Kernel smoothing and better parallelization for phase transitions

leifeld · Feb 4, 2024 · 38eac00 · 38eac00
1 parent ef85c08
commit 38eac00
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Showing 15 changed files with 791 additions and 161 deletions.
diff --git a/bibliography/build.gradle b/bibliography/build.gradle
@@ -1,9 +1,7 @@
 task bibliographyMarkdown {
+    inputs.dir '.'
     doLast {
-        exec {
-            workingDir '.'
-            commandLine 'mkdir', "-p", "$rootDir/build"
-        }
+        mkdir "$rootDir/build"
         exec {
             workingDir '.'
             commandLine 'pandoc', "-t", "gfm", "-s", "--csl", "apa-numeric-superscript-brackets.csl", "--citeproc", "-o", "$rootDir/build/bibliography.md", "bibliography.tex"
@@ -12,59 +10,35 @@ task bibliographyMarkdown {
 }
 
 task bibliographyPdflatex {
+    inputs.dir '.'
     doLast{
-        exec {
-            workingDir '.'
-            commandLine 'mkdir', "-p", "temp"
-        }
-        exec {
-            workingDir '.'
-            commandLine 'mkdir', "-p", "$rootDir/build"
+        mkdir "./temp"
+        mkdir "$rootDir/build"
+        copy {
+            from 'bibliography.tex', 'bibliography.bib'
+            into 'temp'
         }
-        exec {
-            workingDir '.'
-            commandLine 'cp', "bibliography.tex", "temp/"
-        }
-        exec {
-            workingDir '.'
-            commandLine 'cp', "bibliography.bib", "temp/"
-        }
-    }
 
-    doLast {
         exec {
             workingDir 'temp'
             commandLine 'pdflatex', "bibliography.tex"
-        }
-        exec {
-            workingDir 'temp'
             commandLine 'bibtex', "bibliography"
-        }
-        exec {
-            workingDir 'temp'
             commandLine 'pdflatex', "bibliography.tex"
-        }
-        exec {
-            workingDir 'temp'
             commandLine 'pdflatex', "bibliography.tex"
         }
-    }
 
-    doLast {
-        exec {
-            workingDir '.'
-            commandLine 'mv', "temp/bibliography.pdf", "$rootDir/build/"
-        }
-        exec {
-            workingDir '.'
-            commandLine 'rm', "-r", "temp"
+        copy {
+            from 'temp/bibliography.pdf'
+            into "$rootDir/build/"
         }
+        delete 'temp'
     }
 }
 
 task build {
     dependsOn bibliographyMarkdown
     dependsOn bibliographyPdflatex
+    inputs.dir '.'
     def outputDir = file("$rootDir/build/")
     outputs.dir outputDir
 

diff --git a/build/bibliography.md b/build/bibliography.md
@@ -4,7 +4,7 @@ author:
 bibliography:
 - bibliography.bib
 csl: apa-numeric-superscript-brackets.csl
-date: 2024-01-10
+date: 2024-02-04
 title: "Discourse Network Analysis: Bibliography"
 ---
 

diff --git a/dna/build.gradle b/dna/build.gradle
@@ -5,6 +5,8 @@ plugins {
 
 // create jar file, not just .class files
 jar {
+    inputs.dir '.'
+
     // point the manifest to the right class
     manifest {
         attributes 'Main-Class': 'dna.Dna'
@@ -77,4 +79,6 @@ dependencies {
     implementation group: 'me.tongfei', name: 'progressbar', version: '0.9.4'
     // https://mvnrepository.com/artifact/org.ojalgo/ojalgo
     implementation group: 'org.ojalgo', name: 'ojalgo', version: '51.4.1'
+    // https://mvnrepository.com/artifact/org.apache.commons/commons-math3
+    implementation group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'
 }
diff --git a/dna/src/main/java/dna/Dna.java b/dna/src/main/java/dna/Dna.java
@@ -17,7 +17,7 @@ public class Dna {
 	public static Dna dna;
 	public static Logger logger;
 	public static Sql sql;
-	public static final String date = "2024-01-01";
+	public static final String date = "2024-02-04";
 	public static final String version = "3.0.11";
 	public static final String operatingSystem = System.getProperty("os.name");
 	public static File workingDirectory = null;

diff --git a/dna/src/main/java/export/Exporter.java b/dna/src/main/java/export/Exporter.java
diff --git a/rDNA/build.gradle b/rDNA/build.gradle
@@ -1,4 +1,5 @@
 task rDNADocument {
+    inputs.dir 'rDNA'
     doLast {
         exec {
             workingDir 'rDNA'
@@ -9,26 +10,25 @@ task rDNADocument {
 
 task rDNABuild {
     dependsOn rDNADocument
+    inputs.dir 'rDNA'
+    def outputDir = file("$rootDir/build/")
+    doFirst {
+        delete fileTree(dir: outputDir, includes: ['*.tar.gz'])
+    }
     doLast {
-        exec {
-            workingDir '.'
-            commandLine 'mkdir', "-p", "$rootDir/build"
-        }
+        mkdir "$rootDir/build"
         exec {
             workingDir "$rootDir/build/"
             commandLine 'R', "CMD", "build", "../rDNA/rDNA"
         }
     }
-    def outputDir = file("$rootDir/build/")
     outputs.dir outputDir
 }
 
 task rDNACheck {
+    inputs.dir 'rDNA'
     doLast {
-        exec {
-            workingDir '.'
-            commandLine 'mkdir', "-p", "$rootDir/build"
-        }
+        mkdir "$rootDir/build"
         exec {
             workingDir "rDNA"
             commandLine 'R', "-e", "devtools::check(manual = TRUE, check_dir = '../../build/')"
@@ -39,11 +39,9 @@ task rDNACheck {
 }
 
 task rDNATest {
+    inputs.dir 'rDNA'
     doLast {
-        exec {
-            workingDir '.'
-            commandLine 'mkdir', "-p", "$rootDir/build"
-        }
+        mkdir "$rootDir/build"
         exec {
             workingDir "rDNA"
             commandLine 'R', "-e", "devtools::test()"
@@ -57,6 +55,7 @@ task rDNATest {
 
 task build {
     dependsOn rDNABuild
+    inputs.dir 'rDNA'
     def outputDir = file("$rootDir/build/")
     outputs.dir outputDir
     doLast {}

diff --git a/rDNA/rDNA/DESCRIPTION b/rDNA/rDNA/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rDNA
 Version: 3.0.11
-Date: 2023-10-15
+Date: 2024-02-04
 Title: Discourse Network Analysis in R
 Authors@R: 
   c(person(given = "Philip",

diff --git a/rDNA/rDNA/NAMESPACE b/rDNA/rDNA/NAMESPACE
@@ -20,6 +20,7 @@ export(dna_barplot)
 export(dna_closeDatabase)
 export(dna_evaluateBackboneSolution)
 export(dna_getAttributes)
+export(dna_getHeadlessDna)
 export(dna_getVariables)
 export(dna_init)
 export(dna_jar)
@@ -28,6 +29,7 @@ export(dna_network)
 export(dna_openConnectionProfile)
 export(dna_openDatabase)
 export(dna_phaseTransitions)
+export(dna_phaseTransitions2)
 export(dna_printDetails)
 export(dna_queryCoders)
 export(dna_sample)