refreshing preview.
  • Preview API changes: Added a getDisplayName to Renderer and support for extending default preview renderers. Added a renderer manager to preview controlled with new methods in PreviewModel and PreviewController.
  • Add a local scale flag in Ranking API. The value can be set from theRankingController.
  • Add RangeFilter interface in Filters API to help create range filters. The filter system now automatically manages the range values and bounds. The Range object now also supports exclusive intervals.
  • Add a new AttributableFilter filter type. This is useful for filters manipulating Attributable objects regardless whether they belong to a node or edge. Also note new useful abstract plugin implementations have been added to the FiltersPlugin module. Use AbstractFilter for any filter and AbstractAttributeFilter for filters based on attributes. Filter builders are also provided.
  • Update to Netbeans Platform 7.1 and it's new perspective system. The PerspectiveMember SPI has to go away and will break compatibility. Top components now directly declare the perspective they belong to in the @TopComponent.Registration annotation, for instance roles = {"overview"} for the Overview perspective.
  • Add a REPLACE_COLUMN event type in AttributeEvent.
  • New Timeline API exposed as a stable API. Th API controls the Timeline UI component and the animation framework.
  • Add a new TIME_FORMAT event in DynamicModelEvent. The event is triggered when the time format is initialized.
  • Add a getGraphTable() in the AttributeModel. The GraphView elements can also have attributes using the same system as nodes and egdes. The data can be accessed through the Graph.getAttributes() method.