Pulled .circleci and .github template from master. Updated change-log…

… and bumped version.

.circleci/config.yml

@@ -84,17 +84,18 @@ jobs: # a collection of steps
           name: "Publish Release on GitHub"
           command: |
             # Retrieve version
-            VERSION=$(ls ./gradleBuild/distributions/Roddy-*.zip | sed -r 's/.*Roddy-([[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+(-.+)?).zip/\1/')
+            FULL_VERSION=$(ls ./gradleBuild/distributions/Roddy-*.zip | sed -r 's/.*Roddy-([[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+(-test[[:digit:]]+)?).zip/\1/')
+            VERSION=$(echo "$FULL_VERSION" | sed -r 's/([[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+)(-test[[:digit:]]+)?/\1/')
             
-            # Ensure buildversion.txt is up to date
+            # Ensure buildversion.txt is up to date. Only version is supported.
             buildVersionTxt=$(cat ./RoddyCore/buildversion.txt | tr '\n' '.' | sed -r s/\.$//)
             if [[ "$VERSION" != "$buildVersionTxt" ]]; then
               echo "buildversion.txt not updated" >> /dev/stderr
               exit 1
             fi
             
             # Do the actual release
-            ghr -t "$GITHUB_TOKEN" -u "$CIRCLE_PROJECT_USERNAME" -r "$CIRCLE_PROJECT_REPONAME" -c "$CIRCLE_SHA1" -n "$VERSION" "$VERSION" ./gradleBuild/distributions/
+            ghr -t "$GITHUB_TOKEN" -u "$CIRCLE_PROJECT_USERNAME" -r "$CIRCLE_PROJECT_REPONAME" -c "$CIRCLE_SHA1" -n "$FULL_VERSION" "$FULL_VERSION" ./gradleBuild/distributions/
 
 workflows:
   version: 2
@@ -111,15 +112,15 @@ workflows:
             branches: # ignore any commit on any branch by default
               ignore: /.*/
             tags: # unless they match the pattern
-              only: /^\d+\.\d+\.\d+$/
+              only: /^\d+\.\d+\.\d+(-test\d+)?$/
       - build-and-test:
           requires:
             - pre-build
           filters:
             branches:  # ignore any commit on any branch by default
               ignore: /.*/
             tags:  # unless they match the pattern
-              only: /^\d+\.\d+\.\d+$/
+              only: /^\d+\.\d+\.\d+(-test\d+)?$/
       - publish-github-release:
           context:
             - TheRoddyWMS
@@ -129,4 +130,4 @@ workflows:
             branches:  # ignore any commit on any branch by default
               ignore: /.*/
             tags:  # unless they match the pattern
-              only: /^\d+\.\d+\.\d+$/
+              only: /^\d+\.\d+\.\d+(-test\d+)?$/

.github/pull_request_template.md

@@ -2,11 +2,20 @@
 
 ## Check
 
- * [ ] The correct target branch is selected for merging? :sweat_smile:
+ * [ ] Stakeholders agree on the validity of the changes, or are not affected by the change
  * [ ] The merge request title concisely describes the changes
- * [ ] The `README.md` concisely describes the changes classified as major, minor, patch.
- * [ ] If a release is planned, Roddy's release procedure was followed 
-     1. [ ] `buildinfo.txt` was modified to release number
-     2. [ ] `roddy.sh compile` was run to update `RoddyCore/src/de/dkfz/roddy/Constants.java`
-     3. [ ] Both files were checked in after modification
-
+ * [ ] Changes are described in the ChangeLog and classified according to [semantic versioning](#SemanticVersioning) into "major", "minor", "patch" levels.
+ * [ ] The correct target branch is selected for merging :sweat_smile:
+
+This is a pre-release merge request, therefore
+
+ * [ ] Stakeholders agree on the content of the release, or are not affected by the change
+ * [ ] All changes planned to be included in the release are merged into the release branch.
+ * [ ] All changes since the last version are documented in the change-log. Specifically
+   * [ ] Changes included in the release are described.
+   * [ ] Deprecation is justified.
+   * [ ] The resulting new version number is shown.
+ * [ ] The version number has been adapted in the code
+    1. [ ] `buildinfo.txt` was modified to release number
+    2. [ ] `INCREASE_BUILD_VERSION=false roddy.sh compile` was run to update `RoddyCore/src/de/dkfz/roddy/Constants.java`
+    3. [ ] Both files were checked in after modification

CHANGELIST.md

@@ -1,5 +1,15 @@
 # Changelist
 
+* 3.5.11
+
+  - patch: Pure maintenance release (basically same as 3.7.3)
+  - patch: Fix reported release number
+  - patch: Allow release with optional subpatch-level suffixes matching the pattern `-test\d+`. This is obviously for testing only.
+  - patch: Updated PR-template with separated PR and release sections
+
+* 3.5.10
+    - patch: Bumped BatchEuphoria version to 0.0.7-1: A newer LSF release is pickier on the position of the `-o` parameter in `bjobs`. Adapted to this upstream change. Probably code will still work with older LSF versions.
+
 * 3.5.9
 
   - The LocalExecutionService ignored errors of asychronously executed commands. 

RoddyCore/buildversion.txt

@@ -1,2 +1,2 @@
 3.5
-10
+11

RoddyCore/src/de/dkfz/roddy/Constants.java

@@ -16,8 +16,8 @@ public class Constants {
     // Application constants
     /////////////////////////
 
-    public static final String APP_CURRENT_VERSION_STRING = "3.5.10";
-    public static final String APP_CURRENT_VERSION_BUILD_DATE = "Fri Feb 03 13:04:15 CET 2023";
+    public static final String APP_CURRENT_VERSION_STRING = "3.5.11";
+    public static final String APP_CURRENT_VERSION_BUILD_DATE = "Mon Feb 06 14:32:47 CET 2023";
     public static final String APP_PROPERTY_JOB_MANAGER_CLASS = "jobManagerClass";
     public static final String APP_PROPERTY_FILESYSTEM_ACCESS_MANAGER_CLASS = "fileSystemAccessManagerClass";
     public static final String APP_PROPERTY_EXECUTION_SERVICE_CLASS = "executionServiceClass";