Merge pull request #20 from BIOP/fix-process-wait-mac

Rdornier · web-flow · commit 86f3b4691008 · 2026-01-12T17:37:34.000+01:00
Fix process wait mac
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -13,7 +13,7 @@ repositories {
 qupathExtension {
     name = "qupath-extension-spotiflow"
     group = "ch.epfl.biop"
-    version = "0.3.2-SNAPSHOT"
+    version = "0.3.2"
     description = "QuPath extension to use Spotiflow"
     automaticModule = "qupath.ext.biop.spotiflow"
 }
diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>All Classes and Interfaces (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>All Classes and Interfaces (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="class index">
diff --git a/docs/allpackages-index.html b/docs/allpackages-index.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>All Packages (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>All Packages (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="package index">
diff --git a/docs/deprecated-list.html b/docs/deprecated-list.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>Deprecated List (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>Deprecated List (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="deprecated elements">
diff --git a/docs/help-doc.html b/docs/help-doc.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>API Help (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>API Help (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="help">
diff --git a/docs/index-all.html b/docs/index-all.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>Index (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>Index (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="index">
diff --git a/docs/index.html b/docs/index.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>Overview (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>Overview (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="package index">
@@ -48,7 +48,7 @@
 <div class="flex-content">
 <main role="main">
 <div class="header">
-<h1 class="title">qupath-extension-spotiflow 0.3.1 API</h1>
+<h1 class="title">qupath-extension-spotiflow 0.3.2 API</h1>
 </div>
 <div id="all-packages-table">
 <div class="caption"><span>Packages</span></div>
diff --git a/docs/overview-summary.html b/docs/overview-summary.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>qupath-extension-spotiflow 0.3.1 API</title>
+<title>qupath-extension-spotiflow 0.3.2 API</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="index redirect">
diff --git a/docs/overview-tree.html b/docs/overview-tree.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>Class Hierarchy (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>Class Hierarchy (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="class tree">
diff --git a/docs/qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html b/docs/qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>VirtualEnvironmentRunner.EnvType (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>VirtualEnvironmentRunner.EnvType (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.cmd, class: VirtualEnvironmentRunner, enum: EnvType">
diff --git a/docs/qupath/ext/biop/cmd/VirtualEnvironmentRunner.html b/docs/qupath/ext/biop/cmd/VirtualEnvironmentRunner.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>VirtualEnvironmentRunner (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>VirtualEnvironmentRunner (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.cmd, class: VirtualEnvironmentRunner">
diff --git a/docs/qupath/ext/biop/cmd/package-summary.html b/docs/qupath/ext/biop/cmd/package-summary.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>qupath.ext.biop.cmd (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>qupath.ext.biop.cmd (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.cmd">
diff --git a/docs/qupath/ext/biop/cmd/package-tree.html b/docs/qupath/ext/biop/cmd/package-tree.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>qupath.ext.biop.cmd Class Hierarchy (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>qupath.ext.biop.cmd Class Hierarchy (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="tree: package: qupath.ext.biop.cmd">
diff --git a/docs/qupath/ext/biop/spotiflow/Spotiflow.html b/docs/qupath/ext/biop/spotiflow/Spotiflow.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>Spotiflow (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>Spotiflow (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.spotiflow, class: Spotiflow">
diff --git a/docs/qupath/ext/biop/spotiflow/SpotiflowBuilder.html b/docs/qupath/ext/biop/spotiflow/SpotiflowBuilder.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>SpotiflowBuilder (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>SpotiflowBuilder (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.spotiflow, class: SpotiflowBuilder">
diff --git a/docs/qupath/ext/biop/spotiflow/SpotiflowExtension.html b/docs/qupath/ext/biop/spotiflow/SpotiflowExtension.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>SpotiflowExtension (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>SpotiflowExtension (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.spotiflow, class: SpotiflowExtension">
diff --git a/docs/qupath/ext/biop/spotiflow/SpotiflowSetup.html b/docs/qupath/ext/biop/spotiflow/SpotiflowSetup.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>SpotiflowSetup (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>SpotiflowSetup (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.spotiflow, class: SpotiflowSetup">
diff --git a/docs/qupath/ext/biop/spotiflow/package-summary.html b/docs/qupath/ext/biop/spotiflow/package-summary.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>qupath.ext.biop.spotiflow (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>qupath.ext.biop.spotiflow (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="declaration: package: qupath.ext.biop.spotiflow">
diff --git a/docs/qupath/ext/biop/spotiflow/package-tree.html b/docs/qupath/ext/biop/spotiflow/package-tree.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>qupath.ext.biop.spotiflow Class Hierarchy (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>qupath.ext.biop.spotiflow Class Hierarchy (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="tree: package: qupath.ext.biop.spotiflow">
diff --git a/docs/search.html b/docs/search.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>Search (qupath-extension-spotiflow 0.3.1 API)</title>
+<title>Search (qupath-extension-spotiflow 0.3.2 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="description" content="search">
diff --git a/src/main/java/qupath/ext/biop/spotiflow/Spotiflow.java b/src/main/java/qupath/ext/biop/spotiflow/Spotiflow.java
@@ -822,6 +822,9 @@ private void runTraining() throws IOException, InterruptedException {
 
         // Finally, we can run Spotiflow
         veRunner.runCommand(true);
+
+        // Add a waitFor() here to fix MAC Mx chip killing thread issue (#15)
+        veRunner.getProcess().waitFor();
     }
 
     /**
@@ -908,6 +911,9 @@ private ResultsTable runSpotiflowQC() throws IOException, InterruptedException {
         qcRunner.setArguments(spotiflowArguments);
         qcRunner.runCommand(true);
 
+        // Add a waitFor() here to fix MAC Mx chip killing thread issue (#15)
+        qcRunner.getProcess().waitFor();
+
         return ResultsTable.open(qcFile.getAbsolutePath());
     }
 

Original file line number	Diff line number	Diff line change
`@@ -13,7 +13,7 @@ repositories {`
`13`	`13`	`qupathExtension {`
`14`	`14`	`name = "qupath-extension-spotiflow"`
`15`	`15`	`group = "ch.epfl.biop"`
`16`		`- version = "0.3.2-SNAPSHOT"`
	`16`	`+ version = "0.3.2"`
`17`	`17`	`description = "QuPath extension to use Spotiflow"`
`18`	`18`	`automaticModule = "qupath.ext.biop.spotiflow"`
`19`	`19`	`}`