Merge branch 'master' into saturation0123

# Conflicts:
#	dna/src/main/java/export/Exporter.java

.github/workflows/DNA build.yml

@@ -1,6 +1,6 @@
 name: build
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   Bibliography:
@@ -33,7 +33,7 @@ jobs:
       run: pandoc --version
 
     - name: Setup Gradle
-      uses: gradle/gradle-build-action@v2
+      uses: gradle/gradle-build-action@v2.4.2
 
     - name: Execute Gradle build for bibliography
       run: ./gradlew :bibliography:build
@@ -56,7 +56,7 @@ jobs:
         cache: gradle
 
     - name: Setup Gradle
-      uses: gradle/gradle-build-action@v2
+      uses: gradle/gradle-build-action@v2.4.2
 
     - name: Execute Gradle build for DNA
       run: ./gradlew :dna:build
@@ -81,11 +81,16 @@ jobs:
         extra-packages: |
           any::ggplot2
           any::roxygen2
+          any::igraph
+          any::ggraph
+          any::askpass
+          any::cluster
+          any::sna
 
     - uses: gradle/wrapper-validation-action@v1
 
     - name: Setup Gradle
-      uses: gradle/gradle-build-action@v2
+      uses: gradle/gradle-build-action@v2.4.2
 
     - name: Execute Gradle build for rDNA
       run: ./gradlew :rDNA:build

.github/workflows/matrix-chat-message.yml

@@ -0,0 +1,22 @@
+name: Matrix message
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  send-message:
+    runs-on: ubuntu-latest
+    name: Send message via Matrix
+    steps:
+    - name: Send message to DNA Matrix space development room
+      id: matrix-chat-message
+      uses: fadenb/[email protected]
+      with:
+        homeserver: ${{ secrets.MATRIX_SERVER }}
+        token: ${{ secrets.MATRIX_TOKEN }}
+        channel: ${{ secrets.MATRIX_ROOM_ID }}
+        message: |
+          New [commit](https://github.com/leifeld/dna/commit/${{ github.sha }}) in the [dna](https://github.com/leifeld/dna/) GitHub repository (branch: ${{ github.ref_name }}). Commit message: ${{ github.event.head_commit.message }}.

README.md

@@ -12,13 +12,17 @@ The Java software Discourse Network Analyzer (DNA) is a qualitative content anal
 
 - The software comes with an R package called rDNA for remote controlling DNA and for further ways of analyzing the networks.
 
+[DNA 3.0](https://github.com/leifeld/dna/releases) was first released on 12 June 2022. It constitutes a major rewrite from the previous version DNA 2.0 beta 25. DNA 3 comes with many new features and improvements. The [release](https://github.com/leifeld/dna/releases) page contains all the details (scroll to version 3.0.7 for the first DNA 3 release).
+
+If you require the latest (non-release) version of the DNA jar file from GitHub, you can clone the git repository to your computer and execute `./gradlew build` on your terminal or command line. This will build the jar file and store it in the `build/` directory of the cloned repository. Alternatively, you can try to download the latest artifact from the build process under [GitHub Actions](https://github.com/leifeld/dna/actions) by clicking on the latest build and scrolling down to "Artifacts". However, it is usually recommended to use the most recent [release](https://github.com/leifeld/dna/releases/) version.
+
 [![DNA/rDNA build](https://github.com/leifeld/dna/actions/workflows/DNA%20build.yml/badge.svg)](https://github.com/leifeld/dna/actions/workflows/DNA%20build.yml)
 
-## DNA 3.0: current development status
+## rDNA 3.0: Connecting DNA to R
 
-[DNA 3.0](https://github.com/leifeld/dna/releases) was first released on 12 June 2022. It constitutes a major rewrite from the previous version DNA 2.0 beta 25. DNA 3 comes with many new features and improvements. The [release](https://github.com/leifeld/dna/releases) page contains all the details (scroll to version 3.0.7 for the first DNA 3 release).
+The R package rDNA connects DNA to R for data exchange and analysis.
 
