From 722dbdaa8525b7b4521a1641bfa73cfefc0abf04 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Jul 2024 16:45:32 +0000
Subject: [PATCH 1/5] Bump org.apache.maven.plugins:maven-shade-plugin from
 3.4.1 to 3.6.0

Bumps [org.apache.maven.plugins:maven-shade-plugin](https://github.com/apache/maven-shade-plugin) from 3.4.1 to 3.6.0.
- [Release notes](https://github.com/apache/maven-shade-plugin/releases)
- [Commits](https://github.com/apache/maven-shade-plugin/compare/maven-shade-plugin-3.4.1...maven-shade-plugin-3.6.0)

---
updated-dependencies:
- dependency-name: org.apache.maven.plugins:maven-shade-plugin
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 com.ibm.wala.cast.python.ml/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/com.ibm.wala.cast.python.ml/pom.xml b/com.ibm.wala.cast.python.ml/pom.xml
index b3fd1632..a5c6bc7e 100644
--- a/com.ibm.wala.cast.python.ml/pom.xml
+++ b/com.ibm.wala.cast.python.ml/pom.xml
@@ -66,7 +66,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-shade-plugin</artifactId>
-        <version>3.4.1</version>
+        <version>3.6.0</version>
         <configuration>
           <filters>
             <filter>

From ab41e38d2637be418acad405e5028011cdc0327b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Oct 2024 10:02:32 +0000
Subject: [PATCH 2/5] Bump black from 24.8.0 to 24.10.0

Bumps [black](https://github.com/psf/black) from 24.8.0 to 24.10.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.8.0...24.10.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 6876f3ca..ad2b44c0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1 @@
-black==24.8.0
+black==24.10.0

From e90540b4231da605d8c4aa9bbe451d7d1eeb0a82 Mon Sep 17 00:00:00 2001
From: Raffi Khatchadourian <khatchad@hunter.cuny.edu>
Date: Fri, 8 Nov 2024 14:20:48 -0500
Subject: [PATCH 3/5] Add launch configuration.

---
 Apply spotless.launch | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 Apply spotless.launch

diff --git a/Apply spotless.launch b/Apply spotless.launch
new file mode 100644
index 00000000..374c84b1
--- /dev/null
+++ b/Apply spotless.launch	
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.m2e.Maven2LaunchConfigurationType">
+    <intAttribute key="M2_COLORS" value="0"/>
+    <booleanAttribute key="M2_DEBUG_OUTPUT" value="false"/>
+    <stringAttribute key="M2_GOALS" value="spotless:apply"/>
+    <booleanAttribute key="M2_NON_RECURSIVE" value="false"/>
+    <booleanAttribute key="M2_OFFLINE" value="true"/>
+    <stringAttribute key="M2_PROFILES" value=""/>
+    <listAttribute key="M2_PROPERTIES"/>
+    <stringAttribute key="M2_RUNTIME" value="EMBEDDED"/>
+    <booleanAttribute key="M2_SKIP_TESTS" value="true"/>
+    <intAttribute key="M2_THREADS" value="1"/>
+    <booleanAttribute key="M2_UPDATE_SNAPSHOTS" value="false"/>
+    <stringAttribute key="M2_USER_SETTINGS" value=""/>
+    <booleanAttribute key="M2_WORKSPACE_RESOLUTION" value="true"/>
+    <booleanAttribute key="org.eclipse.debug.core.ATTR_FORCE_SYSTEM_CONSOLE_ENCODING" value="false"/>
+    <stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${workspace}"/>
+    <listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+        <listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
+    <stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:/ml}"/>
+</launchConfiguration>

From d60132e2e5606cbf4e83e1686a127053cc69962d Mon Sep 17 00:00:00 2001
From: Raffi Khatchadourian <khatchad@hunter.cuny.edu>
Date: Fri, 8 Nov 2024 15:15:04 -0500
Subject: [PATCH 4/5] Handle null annotation case.

---
 .../source/com/ibm/wala/cast/python/util/Util.java               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/util/Util.java b/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/util/Util.java
index 233fc038..4af60a1b 100644
--- a/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/util/Util.java
+++ b/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/util/Util.java
@@ -107,6 +107,7 @@ public static String removeFileProtocolFromPath(String path) {
    *     presented in the CAst.
    */
   public static Collection<String> getNames(Collection<CAstAnnotation> annotations) {
+    if (annotations == null) return emptyList();
     return annotations.stream().map(Util::getName).flatMap(Optional::stream).toList();
   }
 

From 04eece19a739a7b0476aadbc86a19ef67257b135 Mon Sep 17 00:00:00 2001
From: Raffi Khatchadourian <khatchad@hunter.cuny.edu>
Date: Mon, 11 Nov 2024 14:13:21 -0500
Subject: [PATCH 5/5] Fix version number.

---
 com.ibm.wala.cast.python.ml/run.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/com.ibm.wala.cast.python.ml/run.sh b/com.ibm.wala.cast.python.ml/run.sh
index bcd9476c..f42e8e77 100755
--- a/com.ibm.wala.cast.python.ml/run.sh
+++ b/com.ibm.wala.cast.python.ml/run.sh
@@ -3,4 +3,4 @@
 ME=`realpath $0`
 DIR=`dirname $ME`
 
-cat -u | tee -a /tmp/lsp.in.log | $JAVA_HOME/bin/java -Xdebug -Xrunjdwp:transport=dt_socket,address=127.0.0.1:6660,server=y,suspend=n -jar $DIR/target/com.ibm.wala.cast.python.ml-0.6.0-SNAPSHOT.jar --mode stdio | tee -a /tmp/lsp.out.log
+cat -u | tee -a /tmp/lsp.in.log | $JAVA_HOME/bin/java -Xdebug -Xrunjdwp:transport=dt_socket,address=127.0.0.1:6660,server=y,suspend=n -jar $DIR/target/com.ibm.wala.cast.python.ml-0.38.0-SNAPSHOT.jar --mode stdio | tee -a /tmp/lsp.out.log