Minimum spanning tree plugin by carlschroedl · Pull Request #138 · gephi/gephi-plugins

carlschroedl · 2016-12-18T01:55:34Z

Hello Gephi team! Thanks for the excellent instructions on how to contribute plugins in version 0.9. This pull request upgrades my 0.8-compatible plugin (formerly called SpanningTree) to be compatible with 0.9. Please let me know what you think!

…n-plugin:migrate`

builds successfully.

…n org.gephi:gephi-maven-plugin:validate`

https://github.com/gephi/gephi-toolkit-demos/blob/master/src/main/java/org/gephi/toolkit/demos/ImportExport.java

anything other than null.

attempting to load test graphs to verify.

…g with multiple graph loading.

equality documentation.

line.

aren't part of a minimum spanning tree.

already uses integers. Might change both test data and implementation back to boolean in the future.

'com.carlschroedl.gephi.plugin.minimumspanningtree'

user-facing text.

carlschroedl · 2016-12-18T02:00:33Z

It looks like the only conflict is in the enumeration of plugins in the pom:

    <!-- List of modules -->
    <modules>
        <!-- Add here the paths of all modules (e.g. <module>modules/MyModule</module>) -->
<<<<<<< HEAD
        <module>modules/MinimumSpanningTree</module>
=======
        <module>modules/GeoLayout</module>
        <module>modules/LinkfluencePlugin</module>
        <module>modules/KBraceFilter</module>
        <module>modules/Multimode-Networks</module>
        <module>modules/JsonExporter</module>
        <module>modules/SigmaExporter</module>
        <module>modules/NodeColorManager</module>
        <module>modules/GraphvizLayout</module>
        <module>modules/GraphStreaming</module>
        <module>modules/DesktopStreaming</module>
        <module>modules/StreamingAPI</module>
        <module>modules/StreamingImpl</module>
        <module>modules/JettyWrapper</module>
        <module>modules/StreamingServer</module>
        <module>modules/CircularLayout</module>
        <module>modules/SemanticWebImport</module>
        <module>modules/loxawebsiteexport</module>
        <module>modules/Export-To-Earth</module>
        <module>modules/MapOfCountries</module>
        <module>modules/ScriptingPlugin</module>
        <module>modules/TwitterStreamingImporter</module>
        <module>modules/IsometricLayout</module>
        <module>modules/NetworkSplitter3D</module>
        <module>modules/ExcelCsvImporter</module>
        <module>modules/OracleDriver</module>
        <module>modules/EventGraphLayout</module>
        <module>modules/Lineage</module>
        <module>modules/MdsLayout</module>
        <module>modules/filterfromfile</module>
        <module>modules/GiveColorToNodes</module>
        <module>modules/GiveColorToEdges</module>
        <module>modules/GravityPlugin</module>
        <module>modules/MdsMetric</module>
        <module>modules/VectorCalculator</module>
        <module>modules/PrestigePlugin</module>
>>>>>>> fb3eb2af7db865b64ad3fc02cc0405e708fdd2c6
    </modules>

Is it better for me to resolve this, or for you?

carlschroedl · 2016-12-18T02:08:39Z

...ree/src/main/java/com/carlschroedl/gephi/plugin/minimumspanningtree/GraphTopologyEquals.java

+ * number of edges and nodes.
+ * All other node and edge attributes are ignored in this comparison.
+  */
+public class GraphTopologyEquals {


I created this because I wanted my plugin's tests to assert that the result of running the algorithm was the same as a manually-verified graph loaded from file. Since I'm new to Gephi, I'm wondering if this is necessary. Are there any alternatives built in to Gephi for determining if graphs have equal topologies?

I don't think there are builtin methods for this, but this is a small class. Great that you have tests!

Ok. Cool. Thanks for confirming that I'm not duplicating existing Gephi functionality.

carlschroedl · 2016-12-18T02:25:10Z

modules/MinimumSpanningTree/cover.sh

@@ -0,0 +1,12 @@
+#!/bin/bash


This script is a workaround so that I can view code coverage in NetBeans while developing this plugin. I'm not sure it needs to be included. What do you think?

This file is not necessary but I can omit it in the merge, no problem.