-Please note that the R package rDNA does not have the full functionality of the old 2.0 version yet. It can create networks, but please use the old DNA 2.0 beta 25 for now if you require more complex data management and analysis functionality in R. It is possible to import DNA 2 data into DNA 3 at any point. New R functions will be added in the future.
+Please note that the current version 3.0 does not have the full functionality of the old 2.0 version yet. It can create networks, but please use the old version for now if you require more complex data management and analysis functionality in R. It is possible to import DNA 2 data into DNA 3 at any point (but not the other way around). New R functions will be added in the future.
 
 To install the new rDNA 3 directly from GitHub, try the following code in R:
 
@@ -30,9 +34,24 @@ remotes::install_github("leifeld/dna/rDNA/rDNA@*release",
 
 Note that the package relies on `rJava`, which needs to be installed first.
 
-If you require the latest (non-release) version of the DNA jar file from GitHub, you can clone the git repository to your computer and execute `./gradlew build` on your terminal or command line. This will build the jar file and store it in the directory `dna/build/libs/` of the cloned repository. Alternatively, you can try to download the latest artifact from the build process under [GitHub Actions](https://github.com/leifeld/dna/actions) by clicking on the latest build and scrolling down to "Artifacts". However, it is usually recommended to use the most recent [release](https://github.com/leifeld/dna/releases/) version.
+## Installation of the old rDNA 2.1.18
+For data management, you may still want to use the old rDNA 2.1.18 with DNA 2.0 beta 25. You can install the package directly from GitHub as well. However, you will need to download the correct JAR file and store it either in your working directory or (recommended) in the library path of the installed R package in the "extdata" subdirectory. The following code can do this for you:
+```r
+# install.packages("remotes")
+remotes::install_github("leifeld/dna/[email protected]",
+                        INSTALL_opts = "--no-multiarch")
 
-## Documentation
+# find out where to store the JAR file
+dest <- paste0(dirname(system.file(".", package = "rDNA")),
+               "/extdata/dna-2.0-beta25.jar")
+
+# download JAR file and store in library path
+u <- "https://github.com/leifeld/dna/releases/download/v2.0-beta.25/dna-2.0-beta25.jar"
+download.file(url = u, destfile = dest, mode = "wb")
+
+```
+
+## Documentation and community
 
 - This **tutorial on YouTube** describes installation of DNA, basic data coding, network export, and network analysis using visone. The video clip is 18 minutes long.
 
@@ -46,6 +65,19 @@ If you require the latest (non-release) version of the DNA jar file from GitHub,
 
 - If you have questions or want to report bugs, please create an issue in the [issue tracker](https://github.com/leifeld/dna/issues).
 
+- Join the the DNA community on [Matrix](https://matrix.to/#/#dna:yatrix.org). Matrix is a chat protocol. It's similar to Slack, Discord, or WhatsApp, but without the corporate shackles. It's free, open-source, decentralised, and secure. We have set up a public space called [#dna:yatrix.org](https://matrix.to/#/#dna:yatrix.org) with separate chat rooms for installation, research, and development. It's really easy to join: You first create an account on one of the many Matrix [servers](https://joinmatrix.org/servers/) (we use and recommend [yatrix.org](https://element.yatrix.org/)), then download one of the many Matrix [clients](https://matrix.org/ecosystem/clients/) on your phone, computer, or the web (e.g., Element) to use the account with, and finally join [#dna:yatrix.org](https://matrix.to/#/#dna:yatrix.org). To simplify the process, you can just click on [this invitation link](https://matrix.to/#/#dna:yatrix.org) for some sensible default choices. Make sure you join all four public rooms (you can mute their notifications as needed) and look at the rules in the #dna-welcome room upon arrival.
+
 ## Support the project
 
-Please consider contributing to the project by telling other people about the software, citing our underlying [research](https://www.philipleifeld.com/publications) in your publications, reporting or fixing [issues](https://github.com/leifeld/issues), or starting pull requests.
+Please consider contributing to the project by:
+- telling other people about the software,
+- citing our underlying [research](https://www.philipleifeld.com/publications) in your publications,
+- reporting or fixing [issues](https://github.com/leifeld/issues), or
+- starting pull requests to contribute bug fixes or new functionality.
+
+Some suggestions of new functionality you could add via pull requests:
+- Import filters for loading data from Nvivo, MaxQDA, and other software into DNA.
+- Export filters for exporting networks to Gephi and other network analysis software.
+- Analysis functions or unit tests for the rDNA package.
+- Publications for the bibliography.
+- Bug fixes.