From de8d43b5f7a2746ff3dce4770fdc313372ccf965 Mon Sep 17 00:00:00 2001
From: Nico Stuurman <nico.stuurman@ucsf.edu>
Date: Thu, 21 Aug 2025 09:58:22 -0700
Subject: [PATCH 1/4] Build: transition to maven central deployment.

---
 .github/workflows/build_and_deploy.yml | 13 +++++-----
 java/pom.xml                           | 36 ++++++++++++--------------
 2 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/build_and_deploy.yml b/.github/workflows/build_and_deploy.yml
index 38197d4b..74b123ff 100644
--- a/.github/workflows/build_and_deploy.yml
+++ b/.github/workflows/build_and_deploy.yml
@@ -47,7 +47,7 @@ jobs:
     if: ${{ needs.check-java-version.outputs.changed == 'true' }}
 
       
-    name: Deploy PycroManagerJava.jar to Sonatype OSS
+    name: Deploy PycroManagerJava.jar to Maven central
     runs-on: ubuntu-latest 
 
     steps:
@@ -65,18 +65,17 @@ jobs:
         with: # running setup-java again overwrites the settings.xml
           java-version: 8
           distribution: 'zulu'
-
-          server-id: ossrh
-          server-username: OSSRH_USERNAME
-          server-password: OSSRH_PASSWORD
+          server-id: central
+          server-username: MAVEN_USERNAME
+          server-password: MAVEN_PASSWORD
           gpg-private-key: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}
           gpg-passphrase: MAVEN_GPG_PASSPHRASE
           
       - name: Publish to Apache Maven Central
         run: mvn deploy --file java/pom.xml -Dgpg.passphrase=${{ secrets.MAVEN_GPG_PASSPHRASE }}
         env:
-          OSSRH_USERNAME: ${{ secrets.OSSRH_USERNAME }}
-          OSSRH_PASSWORD: ${{ secrets.OSSRH_PASSWORD }}
+          OSSRH_USERNAME: ${{ secrets.MAVEN_USERNAME }}
+          OSSRH_PASSWORD: ${{ secrets.MAVEN_PASSWORD }}
           MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
 
 
diff --git a/java/pom.xml b/java/pom.xml
index ae5abb19..7c1ad3aa 100644
--- a/java/pom.xml
+++ b/java/pom.xml
@@ -23,7 +23,7 @@
        <developer>
           <id>nicost</id>
           <name>Nico Stuurman</name>
-          <organization>UCSF/HHMI</organization>
+          <organization>UCSF</organization>
        </developer>
     </developers>
   
@@ -55,7 +55,7 @@
       <dependency>
          <groupId>org.micro-manager.acqengj</groupId>
          <artifactId>AcqEngJ</artifactId>
-     <version>0.39.0</version>
+     <version>0.39.2</version>
       </dependency>
       <dependency>
          <groupId>org.micro-manager.ndviewer</groupId>
@@ -111,11 +111,11 @@
            <goal>sign</goal>
           </goals>
              
-                          <configuration>
-                <gpgArguments>
-            <arg>--pinentry-mode</arg>
-            <arg>loopback</arg>
-        </gpgArguments>
+         <configuration>
+           <gpgArguments>
+             <arg>--pinentry-mode</arg>
+             <arg>loopback</arg>
+           </gpgArguments>
          </configuration>
              
          </execution>
@@ -123,17 +123,15 @@
        </plugin>
 
       <plugin>
-      <groupId>org.sonatype.plugins</groupId>
-      <artifactId>nexus-staging-maven-plugin</artifactId>
-      <version>1.6.13</version>
-      <extensions>true</extensions>
-      <configuration>
-       <serverId>ossrh</serverId>
-       <nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
-       <autoReleaseAfterClose>true</autoReleaseAfterClose>
-        <stagingProgressTimeoutMinutes>20</stagingProgressTimeoutMinutes>
-      </configuration>
-
+          <groupId>org.sonatype.central</groupId>
+          <artifactId>central-publishing-maven-plugin</artifactId>
+          <version>0.8.0</version>
+          <extensions>true</extensions>
+          <configuration>
+              <publishingServerId>central</publishingServerId>
+              <autoPublish>true</autoPublish>
+              <waitUntil>published</waitUntil>
+          </configuration>
       </plugin>
     
       </plugins>
@@ -148,4 +146,4 @@
       </repository>
    </distributionManagement>
 
-</project>
\ No newline at end of file
+</project>

From 792349a95f82593745a7e42d51e54d3ab7a6d609 Mon Sep 17 00:00:00 2001
From: Nico Stuurman <nico.stuurman@ucsf.edu>
Date: Thu, 21 Aug 2025 11:09:34 -0700
Subject: [PATCH 2/4] Build: add debug output to conftest.py to see why the
 core is not found while running test on github using github actions.

---
 pycromanager/test/conftest.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pycromanager/test/conftest.py b/pycromanager/test/conftest.py
index 1c5992fc..4a8eb4fe 100644
--- a/pycromanager/test/conftest.py
+++ b/pycromanager/test/conftest.py
@@ -62,6 +62,8 @@ def install_mm():
         # Download an install latest nightly build
         mm_install_dir = download_and_install_mm(destination='auto')
 
+        print('Micro-Manager installed in ' + mm_install_dir)
+
         #### Replace with newer versions of Java libraries ####
         # find pycro-manager/java path
         if os.path.isdir('java'):

From 05c699dfb4866829ca51e0d80e2a029810f324b6 Mon Sep 17 00:00:00 2001
From: Nico Stuurman <nico.stuurman@ucsf.edu>
Date: Thu, 21 Aug 2025 11:28:50 -0700
Subject: [PATCH 3/4] Fix broken tests due to unchecked changes in mmpycores
 API.

---
 pycromanager/test/conftest.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/pycromanager/test/conftest.py b/pycromanager/test/conftest.py
index 4a8eb4fe..c7962f49 100644
--- a/pycromanager/test/conftest.py
+++ b/pycromanager/test/conftest.py
@@ -55,10 +55,12 @@ def install_mm():
     if is_port_in_use(4827):
         print('Using Micro-manager running on port 4827 for testing')
         yield
-    elif find_existing_mm_install():
+    try:
+        path = find_existing_mm_install()
         print('Micro-Manager is already installed, skipping installation')
-        yield find_existing_mm_install()
-    else:
+        yield path
+    except FileNotFoundException:
+        print("No Micro-Manager installation found, installing now")
         # Download an install latest nightly build
         mm_install_dir = download_and_install_mm(destination='auto')
 

From cd1d2c7c0e6d9e186dc41ed06255d26ef175caf7 Mon Sep 17 00:00:00 2001
From: Nico Stuurman <nico.stuurman@ucsf.edu>
Date: Thu, 21 Aug 2025 11:37:21 -0700
Subject: [PATCH 4/4] Build: Error not Exception..

---
 pycromanager/test/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycromanager/test/conftest.py b/pycromanager/test/conftest.py
index c7962f49..66a19938 100644
--- a/pycromanager/test/conftest.py
+++ b/pycromanager/test/conftest.py
@@ -59,7 +59,7 @@ def install_mm():
         path = find_existing_mm_install()
         print('Micro-Manager is already installed, skipping installation')
         yield path
-    except FileNotFoundException:
+    except FileNotFoundError:
         print("No Micro-Manager installation found, installing now")
         # Download an install latest nightly build
         mm_install_dir = download_and_install_mm(destination='auto')