Ok. That works. If it's easier for you, I have no problems with (A): git rm-ing the file on my end, or, if you prefer, I can (B): altogether eliminate the file from the history of this branch and force push to update the pull request. Of course, I don't want to rewrite history if you or another Gephi team member have already pulled this branch down somewhere and started tinkering with it :) Please let me know if I should do either (A) or (B) otherwise I will assume you will exclude it from the merge.

carlschroedl · 2016-12-18T02:26:07Z

modules/MinimumSpanningTree/pom.xml

+
+    <groupId>com.carlschroedl.gephi</groupId>
+    <artifactId>spanning-tree-plugin</artifactId>
+    <version>1.0.0</version>


Is it ok that this is a release version instead of a SNAPSHOT?

No problem, your plugin can declare any version number you want. Just future updates will need to increase it.

Sounds good!

carlschroedl · 2016-12-18T02:31:04Z

modules/MinimumSpanningTree/pom.xml

+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>cobertura-maven-plugin</artifactId>
+                <version>2.6</version>


Unfortunately, when triggering code coverage collection in the NetBeans UI, it disgregards the version of the coverage plugin that is specified in the pom. Instead, NetBeans uses the most recent stable release of the plugin. In this case, there are integration problems between NetBeans 8.2 and the most recent stable release of the cobertura-maven-plugin (2.7). By running the cover.sh script I included above, a user can at least view their code lines painted in red, yellow, or green depending on test coverage. While you can't trigger the collection of code coverage data via the NetBeans UI, you can still view the results in NetBeans.

carlschroedl · 2016-12-18T02:36:23Z

...gTree/src/main/java/com/carlschroedl/gephi/plugin/minimumspanningtree/KruskalsAlgorithm.java

+                + "<br/> The minimum spanning tree can be visualized by creating a Filter on the Attribute \"" + ST_COL_NAME + "\" with value = \"1\"";
+    }
+
+    // <editor-fold defaultstate="collapsed" desc="Inner Helper Classes">


When I was a student I made the unfortunate decision to write many of the following classes as inner classes. I hope to convert these into standalone public classes in a subsequent refactor (carlschroedl#4).

carlschroedl · 2016-12-18T02:40:20Z

...ngTree/src/test/java/com/carlschroedl/gephi/plugin/minimumspanningtree/GraphModelLoader.java

+     * workspace or project after loading.
+     * @param file The file containing a graph
+     * @return the GraphModel
+     */


I wrote this method so that I could concisely and reliably load graphs from file into memory for comparison during my plugin's tests. Is there functionality built-in Gephi to accomplish something like this?

eduramiba · 2016-12-18T14:31:00Z

Thanks for the pull request! I will review it as soon as possible.
Don't worry about that conflict, it always needs to be resolved manually.

carlschroedl · 2016-12-19T01:45:21Z

Thanks for volunteering to resolve the conflict!

carlschroedl · 2016-12-19T02:59:09Z

Apologies, this pull request includes several test resources that are not used. The only ones used are:

wiki_kruskal_example_initial.graphml
wiki_kruskal_example_mst.graphml

The following are not used:

wiki_kruskal_example.gephi
wiki_kruskal_example_initial.csv
wiki_kruskal_example_initial.gdf
wiki_kruskal_example_initial.gexf
wiki_kruskal_example_initial.svg
wiki_kruskal_example_mst.csv
wiki_kruskal_example_mst.gdf
wiki_kruskal_example_mst.gml
wiki_kruskal_example_mst.svg
wiki_kruskal_example_with_mst.gephi

I believe it is prudent to delete the unused test resources. Just like I mentioned above, I can do that by either (A): simply git rm-ing the file on my end, or, if you prefer, I can (B): altogether eliminate the file from the history of this branch and force push to update the pull request. Which do you prefer?

carlschroedl · 2016-12-19T03:05:02Z

I should mention that I've rewritten history many times in the past with native git as well as with BFG Repo-Cleaner, so there's no need to worry about me accidentally destroying the good parts of the history while eliminating the bad parts. In other words, don't be afraid that I will screw up option (B) and delete the plugin :)

eduramiba · 2016-12-19T10:19:34Z

Hi,
I don't mind if you rewrite history, I have not cloned it yet.

