Merge branch 'release/v3.0.11'

.circleci/config.yml

@@ -0,0 +1,71 @@
+version: 2.1
+jobs:
+  build:
+    docker:
+      - image: circleci/openjdk:8-jdk
+
+    working_directory: ~/mixcr
+
+    environment:
+      MAX_MEMORY_OVERRIDE: 3500
+      MAVEN_OPTS: -Xmx3g
+
+    steps:
+      - checkout
+
+      - run:
+          name: Downloading git submodules
+          command: git submodule update --init --recursive
+
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "pom.xml" }}-{{ checksum "milib/pom.xml" }}-{{ checksum "repseqio/pom.xml" }}
+            - v1-dependencies-
+
+      - run:
+          name: Building MiLib
+          working_directory: milib
+          command: mvn clean install -DskipTests --batch-mode
+
+      - restore_cache:
+          keys:
+            - v1-repseqio-cache-{{ checksum "repseqio/.gitmodules" }}
+            - v1-repseqio-cache-
+
+      - run:
+          name: Building RepseqIO
+          working_directory: repseqio
+          command: mvn clean install -DskipTests --batch-mode
+
+      - save_cache:
+          paths:
+            - repseqio/.cache
+          key: v1-repseqio-cache-{{ checksum "repseqio/.gitmodules" }}
+
+      - restore_cache:
+          key: v1-test-data-{{ checksum "ensure-test-data.sh" }}
+
+      - run:
+          name: Downloading test data
+          command: ./ensure-test-data.sh
+
+      - save_cache:
+          paths:
+            - src/test/resources/sequences/big/
+          key: v1-test-data-{{ checksum "ensure-test-data.sh" }}
+
+      - run:
+          name: Building and testing MiXCR
+          command: mvn clean install
+
+      - store_test_results:
+          path: target/surefire-reports
+
+      - save_cache:
+          paths:
+            - ~/.m2
+          key: v1-dependencies-{{ checksum "pom.xml" }}-{{ checksum "milib/pom.xml" }}-{{ checksum "repseqio/pom.xml" }}
+
+      - run:
+          name: Running MiXCR Integration tests
+          command: ./itests.sh test

CHANGELOG

@@ -1,4 +1,15 @@
 
+MiXCR 3.0.11 (24 Oct 2019)
+========================
+
+-- Fixes exception in `assemble` for multi-assembling-feature cases with zero length sequences
+-- Fixes empty `FR3` imputed sequence in cases with zero assembled nucleotides on the 5' side of 
+   CDR3
+-- MiXCR execution script optimized for Docker (Java 11 is recommended for running MiXCR in 
+   container environment)
+-- Other fixes for MiXCR script
+
+
 MiXCR 3.0.10 (12 Sep 2019)
 ========================