Actually, remove unnecessary files if you can please. If the files are just small examples or similar we can merge them.

By the way, it's possible to include demo screenshots for your plugin that will appear in the new plugins site. Just drop them in src/img folder like https://github.com/gephi/gephi-plugins/tree/geolayout-plugin/modules/GeoLayout/src/img

carlschroedl · 2016-12-20T00:03:22Z

Thanks! I will rewrite history to remove the unnecessary files. I didn't know about the src/img feature. I will add a couple images.

carlschroedl · 2016-12-23T18:34:41Z

The earliest I can resume work on this pull request is January 5th.

carlschroedl · 2017-01-18T03:46:09Z

Closing this in case there are stale refs. Have opened #140 for the cleaned history.

Typos on #136 & #138 & #146

carlschroedl added 30 commits October 31, 2016 17:47

Checkpoint: Immediately after migrating via `mvn org.gephi:gephi-mave…

387fa5e

…n-plugin:migrate`

First pass at fixing 0.8 to 0.9 API differences. The SpanningTree module

bb16b82

builds successfully.

Correcting Plugin metdata. Now passes gephi plugin validation via `mv…

e8ba8a9

…n org.gephi:gephi-maven-plugin:validate`

Adding jUnit, test skeleton

e6f49d0

Moving example data to paths paralleling package structure

77627a3

Broken checkpoint -- starting to import data based off example from

d6e657a

https://github.com/gephi/gephi-toolkit-demos/blob/master/src/main/java/org/gephi/toolkit/demos/ImportExport.java

Broken checkpoint. Can't get ImportController#importFile() to return

ef6237b

anything other than null.

Merge branch 'master' into spanning-tree-integration-test

fc76ce9

Dependency additions to enable importing graphs from file

2eff609

Broken checkpoint: building graph edge&node equality checker and

67d06d9

attempting to load test graphs to verify.

Could not open *.gephi files. Switching to Graph ML. Now experimentin…

10c84df

…g with multiple graph loading.

Successfully loaded two graphs simultaneously

86a73b2

Formatting, removing unused imports.

b322cfb

Moved graph equality comparison to another class.

f58094e

Refactored loading functionality into a separate file. Improved graph

e4b8ceb

equality documentation.

Discovered and fixed bug via new tests.

e28b4dc

Cleanup and small test addition.

61137ba

Adding ability to report test coverage. Increasing test coverage to new

46a4dcc

line.

Complete line coverage achieved for GraphTopologyEquals.

643871b

Successfully implemented a post-alorithm filter to exclude edges that

783b599

aren't part of a minimum spanning tree.

Reducing specificity

0cd76b8

Refactoring MST edge filtering into its own method.

d04f2f4

Removed unused imports

ee0b151

Switching back to integer spanning tree attribute because the test data

64c34c4

already uses integers. Might change both test data and implementation back to boolean in the future.

Re-branding as "Minimum Spanning Tree Plugin" at the maven level.

39e828f

Rebranding to 'MinimumSpanningTree' at the file system level

6bce82a

Updating rebranded module path in the parent pom

6c4f4d1

Rebranding java packages to

93a9a2d

'com.carlschroedl.gephi.plugin.minimumspanningtree'

Updating public packages with rebranding.

679e7bf

Rebranding as MinimumSpanningTree at the class name levl. Also rebranded

da42c77

user-facing text.

fixing typo in user-facing text

bd39daa

carlschroedl commented Dec 18, 2016

View reviewed changes

Documenting and generalizing utility script

d6ac100

carlschroedl commented Dec 18, 2016

View reviewed changes

carlschroedl force-pushed the minimum-spanning-tree-plugin branch from 073b440 to d6ac100 Compare January 18, 2017 03:11

carlschroedl closed this Jan 18, 2017

carlschroedl mentioned this pull request Jan 18, 2017

Minimum spanning tree plugin (cleaned history) #140

Merged

kant added a commit to kant/gephi-plugins that referenced this pull request Oct 28, 2018

Typos on gephi#136 & gephi#138 & gephi#146

6c5cffb

eduramiba added a commit that referenced this pull request Oct 28, 2018

Merge pull request #198 from kant/patch-1

e5a5631

Typos on #136 & #138 & #146

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